emdbXMLTranslator package

Submodules

emdbXMLTranslator.diff_all module

diff_all.py

Diff v1.9 files with 1.9 files translated from 2.0 files

TODO:

Version history:

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

emdbXMLTranslator.diff_all.diff_all(v19Dir, v20To19Dir, outDir)[source]
emdbXMLTranslator.diff_all.main()[source]

Diff v1.9 files with 1.9 files translated from 2.0 files

emdbXMLTranslator.emdb_19 module

class emdbXMLTranslator.emdb_19.accVoltType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='accVoltType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='accVoltType')[source]
exportChildren(outfile, level, namespace_='', name_='accVoltType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ec90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ecd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.adminType(lastUpdate=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Information relevant for administration purposes. Not for public release

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='adminType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='adminType')[source]
exportChildren(outfile, level, namespace_='', name_='adminType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_lastUpdate()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604f90>]
set_lastUpdate(lastUpdate)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.anglType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='anglType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='anglType')[source]
exportChildren(outfile, level, namespace_='', name_='anglType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ea90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ead0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.axisOrderType(axisOrderFast=None, axisOrderMedium=None, axisOrderSlow=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axisOrderType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axisOrderType')[source]
exportChildren(outfile, level, namespace_='', name_='axisOrderType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_axisOrderFast()[source]
get_axisOrderMedium()[source]
get_axisOrderSlow()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6477d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647810>]
set_axisOrderFast(axisOrderFast)[source]
set_axisOrderMedium(axisOrderMedium)[source]
set_axisOrderSlow(axisOrderSlow)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.bufferType(ph=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='bufferType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='bufferType')[source]
exportChildren(outfile, level, namespace_='', name_='bufferType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_ph()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e290>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e2d0>]
set_details(details)[source]
set_ph(ph)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.cAngleType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cAngleType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cAngleType')[source]
exportChildren(outfile, level, namespace_='', name_='cAngleType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fb50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fb90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.cType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cType')[source]
exportChildren(outfile, level, namespace_='', name_='cType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f990>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.cellCompType(sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, oligomericDetails=None, numCopies=None, recombinantExpFlag=None, natSource=None, engSource=None, details=None, externalReferences=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cellCompType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cellCompType')[source]
exportChildren(outfile, level, namespace_='', name_='cellCompType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_engSource()[source]
get_externalReferences()[source]
get_natSource()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
get_recombinantExpFlag()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_synSpeciesName()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62eb90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ebd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ec10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ec50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ec90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ecd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ed10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ed50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ed90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62edd0>]
set_details(details)[source]
set_engSource(engSource)[source]
set_externalReferences(externalReferences)[source]
set_natSource(natSource)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
set_recombinantExpFlag(recombinantExpFlag)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.cellType(cellA=None, cellB=None, cellC=None, cellAlpha=None, cellBeta=None, cellGamma=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cellType')[source]
exportChildren(outfile, level, namespace_='', name_='cellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cellA()[source]
get_cellAlpha()[source]
get_cellB()[source]
get_cellBeta()[source]
get_cellC()[source]
get_cellGamma()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f290>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f2d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f350>]
set_cellA(cellA)[source]
set_cellAlpha(cellAlpha)[source]
set_cellB(cellB)[source]
set_cellBeta(cellBeta)[source]
set_cellC(cellC)[source]
set_cellGamma(cellGamma)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.contactType(firstName=None, middleName=None, familyName=None, email=None, phone=None, fax=None, address=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contactType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contactType')[source]
exportChildren(outfile, level, namespace_='', name_='contactType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_address()[source]
get_email()[source]
get_familyName()[source]
get_fax()[source]
get_firstName()[source]
get_middleName()[source]
get_phone()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6183d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618410>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618490>]
set_address(address)[source]
set_email(email)[source]
set_familyName(familyName)[source]
set_fax(fax)[source]
set_firstName(firstName)[source]
set_middleName(middleName)[source]
set_phone(phone)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.contourLevelType(source=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contourLevelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contourLevelType')[source]
exportChildren(outfile, level, namespace_='', name_='contourLevelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_source()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c658090>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6580d0>]
set_source(source)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.crystSizeType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystSizeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystSizeType')[source]
exportChildren(outfile, level, namespace_='', name_='crystSizeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e6d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.csType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='csType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='csType')[source]
exportChildren(outfile, level, namespace_='', name_='csType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ed90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63edd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.defocusType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='defocusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='defocusType')[source]
exportChildren(outfile, level, namespace_='', name_='defocusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647150>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.depType(status=None, depositionDate=None, depositionSite=None, processingSite=None, headerReleaseDate=None, mapReleaseDate=None, obsoletedDate=None, supersededByList=None, replaceExistingEntry=None, obsoleteList=None, details=None, inFrameEMDBId=None, title=None, authors=None, keywords=None, fittedPDBEntryIdList=None, primaryReference=None, secondaryReference=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Contains context information relevant to the EMD entry record

add_secondaryReference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='depType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='depType')[source]
exportChildren(outfile, level, namespace_='', name_='depType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_authors()[source]
get_depositionDate()[source]
get_depositionSite()[source]
get_details()[source]
get_fittedPDBEntryIdList()[source]
get_headerReleaseDate()[source]
get_inFrameEMDBId()[source]
get_keywords()[source]
get_mapReleaseDate()[source]
get_obsoleteList()[source]
get_obsoletedDate()[source]
get_primaryReference()[source]
get_processingSite()[source]
get_replaceExistingEntry()[source]
get_secondaryReference()[source]
get_status()[source]
get_supersededByList()[source]
get_title()[source]
hasContent_()[source]
insert_secondaryReference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b0d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b150>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b190>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b1d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b290>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b2d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b3d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b410>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b4d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b510>]
replace_secondaryReference_at(index, value)[source]
set_authors(authors)[source]
set_depositionDate(depositionDate)[source]
set_depositionSite(depositionSite)[source]
set_details(details)[source]
set_fittedPDBEntryIdList(fittedPDBEntryIdList)[source]
set_headerReleaseDate(headerReleaseDate)[source]
set_inFrameEMDBId(inFrameEMDBId)[source]
set_keywords(keywords)[source]
set_mapReleaseDate(mapReleaseDate)[source]
set_obsoleteList(obsoleteList)[source]
set_obsoletedDate(obsoletedDate)[source]
set_primaryReference(primaryReference)[source]
set_processingSite(processingSite)[source]
set_replaceExistingEntry(replaceExistingEntry)[source]
set_secondaryReference(secondaryReference)[source]
set_status(status)[source]
set_supersededByList(supersededByList)[source]
set_title(title)[source]
subclass = None
superclass = None
validate_depositionSiteType(value)[source]
validate_emdbEntryIdType(value)[source]
validate_emdbEntryIdType_patterns_ = [['^EMD-\\d{4,}(, EMD-\\d{4,})*$']]
validate_processingSiteType(value)[source]
class emdbXMLTranslator.emdb_19.diamType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='diamType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='diamType')[source]
exportChildren(outfile, level, namespace_='', name_='diamType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e990>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e9d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.dimensionType(numRows=None, numColumns=None, numSections=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='dimensionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='dimensionType')[source]
exportChildren(outfile, level, namespace_='', name_='dimensionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_numColumns()[source]
get_numRows()[source]
get_numSections()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6478d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647950>]
set_numColumns(numColumns)[source]
set_numRows(numRows)[source]
set_numSections(numSections)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.eDoseType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='eDoseType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='eDoseType')[source]
exportChildren(outfile, level, namespace_='', name_='eDoseType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ee90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63eed0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.eWindowType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='eWindowType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='eWindowType')[source]
exportChildren(outfile, level, namespace_='', name_='eWindowType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ef90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63efd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.emdbListType(entry=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_entry(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='emdbListType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='emdbListType')[source]
exportChildren(outfile, level, namespace_='', name_='emdbListType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_entry()[source]
hasContent_()[source]
insert_entry_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fc50>]
replace_entry_at(index, value)[source]
set_entry(entry)[source]
subclass = None
superclass = None
validate_emdbType(value)[source]
validate_emdbType_patterns_ = [['^EMD-\\d{4,}$']]
class emdbXMLTranslator.emdb_19.engSrcType(expSystem=None, expSystemStrain=None, expSystemCell=None, vector=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='engSrcType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='engSrcType')[source]
exportChildren(outfile, level, namespace_='', name_='engSrcType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_expSystem()[source]
get_expSystemCell()[source]
get_expSystemStrain()[source]
get_vector()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e150>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e190>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e1d0>]
set_expSystem(expSystem)[source]
set_expSystemCell(expSystemCell)[source]
set_expSystemStrain(expSystemStrain)[source]
set_vector(vector)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.entryType(version=None, accessCode=None, admin=None, deposition=None, map=None, supplement=None, sample=None, experiment=None, processing=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Electron Microscopy Database record identified by its accession code

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='entryType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='entryType')[source]
exportChildren(outfile, level, namespace_='', name_='entryType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_accessCode()[source]
get_admin()[source]
get_deposition()[source]
get_experiment()[source]
get_map()[source]
get_processing()[source]
get_sample()[source]
get_supplement()[source]
get_version()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604cd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604d10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604d50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604d90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604dd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604e10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604e50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604e90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c604ed0>]
set_accessCode(accessCode)[source]
set_admin(admin)[source]
set_deposition(deposition)[source]
set_experiment(experiment)[source]
set_map(map)[source]
set_processing(processing)[source]
set_sample(sample)[source]
set_supplement(supplement)[source]
set_version(version)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.expType(vitrification=None, imaging=None, imageAcquisition=None, fitting=None, specimenPreparation=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Experimental techniques used to derive the density map.

add_fitting(value)[source]
add_imageAcquisition(value)[source]
add_imaging(value)[source]
add_vitrification(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='expType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='expType')[source]
exportChildren(outfile, level, namespace_='', name_='expType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fitting()[source]
get_imageAcquisition()[source]
get_imaging()[source]
get_specimenPreparation()[source]
get_vitrification()[source]
hasContent_()[source]
insert_fitting_at(index, value)[source]
insert_imageAcquisition_at(index, value)[source]
insert_imaging_at(index, value)[source]
insert_vitrification_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bcd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bd10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bd50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bd90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bdd0>]
replace_fitting_at(index, value)[source]
replace_imageAcquisition_at(index, value)[source]
replace_imaging_at(index, value)[source]
replace_vitrification_at(index, value)[source]
set_fitting(fitting)[source]
set_imageAcquisition(imageAcquisition)[source]
set_imaging(imaging)[source]
set_specimenPreparation(specimenPreparation)[source]
set_vitrification(vitrification)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.externalRefType(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='externalRefType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='externalRefType')[source]
exportChildren(outfile, level, namespace_='', name_='externalRefType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618250>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.externalReferencesType(refUniProt=None, refGo=None, refInterpro=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_refGo(value)[source]
add_refInterpro(value)[source]
add_refUniProt(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='externalReferencesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='externalReferencesType')[source]
exportChildren(outfile, level, namespace_='', name_='externalReferencesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_refGo()[source]
get_refInterpro()[source]
get_refUniProt()[source]
hasContent_()[source]
insert_refGo_at(index, value)[source]
insert_refInterpro_at(index, value)[source]
insert_refUniProt_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636cd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636d10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636d50>]
replace_refGo_at(index, value)[source]
replace_refInterpro_at(index, value)[source]
replace_refUniProt_at(index, value)[source]
set_refGo(refGo)[source]
set_refInterpro(refInterpro)[source]
set_refUniProt(refUniProt)[source]
subclass = None
superclass = None
validate_goIdType(value)[source]
validate_goIdType_patterns_ = [['^GO:\\d{7}$']]
validate_iprIdType(value)[source]
validate_iprIdType_patterns_ = [['^IPR\\d{6}$']]
validate_uniProtType(value)[source]
validate_uniProtType_patterns_ = [['^[A-Z][\\dA-Z]{5}$']]
class emdbXMLTranslator.emdb_19.figSetType(figure=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_figure(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='figSetType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='figSetType')[source]
exportChildren(outfile, level, namespace_='', name_='figSetType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_figure()[source]
hasContent_()[source]
insert_figure_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626350>]
replace_figure_at(index, value)[source]
set_figure(figure)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.figType(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='figType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='figType')[source]
exportChildren(outfile, level, namespace_='', name_='figType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626550>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626590>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.fittingType(pdbEntryIdList=None, software=None, refProtocol=None, targetCriteria=None, overallBValue=None, refSpace=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Fitting procedure details for coordinates.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fittingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fittingType')[source]
exportChildren(outfile, level, namespace_='', name_='fittingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_overallBValue()[source]
get_pdbEntryIdList()[source]
get_refProtocol()[source]
get_refSpace()[source]
get_software()[source]
get_targetCriteria()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612150>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612190>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6121d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612290>]
set_details(details)[source]
set_overallBValue(overallBValue)[source]
set_pdbEntryIdList(pdbEntryIdList)[source]
set_refProtocol(refProtocol)[source]
set_refSpace(refSpace)[source]
set_software(software)[source]
set_targetCriteria(targetCriteria)[source]
subclass = None
superclass = None
validate_refProtocolType(value)[source]
validate_refSpaceType(value)[source]
class emdbXMLTranslator.emdb_19.fscSetType(fsc=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_fsc(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fscSetType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fscSetType')[source]
exportChildren(outfile, level, namespace_='', name_='fscSetType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fsc()[source]
hasContent_()[source]
insert_fsc_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626450>]
replace_fsc_at(index, value)[source]
set_fsc(fsc)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.fscType(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fscType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fscType')[source]
exportChildren(outfile, level, namespace_='', name_='fscType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626690>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.helixParamType(deltaPhi=None, deltaZ=None, hand=None, axialSymmetry=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helixParamType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helixParamType')[source]
exportChildren(outfile, level, namespace_='', name_='helixParamType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_axialSymmetry()[source]
get_deltaPhi()[source]
get_deltaZ()[source]
get_hand()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ec10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ec50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ec90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ecd0>]
set_axialSymmetry(axialSymmetry)[source]
set_deltaPhi(deltaPhi)[source]
set_deltaZ(deltaZ)[source]
set_hand(hand)[source]
subclass = None
superclass = None
validate_handType(value)[source]
class emdbXMLTranslator.emdb_19.helixType(details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helixType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helixType')[source]
exportChildren(outfile, level, namespace_='', name_='helixType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ed90>]
set_details(details)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.imgScanType(numDigitalImages=None, scanner=None, samplingSize=None, odRange=None, URLRawData=None, quantBitNumber=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='imgScanType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='imgScanType')[source]
exportChildren(outfile, level, namespace_='', name_='imgScanType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_URLRawData()[source]
get_details()[source]
get_numDigitalImages()[source]
get_odRange()[source]
get_quantBitNumber()[source]
get_samplingSize()[source]
get_scanner()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e290>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e2d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e390>]
set_URLRawData(URLRawData)[source]
set_details(details)[source]
set_numDigitalImages(numDigitalImages)[source]
set_odRange(odRange)[source]
set_quantBitNumber(quantBitNumber)[source]
set_samplingSize(samplingSize)[source]
set_scanner(scanner)[source]
subclass = None
superclass = None
validate_scannerType(value)[source]
class emdbXMLTranslator.emdb_19.imgType(astigmatism=None, electronSource=None, electronDose=None, energyFilter=None, imagingMode=None, nominalDefocusMin=None, nominalDefocusMax=None, illuminationMode=None, specimenHolder=None, details=None, detector=None, nominalCs=None, tiltAngleMin=None, calibratedMagnification=None, tiltAngleMax=None, temperature=None, temperatureMin=None, temperatureMax=None, microscope=None, date=None, specimenHolderModel=None, acceleratingVoltage=None, nominalMagnification=None, energyWindow=None, detectorDistance=None, electronBeamTiltParams=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='imgType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='imgType')[source]
exportChildren(outfile, level, namespace_='', name_='imgType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_acceleratingVoltage()[source]
get_astigmatism()[source]
get_calibratedMagnification()[source]
get_date()[source]
get_details()[source]
get_detector()[source]
get_detectorDistance()[source]
get_electronBeamTiltParams()[source]
get_electronDose()[source]
get_electronSource()[source]
get_energyFilter()[source]
get_energyWindow()[source]
get_illuminationMode()[source]
get_imagingMode()[source]
get_microscope()[source]
get_nominalCs()[source]
get_nominalDefocusMax()[source]
get_nominalDefocusMin()[source]
get_nominalMagnification()[source]
get_specimenHolder()[source]
get_specimenHolderModel()[source]
get_temperature()[source]
get_temperatureMax()[source]
get_temperatureMin()[source]
get_tiltAngleMax()[source]
get_tiltAngleMin()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618a90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618ad0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618b10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618b50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618b90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618bd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618c10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618c50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618c90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618cd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618d10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618d50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618d90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618dd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618e10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618e50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618e90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618ed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618f10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618f50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618f90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618fd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e050>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e090>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e0d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e110>]
set_acceleratingVoltage(acceleratingVoltage)[source]
set_astigmatism(astigmatism)[source]
set_calibratedMagnification(calibratedMagnification)[source]
set_date(date)[source]
set_details(details)[source]
set_detector(detector)[source]
set_detectorDistance(detectorDistance)[source]
set_electronBeamTiltParams(electronBeamTiltParams)[source]
set_electronDose(electronDose)[source]
set_electronSource(electronSource)[source]
set_energyFilter(energyFilter)[source]
set_energyWindow(energyWindow)[source]
set_illuminationMode(illuminationMode)[source]
set_imagingMode(imagingMode)[source]
set_microscope(microscope)[source]
set_nominalCs(nominalCs)[source]
set_nominalDefocusMax(nominalDefocusMax)[source]
set_nominalDefocusMin(nominalDefocusMin)[source]
set_nominalMagnification(nominalMagnification)[source]
set_specimenHolder(specimenHolder)[source]
set_specimenHolderModel(specimenHolderModel)[source]
set_temperature(temperature)[source]
set_temperatureMax(temperatureMax)[source]
set_temperatureMin(temperatureMin)[source]
set_tiltAngleMax(tiltAngleMax)[source]
set_tiltAngleMin(tiltAngleMin)[source]
subclass = None
superclass = None
validate_detectorType(value)[source]
validate_eSourceType(value)[source]
validate_illumType(value)[source]
validate_imgModeType(value)[source]
validate_microscopeType(value)[source]
validate_specimenHolderType(value)[source]
class emdbXMLTranslator.emdb_19.jrnlArtType(authors=None, articleTitle=None, journal=None, volume=None, firstPage=None, lastPage=None, year=None, externalReference=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_externalReference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='jrnlArtType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='jrnlArtType')[source]
exportChildren(outfile, level, namespace_='', name_='jrnlArtType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_articleTitle()[source]
get_authors()[source]
get_externalReference()[source]
get_firstPage()[source]
get_journal()[source]
get_lastPage()[source]
get_volume()[source]
get_year()[source]
hasContent_()[source]
insert_externalReference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612bd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612c10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612c50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612c90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612cd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612d10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612d50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612d90>]
replace_externalReference_at(index, value)[source]
set_articleTitle(articleTitle)[source]
set_authors(authors)[source]
set_externalReference(externalReference)[source]
set_firstPage(firstPage)[source]
set_journal(journal)[source]
set_lastPage(lastPage)[source]
set_volume(volume)[source]
set_year(year)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.labelType(formula=None, oligomericDetails=None, numCopies=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='labelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='labelType')[source]
exportChildren(outfile, level, namespace_='', name_='labelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_formula()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636410>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636490>]
set_formula(formula)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.layerLineType(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='layerLineType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='layerLineType')[source]
exportChildren(outfile, level, namespace_='', name_='layerLineType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e150>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.lengthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='lengthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='lengthType')[source]
exportChildren(outfile, level, namespace_='', name_='lengthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e7d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.ligandType(sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, oligomericDetails=None, numCopies=None, recombinantExpFlag=None, natSource=None, engSource=None, details=None, externalReferences=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ligandType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ligandType')[source]
exportChildren(outfile, level, namespace_='', name_='ligandType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_engSource()[source]
get_externalReferences()[source]
get_natSource()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
get_recombinantExpFlag()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_synSpeciesName()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636150>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636190>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6361d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636290>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6362d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636350>]
set_details(details)[source]
set_engSource(engSource)[source]
set_externalReferences(externalReferences)[source]
set_natSource(natSource)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
set_recombinantExpFlag(recombinantExpFlag)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.limType(valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='limType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='limType')[source]
exportChildren(outfile, level, namespace_='', name_='limType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f850>]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.limitType(limitRow=None, limitCol=None, limitSec=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='limitType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='limitType')[source]
exportChildren(outfile, level, namespace_='', name_='limitType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_limitCol()[source]
get_limitRow()[source]
get_limitSec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f690>]
set_limitCol(limitCol)[source]
set_limitRow(limitRow)[source]
set_limitSec(limitSec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.mapFileType(sizeKb=None, type_=None, format=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mapFileType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mapFileType')[source]
exportChildren(outfile, level, namespace_='', name_='mapFileType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_format()[source]
get_sizeKb()[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6473d0>]
set_format(format)[source]
set_sizeKb(sizeKb)[source]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.mapType(file=None, dataType=None, dimensions=None, origin=None, limit=None, spacing=None, cell=None, axisOrder=None, statistics=None, spaceGroupNumber=None, details=None, pixelSpacing=None, contourLevel=None, annotationDetails=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Information on the volume density map

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mapType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mapType')[source]
exportChildren(outfile, level, namespace_='', name_='mapType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_annotationDetails()[source]
get_axisOrder()[source]
get_cell()[source]
get_contourLevel()[source]
get_dataType()[source]
get_details()[source]
get_dimensions()[source]
get_file()[source]
get_limit()[source]
get_origin()[source]
get_pixelSpacing()[source]
get_spaceGroupNumber()[source]
get_spacing()[source]
get_statistics()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b6d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b7d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b810>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b850>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b8d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60b950>]
set_annotationDetails(annotationDetails)[source]
set_axisOrder(axisOrder)[source]
set_cell(cell)[source]
set_contourLevel(contourLevel)[source]
set_dataType(dataType)[source]
set_details(details)[source]
set_dimensions(dimensions)[source]
set_file(file)[source]
set_limit(limit)[source]
set_origin(origin)[source]
set_pixelSpacing(pixelSpacing)[source]
set_spaceGroupNumber(spaceGroupNumber)[source]
set_spacing(spacing)[source]
set_statistics(statistics)[source]
subclass = None
superclass = None
validate_mapDataType(value)[source]
class emdbXMLTranslator.emdb_19.mskFileType(sizeKb=None, type_=None, format=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mskFileType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mskFileType')[source]
exportChildren(outfile, level, namespace_='', name_='mskFileType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_format()[source]
get_sizeKb()[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6474d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647510>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647550>]
set_format(format)[source]
set_sizeKb(sizeKb)[source]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.mskSetType(mask=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_mask(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mskSetType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mskSetType')[source]
exportChildren(outfile, level, namespace_='', name_='mskSetType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_mask()[source]
hasContent_()[source]
insert_mask_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626750>]
replace_mask_at(index, value)[source]
set_mask(mask)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.mskType(file=None, dataType=None, dimensions=None, spacing=None, origin=None, limit=None, cell=None, axisOrder=None, statistics=None, pixelSpacing=None, details=None, annotationDetails=None, spaceGroupNumber=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mskType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mskType')[source]
exportChildren(outfile, level, namespace_='', name_='mskType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_annotationDetails()[source]
get_axisOrder()[source]
get_cell()[source]
get_dataType()[source]
get_details()[source]
get_dimensions()[source]
get_file()[source]
get_limit()[source]
get_origin()[source]
get_pixelSpacing()[source]
get_spaceGroupNumber()[source]
get_spacing()[source]
get_statistics()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626850>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6268d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626990>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6269d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626a10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626a50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626a90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626ad0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626b10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626b50>]
set_annotationDetails(annotationDetails)[source]
set_axisOrder(axisOrder)[source]
set_cell(cell)[source]
set_dataType(dataType)[source]
set_details(details)[source]
set_dimensions(dimensions)[source]
set_file(file)[source]
set_limit(limit)[source]
set_origin(origin)[source]
set_pixelSpacing(pixelSpacing)[source]
set_spaceGroupNumber(spaceGroupNumber)[source]
set_spacing(spacing)[source]
set_statistics(statistics)[source]
subclass = None
superclass = None
validate_mapDataType(value)[source]
class emdbXMLTranslator.emdb_19.mwType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mwType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mwType')[source]
exportChildren(outfile, level, namespace_='', name_='mwType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e3d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.natSrcType(cell=None, organelle=None, organOrTissue=None, cellLocation=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natSrcType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natSrcType')[source]
exportChildren(outfile, level, namespace_='', name_='natSrcType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_cellLocation()[source]
get_organOrTissue()[source]
get_organelle()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636f50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636f90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636fd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e050>]
set_cell(cell)[source]
set_cellLocation(cellLocation)[source]
set_organOrTissue(organOrTissue)[source]
set_organelle(organelle)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.natSrcVirusType(hostCategory=None, hostSpecies=None, hostSpeciesStrain=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natSrcVirusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natSrcVirusType')[source]
exportChildren(outfile, level, namespace_='', name_='natSrcVirusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_hostCategory()[source]
get_hostSpecies()[source]
get_hostSpeciesStrain()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636e10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636e50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636e90>]
set_hostCategory(hostCategory)[source]
set_hostSpecies(hostSpecies)[source]
set_hostSpeciesStrain(hostSpeciesStrain)[source]
subclass = None
superclass = None
validate_hostCategoryType(value)[source]
class emdbXMLTranslator.emdb_19.nonJrnlArtType(authors=None, chapterTitle=None, book=None, thesisTitle=None, editor=None, publisher=None, publisherLocation=None, volume=None, firstPage=None, lastPage=None, year=None, externalReference=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_externalReference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='nonJrnlArtType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='nonJrnlArtType')[source]
exportChildren(outfile, level, namespace_='', name_='nonJrnlArtType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_authors()[source]
get_book()[source]
get_chapterTitle()[source]
get_editor()[source]
get_externalReference()[source]
get_firstPage()[source]
get_lastPage()[source]
get_publisher()[source]
get_publisherLocation()[source]
get_thesisTitle()[source]
get_volume()[source]
get_year()[source]
hasContent_()[source]
insert_externalReference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612e50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612e90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612ed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612f10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612f50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612f90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612fd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618050>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618090>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6180d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618150>]
replace_externalReference_at(index, value)[source]
set_authors(authors)[source]
set_book(book)[source]
set_chapterTitle(chapterTitle)[source]
set_editor(editor)[source]
set_externalReference(externalReference)[source]
set_firstPage(firstPage)[source]
set_lastPage(lastPage)[source]
set_publisher(publisher)[source]
set_publisherLocation(publisherLocation)[source]
set_thesisTitle(thesisTitle)[source]
set_volume(volume)[source]
set_year(year)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.nuclAcidType(sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, syntheticFlag=None, sequence=None, class_=None, structure=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='nuclAcidType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='nuclAcidType')[source]
exportChildren(outfile, level, namespace_='', name_='nuclAcidType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_class()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_sequence()[source]
get_structure()[source]
get_synSpeciesName()[source]
get_syntheticFlag()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ee90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62eed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ef10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ef50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ef90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62efd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636050>]
set_class(class_)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_sequence(sequence)[source]
set_structure(structure)[source]
set_synSpeciesName(synSpeciesName)[source]
set_syntheticFlag(syntheticFlag)[source]
subclass = None
superclass = None
validate_naClassType(value)[source]
validate_naStructType(value)[source]
class emdbXMLTranslator.emdb_19.origType(valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='origType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='origType')[source]
exportChildren(outfile, level, namespace_='', name_='origType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e890>]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.originType(originRow=None, originCol=None, originSec=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='originType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='originType')[source]
exportChildren(outfile, level, namespace_='', name_='originType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_originCol()[source]
get_originRow()[source]
get_originSec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647f10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647f50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647f90>]
set_originCol(originCol)[source]
set_originRow(originRow)[source]
set_originSec(originSec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.pdbidList2Type(pdbEntryId=None, pdbChainId=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_pdbChainId(value)[source]
add_pdbEntryId(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pdbidList2Type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pdbidList2Type')[source]
exportChildren(outfile, level, namespace_='', name_='pdbidList2Type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_pdbChainId()[source]
get_pdbEntryId()[source]
hasContent_()[source]
insert_pdbChainId_at(index, value)[source]
insert_pdbEntryId_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fe50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fe90>]
replace_pdbChainId_at(index, value)[source]
replace_pdbEntryId_at(index, value)[source]
set_pdbChainId(pdbChainId)[source]
set_pdbEntryId(pdbEntryId)[source]
subclass = None
superclass = None
validate_pdbidType(value)[source]
validate_pdbidType_patterns_ = [['^\\d[0-9a-zA-Z]{3}$']]
class emdbXMLTranslator.emdb_19.pdbidListType(fittedPDBEntryId=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_fittedPDBEntryId(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pdbidListType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pdbidListType')[source]
exportChildren(outfile, level, namespace_='', name_='pdbidListType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fittedPDBEntryId()[source]
hasContent_()[source]
insert_fittedPDBEntryId_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fd50>]
replace_fittedPDBEntryId_at(index, value)[source]
set_fittedPDBEntryId(fittedPDBEntryId)[source]
subclass = None
superclass = None
validate_pdbidType(value)[source]
validate_pdbidType_patterns_ = [['^\\d[0-9a-zA-Z]{3}$']]
class emdbXMLTranslator.emdb_19.pixType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pixType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pixType')[source]
exportChildren(outfile, level, namespace_='', name_='pixType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f790>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.pixelSpacingType(pixelX=None, pixelY=None, pixelZ=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pixelSpacingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pixelSpacingType')[source]
exportChildren(outfile, level, namespace_='', name_='pixelSpacingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_pixelX()[source]
get_pixelY()[source]
get_pixelZ()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647dd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647e10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647e50>]
set_pixelX(pixelX)[source]
set_pixelY(pixelY)[source]
set_pixelZ(pixelZ)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.prRefType(journalArticle=None, nonJournalArticle=None, published=None)[source]

Bases: emdbXMLTranslator.emdb_19.pubType

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='prRefType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='prRefType')[source]
exportChildren(outfile, level, namespace_='', name_='prRefType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_published()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612b10>]
set_published(published)[source]
subclass = None
superclass

alias of pubType

class emdbXMLTranslator.emdb_19.processType(method=None, reconstruction=None, twoDCrystal=None, helical=None, subtomogramAveraging=None, tomography=None, singleParticle=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Digital processing of the image data.

add_reconstruction(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='processType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='processType')[source]
exportChildren(outfile, level, namespace_='', name_='processType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helical()[source]
get_method()[source]
get_reconstruction()[source]
get_singleParticle()[source]
get_subtomogramAveraging()[source]
get_tomography()[source]
get_twoDCrystal()[source]
hasContent_()[source]
insert_reconstruction_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60be90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bf10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bf50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bf90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bfd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612050>]
replace_reconstruction_at(index, value)[source]
set_helical(helical)[source]
set_method(method)[source]
set_reconstruction(reconstruction)[source]
set_singleParticle(singleParticle)[source]
set_subtomogramAveraging(subtomogramAveraging)[source]
set_tomography(tomography)[source]
set_twoDCrystal(twoDCrystal)[source]
subclass = None
superclass = None
validate_methodType(value)[source]
class emdbXMLTranslator.emdb_19.proteinType(sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, oligomericDetails=None, numCopies=None, recombinantExpFlag=None, natSource=None, engSource=None, details=None, externalReferences=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='proteinType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='proteinType')[source]
exportChildren(outfile, level, namespace_='', name_='proteinType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_engSource()[source]
get_externalReferences()[source]
get_natSource()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
get_recombinantExpFlag()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_synSpeciesName()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e8d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e990>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e9d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ea10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ea50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ea90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62ead0>]
set_details(details)[source]
set_engSource(engSource)[source]
set_externalReferences(externalReferences)[source]
set_natSource(natSource)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
set_recombinantExpFlag(recombinantExpFlag)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.pubType(journalArticle=None, nonJournalArticle=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pubType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pubType')[source]
exportChildren(outfile, level, namespace_='', name_='pubType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_extensiontype_()[source]
get_journalArticle()[source]
get_nonJournalArticle()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612a10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612a50>]
set_extensiontype_(extensiontype_)[source]
set_journalArticle(journalArticle)[source]
set_nonJournalArticle(nonJournalArticle)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.reconsType(algorithm=None, software=None, ctfCorrection=None, resolutionByAuthor=None, resolutionMethod=None, details=None, eulerAnglesDetails=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='reconsType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='reconsType')[source]
exportChildren(outfile, level, namespace_='', name_='reconsType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_algorithm()[source]
get_ctfCorrection()[source]
get_details()[source]
get_eulerAnglesDetails()[source]
get_resolutionByAuthor()[source]
get_resolutionMethod()[source]
get_software()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e4d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e510>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e550>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e590>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e5d0>]
set_algorithm(algorithm)[source]
set_ctfCorrection(ctfCorrection)[source]
set_details(details)[source]
set_eulerAnglesDetails(eulerAnglesDetails)[source]
set_resolutionByAuthor(resolutionByAuthor)[source]
set_resolutionMethod(resolutionMethod)[source]
set_software(software)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.riboTypeEu(eukaryote=None, sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, oligomericDetails=None, numCopies=None, recombinantExpFlag=None, natSource=None, engSource=None, details=None, externalReferences=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='riboTypeEu', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='riboTypeEu')[source]
exportChildren(outfile, level, namespace_='', name_='riboTypeEu', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_engSource()[source]
get_eukaryote()[source]
get_externalReferences()[source]
get_natSource()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
get_recombinantExpFlag()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_synSpeciesName()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636550>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636590>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6365d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6366d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6367d0>]
set_details(details)[source]
set_engSource(engSource)[source]
set_eukaryote(eukaryote)[source]
set_externalReferences(externalReferences)[source]
set_natSource(natSource)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
set_recombinantExpFlag(recombinantExpFlag)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.riboTypePro(prokaryote=None, sciSpeciesName=None, sciSpeciesStrain=None, synSpeciesName=None, oligomericDetails=None, numCopies=None, recombinantExpFlag=None, natSource=None, engSource=None, details=None, externalReferences=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='riboTypePro', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='riboTypePro')[source]
exportChildren(outfile, level, namespace_='', name_='riboTypePro', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_engSource()[source]
get_externalReferences()[source]
get_natSource()[source]
get_numCopies()[source]
get_oligomericDetails()[source]
get_prokaryote()[source]
get_recombinantExpFlag()[source]
get_sciSpeciesName()[source]
get_sciSpeciesStrain()[source]
get_synSpeciesName()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6368d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636990>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6369d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636a10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636a50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636a90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636ad0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636b10>]
set_details(details)[source]
set_engSource(engSource)[source]
set_externalReferences(externalReferences)[source]
set_natSource(natSource)[source]
set_numCopies(numCopies)[source]
set_oligomericDetails(oligomericDetails)[source]
set_prokaryote(prokaryote)[source]
set_recombinantExpFlag(recombinantExpFlag)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.samplConcType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='samplConcType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='samplConcType')[source]
exportChildren(outfile, level, namespace_='', name_='samplConcType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e4d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.samplSizeType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='samplSizeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='samplSizeType')[source]
exportChildren(outfile, level, namespace_='', name_='samplSizeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63eb90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63ebd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.samplType(numComponents=None, name=None, compDegree=None, molWtTheo=None, details=None, molWtMethod=None, molWtExp=None, sampleComponentList=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Nature of the biological sample studied. [/emdEntry/sample]

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='samplType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='samplType')[source]
exportChildren(outfile, level, namespace_='', name_='samplType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_compDegree()[source]
get_details()[source]
get_molWtExp()[source]
get_molWtMethod()[source]
get_molWtTheo()[source]
get_name()[source]
get_numComponents()[source]
get_sampleComponentList()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60ba10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60ba50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60ba90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bad0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bb10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bb50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bb90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c60bbd0>]
set_compDegree(compDegree)[source]
set_details(details)[source]
set_molWtExp(molWtExp)[source]
set_molWtMethod(molWtMethod)[source]
set_molWtTheo(molWtTheo)[source]
set_name(name)[source]
set_numComponents(numComponents)[source]
set_sampleComponentList(sampleComponentList)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.sciSpeciesType(ncbiTaxId=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sciSpeciesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sciSpeciesType')[source]
exportChildren(outfile, level, namespace_='', name_='sciSpeciesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ncbiTaxId()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636bd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c636c10>]
set_ncbiTaxId(ncbiTaxId)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.shellType(id=None, nameElement=None, diameter=None, tNumber=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='shellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='shellType')[source]
exportChildren(outfile, level, namespace_='', name_='shellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_diameter()[source]
get_id()[source]
get_nameElement()[source]
get_tNumber()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e7d0>]
set_diameter(diameter)[source]
set_id(id)[source]
set_nameElement(nameElement)[source]
set_tNumber(tNumber)[source]
subclass = None
superclass = None
validate_floatOrNAType(value)[source]
class emdbXMLTranslator.emdb_19.singPartType(appliedSymmetry=None, numProjections=None, numClassAverages=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='singPartType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='singPartType')[source]
exportChildren(outfile, level, namespace_='', name_='singPartType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_appliedSymmetry()[source]
get_details()[source]
get_numClassAverages()[source]
get_numProjections()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ee90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61eed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ef10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ef50>]
set_appliedSymmetry(appliedSymmetry)[source]
set_details(details)[source]
set_numClassAverages(numClassAverages)[source]
set_numProjections(numProjections)[source]
subclass = None
superclass = None
validate_pointGroupSymmetryType(value)[source]
validate_pointGroupSymmetryType_patterns_ = [['^C\\d+|D\\d+|O|T|I$']]
class emdbXMLTranslator.emdb_19.slcCType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcCType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcCType')[source]
exportChildren(outfile, level, namespace_='', name_='slcCType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fa50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64fa90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcCellType(cellA=None, cellB=None, cellC=None, cellAlpha=None, cellBeta=None, cellGamma=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcCellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcCellType')[source]
exportChildren(outfile, level, namespace_='', name_='slcCellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cellA()[source]
get_cellAlpha()[source]
get_cellB()[source]
get_cellBeta()[source]
get_cellC()[source]
get_cellGamma()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f410>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f4d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f510>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f550>]
set_cellA(cellA)[source]
set_cellAlpha(cellAlpha)[source]
set_cellB(cellB)[source]
set_cellBeta(cellBeta)[source]
set_cellC(cellC)[source]
set_cellGamma(cellGamma)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcDimensionType(numRows=None, numColumns=None, numSections=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcDimensionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcDimensionType')[source]
exportChildren(outfile, level, namespace_='', name_='slcDimensionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_numColumns()[source]
get_numRows()[source]
get_numSections()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647a10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647a50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647a90>]
set_numColumns(numColumns)[source]
set_numRows(numRows)[source]
set_numSections(numSections)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcFileType(sizeKb=None, type_=None, format=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcFileType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcFileType')[source]
exportChildren(outfile, level, namespace_='', name_='slcFileType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_format()[source]
get_sizeKb()[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6476d0>]
set_format(format)[source]
set_sizeKb(sizeKb)[source]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcSetType(slice=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_slice(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcSetType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcSetType')[source]
exportChildren(outfile, level, namespace_='', name_='slcSetType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_slice()[source]
hasContent_()[source]
insert_slice_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626c10>]
replace_slice_at(index, value)[source]
set_slice(slice)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcSpacingType(spacingRow=None, spacingCol=None, spacingSec=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcSpacingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcSpacingType')[source]
exportChildren(outfile, level, namespace_='', name_='slcSpacingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_spacingCol()[source]
get_spacingRow()[source]
get_spacingSec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647c90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647cd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647d10>]
set_spacingCol(spacingCol)[source]
set_spacingRow(spacingRow)[source]
set_spacingSec(spacingSec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.slcType(file=None, dataType=None, dimensions=None, spacing=None, origin=None, limit=None, cell=None, axisOrder=None, statistics=None, pixelSpacing=None, details=None, annotationDetails=None, spaceGroupNumber=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slcType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slcType')[source]
exportChildren(outfile, level, namespace_='', name_='slcType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_annotationDetails()[source]
get_axisOrder()[source]
get_cell()[source]
get_dataType()[source]
get_details()[source]
get_dimensions()[source]
get_file()[source]
get_limit()[source]
get_origin()[source]
get_pixelSpacing()[source]
get_spaceGroupNumber()[source]
get_spacing()[source]
get_statistics()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626d10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626d50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626d90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626dd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626e10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626e50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626e90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626ed0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626f10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626f50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626f90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626fd0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e050>]
set_annotationDetails(annotationDetails)[source]
set_axisOrder(axisOrder)[source]
set_cell(cell)[source]
set_dataType(dataType)[source]
set_details(details)[source]
set_dimensions(dimensions)[source]
set_file(file)[source]
set_limit(limit)[source]
set_origin(origin)[source]
set_pixelSpacing(pixelSpacing)[source]
set_spaceGroupNumber(spaceGroupNumber)[source]
set_spacing(spacing)[source]
set_statistics(statistics)[source]
subclass = None
superclass = None
validate_mapDataType(value)[source]
class emdbXMLTranslator.emdb_19.smplCompListType(sampleComponent=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

List of individual sample components. [/emdEntry/sample/sampleComponentList]

add_sampleComponent(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='smplCompListType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='smplCompListType')[source]
exportChildren(outfile, level, namespace_='', name_='smplCompListType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_sampleComponent()[source]
hasContent_()[source]
insert_sampleComponent_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6124d0>]
replace_sampleComponent_at(index, value)[source]
set_sampleComponent(sampleComponent)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.smplCompType(componentID=None, entry=None, sciName=None, synName=None, molWtTheo=None, molWtExp=None, details=None, protein=None, cellular_component=None, virus=None, nucleic_acid=None, ligand=None, label=None, ribosome_eukaryote=None, ribosome_prokaryote=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

A single sample component. [/emdEntry/sample/sampleComponentList/sampleComponent]

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='smplCompType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='smplCompType')[source]
exportChildren(outfile, level, namespace_='', name_='smplCompType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cellular_component()[source]
get_componentID()[source]
get_details()[source]
get_entry()[source]
get_label()[source]
get_ligand()[source]
get_molWtExp()[source]
get_molWtTheo()[source]
get_nucleic_acid()[source]
get_protein()[source]
get_ribosome_eukaryote()[source]
get_ribosome_prokaryote()[source]
get_sciName()[source]
get_synName()[source]
get_virus()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6125d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6126d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6127d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612810>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612850>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6128d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612950>]
set_cellular_component(cellular_component)[source]
set_componentID(componentID)[source]
set_details(details)[source]
set_entry(entry)[source]
set_label(label)[source]
set_ligand(ligand)[source]
set_molWtExp(molWtExp)[source]
set_molWtTheo(molWtTheo)[source]
set_nucleic_acid(nucleic_acid)[source]
set_protein(protein)[source]
set_ribosome_eukaryote(ribosome_eukaryote)[source]
set_ribosome_prokaryote(ribosome_prokaryote)[source]
set_sciName(sciName)[source]
set_synName(synName)[source]
set_virus(virus)[source]
subclass = None
superclass = None
validate_cmpntClassType(value)[source]
class emdbXMLTranslator.emdb_19.smplPrepType(specimenState=None, specimenConc=None, buffer=None, staining=None, specimenSupportDetails=None, twoDCrystalParameters=None, threeDCrystalParameters=None, helicalParameters=None, crystalGrowDetails=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='smplPrepType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='smplPrepType')[source]
exportChildren(outfile, level, namespace_='', name_='smplPrepType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_buffer()[source]
get_crystalGrowDetails()[source]
get_helicalParameters()[source]
get_specimenConc()[source]
get_specimenState()[source]
get_specimenSupportDetails()[source]
get_staining()[source]
get_threeDCrystalParameters()[source]
get_twoDCrystalParameters()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618550>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618590>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6185d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618650>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6186d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618750>]
set_buffer(buffer)[source]
set_crystalGrowDetails(crystalGrowDetails)[source]
set_helicalParameters(helicalParameters)[source]
set_specimenConc(specimenConc)[source]
set_specimenState(specimenState)[source]
set_specimenSupportDetails(specimenSupportDetails)[source]
set_staining(staining)[source]
set_threeDCrystalParameters(threeDCrystalParameters)[source]
set_twoDCrystalParameters(twoDCrystalParameters)[source]
subclass = None
superclass = None
validate_specimenType(value)[source]
class emdbXMLTranslator.emdb_19.spacingType(spacingRow=None, spacingCol=None, spacingSec=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='spacingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='spacingType')[source]
exportChildren(outfile, level, namespace_='', name_='spacingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_spacingCol()[source]
get_spacingRow()[source]
get_spacingSec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647b50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647b90>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647bd0>]
set_spacingCol(spacingCol)[source]
set_spacingRow(spacingRow)[source]
set_spacingSec(spacingSec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.statisticsType(minimum=None, maximum=None, average=None, std=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='statisticsType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='statisticsType')[source]
exportChildren(outfile, level, namespace_='', name_='statisticsType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average()[source]
get_maximum()[source]
get_minimum()[source]
get_std()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f090>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f0d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f110>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64f150>]
set_average(average)[source]
set_maximum(maximum)[source]
set_minimum(minimum)[source]
set_std(std)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.statusType(prior=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='statusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='statusType')[source]
exportChildren(outfile, level, namespace_='', name_='statusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_prior()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64ff50>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c64ff90>]
set_prior(prior)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
validate_status(value)[source]
class emdbXMLTranslator.emdb_19.structFactType(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='structFactType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='structFactType')[source]
exportChildren(outfile, level, namespace_='', name_='structFactType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e250>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.subTomType(appliedSymmetry=None, numSubtomograms=None, numClassAverages=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='subTomType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='subTomType')[source]
exportChildren(outfile, level, namespace_='', name_='subTomType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_appliedSymmetry()[source]
get_details()[source]
get_numClassAverages()[source]
get_numSubtomograms()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626050>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626090>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6260d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626110>]
set_appliedSymmetry(appliedSymmetry)[source]
set_details(details)[source]
set_numClassAverages(numClassAverages)[source]
set_numSubtomograms(numSubtomograms)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.supplType(maskSet=None, sliceSet=None, figureSet=None, fscSet=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

Supplemental data sets.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='supplType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='supplType')[source]
exportChildren(outfile, level, namespace_='', name_='supplType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_figureSet()[source]
get_fscSet()[source]
get_maskSet()[source]
get_sliceSet()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6123d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c612410>]
set_figureSet(figureSet)[source]
set_fscSet(fscSet)[source]
set_maskSet(maskSet)[source]
set_sliceSet(sliceSet)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.tempType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tempType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tempType')[source]
exportChildren(outfile, level, namespace_='', name_='tempType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e590>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c63e5d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.threeDxtalParamType(aLength=None, bLength=None, cLength=None, alpha=None, beta=None, gamma=None, spaceGroup=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='threeDxtalParamType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='threeDxtalParamType')[source]
exportChildren(outfile, level, namespace_='', name_='threeDxtalParamType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_aLength()[source]
get_alpha()[source]
get_bLength()[source]
get_beta()[source]
get_cLength()[source]
get_gamma()[source]
get_spaceGroup()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e8d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e990>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e9d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ea10>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61ea50>]
set_aLength(aLength)[source]
set_alpha(alpha)[source]
set_bLength(bLength)[source]
set_beta(beta)[source]
set_cLength(cLength)[source]
set_gamma(gamma)[source]
set_spaceGroup(spaceGroup)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.tiltType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tiltType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tiltType')[source]
exportChildren(outfile, level, namespace_='', name_='tiltType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c647250>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_19.tomogrType(appliedSymmetry=None, tiltAngleIncrement=None, numSections=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tomogrType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tomogrType')[source]
exportChildren(outfile, level, namespace_='', name_='tomogrType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_appliedSymmetry()[source]
get_details()[source]
get_numSections()[source]
get_tiltAngleIncrement()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6261d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626210>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626250>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c626290>]
set_appliedSymmetry(appliedSymmetry)[source]
set_details(details)[source]
set_numSections(numSections)[source]
set_tiltAngleIncrement(tiltAngleIncrement)[source]
subclass = None
superclass = None
validate_pointGroupSymmetryType(value)[source]
validate_pointGroupSymmetryType_patterns_ = [['^C\\d+|D\\d+|O|T|I$']]
class emdbXMLTranslator.emdb_19.twoDxtalParamType(aLength=None, bLength=None, cLength=None, alpha=None, beta=None, gamma=None, planeGroup=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='twoDxtalParamType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='twoDxtalParamType')[source]
exportChildren(outfile, level, namespace_='', name_='twoDxtalParamType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_aLength()[source]
get_alpha()[source]
get_bLength()[source]
get_beta()[source]
get_cLength()[source]
get_gamma()[source]
get_planeGroup()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e690>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e6d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e710>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e750>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e790>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e7d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61e810>]
set_aLength(aLength)[source]
set_alpha(alpha)[source]
set_bLength(bLength)[source]
set_beta(beta)[source]
set_cLength(cLength)[source]
set_gamma(gamma)[source]
set_planeGroup(planeGroup)[source]
subclass = None
superclass = None
validate_plGrpType(value)[source]
class emdbXMLTranslator.emdb_19.virusType(sciSpeciesName=None, synSpeciesName=None, sciSpeciesSerotype=None, sciSpeciesSerocomplex=None, sciSpeciesSubspecies=None, sciSpeciesStrain=None, empty=None, enveloped=None, isolate=None, class_=None, externalReferences=None, natSource=None, engSource=None, shell=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

add_engSource(value)[source]
add_externalReferences(value)[source]
add_natSource(value)[source]
add_shell(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='virusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='virusType')[source]
exportChildren(outfile, level, namespace_='', name_='virusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_class()[source]
get_empty()[source]
get_engSource()[source]
get_enveloped()[source]
get_externalReferences()[source]
get_isolate()[source]
get_natSource()[source]
get_sciSpeciesName()[source]
get_sciSpeciesSerocomplex()[source]
get_sciSpeciesSerotype()[source]
get_sciSpeciesStrain()[source]
get_sciSpeciesSubspecies()[source]
get_shell()[source]
get_synSpeciesName()[source]
hasContent_()[source]
insert_engSource_at(index, value)[source]
insert_externalReferences_at(index, value)[source]
insert_natSource_at(index, value)[source]
insert_shell_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e310>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e350>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e390>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e3d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e410>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e450>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e490>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e4d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e510>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e550>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e590>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e5d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e610>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c62e650>]
replace_engSource_at(index, value)[source]
replace_externalReferences_at(index, value)[source]
replace_natSource_at(index, value)[source]
replace_shell_at(index, value)[source]
set_class(class_)[source]
set_empty(empty)[source]
set_engSource(engSource)[source]
set_enveloped(enveloped)[source]
set_externalReferences(externalReferences)[source]
set_isolate(isolate)[source]
set_natSource(natSource)[source]
set_sciSpeciesName(sciSpeciesName)[source]
set_sciSpeciesSerocomplex(sciSpeciesSerocomplex)[source]
set_sciSpeciesSerotype(sciSpeciesSerotype)[source]
set_sciSpeciesStrain(sciSpeciesStrain)[source]
set_sciSpeciesSubspecies(sciSpeciesSubspecies)[source]
set_shell(shell)[source]
set_synSpeciesName(synSpeciesName)[source]
subclass = None
superclass = None
validate_virusClassType(value)[source]
validate_virusIsolType(value)[source]
class emdbXMLTranslator.emdb_19.vitrifType(cryogenName=None, humidity=None, temperature=None, instrument=None, method=None, timeResolvedState=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='vitrifType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='vitrifType')[source]
exportChildren(outfile, level, namespace_='', name_='vitrifType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_cryogenName()[source]
get_details()[source]
get_humidity()[source]
get_instrument()[source]
get_method()[source]
get_temperature()[source]
get_timeResolvedState()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618810>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618850>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618890>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c6188d0>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618910>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618950>, <emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c618990>]
set_cryogenName(cryogenName)[source]
set_details(details)[source]
set_humidity(humidity)[source]
set_instrument(instrument)[source]
set_method(method)[source]
set_temperature(temperature)[source]
set_timeResolvedState(timeResolvedState)[source]
subclass = None
superclass = None
validate_cryogenType(value)[source]
validate_vitrInstrType(value)[source]
class emdbXMLTranslator.emdb_19.xtal2DType(details=None)[source]

Bases: emdbXMLTranslator.emdb_19.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='xtal2DType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='xtal2DType')[source]
exportChildren(outfile, level, namespace_='', name_='xtal2DType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_19.MemberSpec_ object at 0x10c61eb10>]
set_details(details)[source]
subclass = None
superclass = None

emdbXMLTranslator.emdb_19_to_json module

emdb_19_to_json

Reads in a EMDB header file following 1.9 schema and outputs summary information as a JSON. This is an stub example to show how to use emdb_19.py to read the header file.

TODO:

Version history:

Copyright [2014-2015] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

class emdbXMLTranslator.emdb_19_to_json.EMDBXML19JSONTranslator[source]

Class for translating summary info from EMDB 1.9 to a JSON file

setWarningLevel(level)[source]

Set the level of logging warnings. 0 = no warnings, 3 = max warnings, 1 = default

Parameters @param level: warning level 0 -> 3

translate(inputFile, outputFile)[source]

Translate EMDB 1.9 to a JSON. Summary info only

Parameters @param inputFile: input file in EMDB 1.9 XML @param outputFile: output JSON file

warn(level, msg)[source]

Log a warning message but take into account the warningLevel

Parameters: @param level: only messages with level >= warningLevel are printed @param msg: warning message

emdbXMLTranslator.emdb_19_to_json.main()[source]

Extract summary info from EMDB XML 1.9 file to JSON

emdbXMLTranslator.emdb_20_to_json module

emdb_20_to_json

Reads in a EMDB header file following 2.0 schema and outputs summary information as a JSON. This is an stub example to show how to use emdb_da.py to read the header file.

TODO:

Version history:

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

class emdbXMLTranslator.emdb_20_to_json.EMDBXML20JSONTranslator[source]

Class for translating summary info from EMDB 2.0 to a JSON file

setWarningLevel(level)[source]

Set the level of logging warnings. 0 = no warnings, 3 = max warnings, 1 = default

Parameters @param level: warning level 0 -> 3

translate(inputFile, outputFile)[source]

Translate EMDB 2.0 to a JSON. Summary info only

Parameters @param inputFile: input file in EMDB 2.0 XML @param outputFile: output JSON file

warn(level, msg)[source]

Log a warning message but take into account the warningLevel

Parameters: @param level: only messages with level >= warningLevel are printed @param msg: warning message

emdbXMLTranslator.emdb_20_to_json.main()[source]

Extract summary info from EMDB XML 2.0 file to JSON

emdbXMLTranslator.emdb_da module

class emdbXMLTranslator.emdb_da.acceleration_voltageType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='acceleration_voltageType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='acceleration_voltageType')[source]
exportChildren(outfile, level, namespace_='', name_='acceleration_voltageType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de7d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.additional_map_listType(additional_map=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_additional_map(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='additional_map_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='additional_map_listType')[source]
exportChildren(outfile, level, namespace_='', name_='additional_map_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_additional_map()[source]
hasContent_()[source]
insert_additional_map_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770f90>]
replace_additional_map_at(index, value)[source]
set_additional_map(additional_map)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.address_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='address_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='address_type')[source]
exportChildren(outfile, level, namespace_='', name_='address_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.admin_type(status_history_list=None, current_status=None, sites=None, key_dates=None, obsolete_list=None, superseded_by_list=None, grant_support=None, contact_author=None, title=None, authors_list=None, details=None, keywords=None, replace_existing_entry=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

for pdbx categories with “PDB” in name, we should request duplicate categories with “EMDB” substituted

add_contact_author(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='admin_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='admin_type')[source]
exportChildren(outfile, level, namespace_='', name_='admin_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_authors_list()[source]
get_contact_author()[source]
get_current_status()[source]
get_details()[source]
get_grant_support()[source]
get_key_dates()[source]
get_keywords()[source]
get_obsolete_list()[source]
get_replace_existing_entry()[source]
get_sites()[source]
get_status_history_list()[source]
get_superseded_by_list()[source]
get_title()[source]
hasContent_()[source]
insert_contact_author_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9de550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda0d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda250>]
replace_contact_author_at(index, value)[source]
set_authors_list(authors_list)[source]
set_contact_author(contact_author)[source]
set_current_status(current_status)[source]
set_details(details)[source]
set_grant_support(grant_support)[source]
set_key_dates(key_dates)[source]
set_keywords(keywords)[source]
set_obsolete_list(obsolete_list)[source]
set_replace_existing_entry(replace_existing_entry)[source]
set_sites(sites)[source]
set_status_history_list(status_history_list)[source]
set_superseded_by_list(superseded_by_list)[source]
set_title(title)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.alignment_procedureType(none=None, basic=None, zemlin_tableau=None, coma_free=None, other=None, legacy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='alignment_procedureType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='alignment_procedureType')[source]
exportChildren(outfile, level, namespace_='', name_='alignment_procedureType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_basic()[source]
get_coma_free()[source]
get_legacy()[source]
get_none()[source]
get_other()[source]
get_zemlin_tableau()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e73d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7450>]
set_basic(basic)[source]
set_coma_free(coma_free)[source]
set_legacy(legacy)[source]
set_none(none)[source]
set_other(other)[source]
set_zemlin_tableau(zemlin_tableau)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.ammonium_molybdate[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ammonium_molybdate', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ammonium_molybdate')[source]
exportChildren(outfile, level, namespace_='', name_='ammonium_molybdate', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.amplitude_correctionType(factor=None, correction_space=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='amplitude_correctionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='amplitude_correctionType')[source]
exportChildren(outfile, level, namespace_='', name_='amplitude_correctionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_correction_space()[source]
get_factor()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a2d0>]
set_correction_space(correction_space)[source]
set_factor(factor)[source]
subclass = None
superclass = None
validate_correction_space_type(value)[source]
class emdbXMLTranslator.emdb_da.angleType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angleType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angleType')[source]
exportChildren(outfile, level, namespace_='', name_='angleType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5cd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.angle_assignment_type(type_=None, projection_matching_processing=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angle_assignment_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angle_assignment_type')[source]
exportChildren(outfile, level, namespace_='', name_='angle_assignment_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_projection_matching_processing()[source]
get_software_list()[source]
get_type()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d650>]
set_details(details)[source]
set_projection_matching_processing(projection_matching_processing)[source]
set_software_list(software_list)[source]
set_type(type_)[source]
subclass = None
superclass = None
validate_typeType8(value)[source]
class emdbXMLTranslator.emdb_da.angle_incrementType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angle_incrementType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angle_incrementType')[source]
exportChildren(outfile, level, namespace_='', name_='angle_incrementType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f08d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.angular_samplingType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angular_samplingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angular_samplingType')[source]
exportChildren(outfile, level, namespace_='', name_='angular_samplingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a510>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.angular_samplingType12(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angular_samplingType12', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angular_samplingType12')[source]
exportChildren(outfile, level, namespace_='', name_='angular_samplingType12', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cf10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cf50>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.angular_samplingType9(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='angular_samplingType9', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='angular_samplingType9')[source]
exportChildren(outfile, level, namespace_='', name_='angular_samplingType9', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7442d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.annotatorType(private=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='annotatorType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='annotatorType')[source]
exportChildren(outfile, level, namespace_='', name_='annotatorType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_private()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3ed0>]
set_private(private)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.applied_symmetry_type(space_group=None, point_group=None, helical_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='applied_symmetry_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='applied_symmetry_type')[source]
exportChildren(outfile, level, namespace_='', name_='applied_symmetry_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helical_parameters()[source]
get_point_group()[source]
get_space_group()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6858d0>]
set_helical_parameters(helical_parameters)[source]
set_point_group(point_group)[source]
set_space_group(space_group)[source]
subclass = None
superclass = None
validate_plane_and_space_group_type(value)[source]
validate_point_groupType(value)[source]
validate_point_groupType_patterns_ = [['^C\\d+|D\\d+|O|T|I$'], ['^C\\d+|D\\d+|O|T|I$']]
class emdbXMLTranslator.emdb_da.auro_glucothionate[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='auro_glucothionate', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='auro_glucothionate')[source]
exportChildren(outfile, level, namespace_='', name_='auro_glucothionate', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.author_order_type(order=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='author_order_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='author_order_type')[source]
exportChildren(outfile, level, namespace_='', name_='author_order_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_order()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696ad0>]
set_order(order)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.authors_listType(author=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_author(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='authors_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='authors_listType')[source]
exportChildren(outfile, level, namespace_='', name_='authors_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_author()[source]
hasContent_()[source]
insert_author_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3cd0>]
replace_author_at(index, value)[source]
set_author(author)[source]
subclass = None
superclass = None
validate_author_type(value)[source]
validate_author_type_patterns_ = [["^[A-Za-z '\\-]+ [A-Z\\-]+$"]]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd3d0>]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6969d0>]
validate_linkType_patterns_ = [['^(https?|ftp)://.*$']]
class emdbXMLTranslator.emdb_da.average[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='average', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='average')[source]
exportChildren(outfile, level, namespace_='', name_='average', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.average_electron_dose_per_imageType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='average_electron_dose_per_imageType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='average_electron_dose_per_imageType')[source]
exportChildren(outfile, level, namespace_='', name_='average_electron_dose_per_imageType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f05d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.average_exposure_timeType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='average_exposure_timeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='average_exposure_timeType')[source]
exportChildren(outfile, level, namespace_='', name_='average_exposure_timeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f04d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.axis2Type(min_angle=None, max_angle=None, angle_increment=None, axis_rotation=None)[source]

Bases: emdbXMLTranslator.emdb_da.axis_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axis2Type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axis2Type')[source]
exportChildren(outfile, level, namespace_='', name_='axis2Type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_axis_rotation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0990>]
set_axis_rotation(axis_rotation)[source]
subclass = None
superclass

alias of axis_type

class emdbXMLTranslator.emdb_da.axis_orderType(fast=None, medium=None, slow=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axis_orderType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axis_orderType')[source]
exportChildren(outfile, level, namespace_='', name_='axis_orderType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fast()[source]
get_medium()[source]
get_slow()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767390>]
set_fast(fast)[source]
set_medium(medium)[source]
set_slow(slow)[source]
subclass = None
superclass = None
validate_fastType(value)[source]
validate_fastType_patterns_ = [['^X|Y|Z$']]
validate_mediumType(value)[source]
validate_mediumType_patterns_ = [['^X|Y|Z$']]
validate_slowType(value)[source]
validate_slowType_patterns_ = [['^X|Y|Z$']]
class emdbXMLTranslator.emdb_da.axis_rotation[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Rotation of axis relative to axis1

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axis_rotation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axis_rotation')[source]
exportChildren(outfile, level, namespace_='', name_='axis_rotation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.axis_rotationType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axis_rotationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axis_rotationType')[source]
exportChildren(outfile, level, namespace_='', name_='axis_rotationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0ad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0b10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.axis_type(min_angle=None, max_angle=None, angle_increment=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='axis_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='axis_type')[source]
exportChildren(outfile, level, namespace_='', name_='axis_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angle_increment()[source]
get_extensiontype_()[source]
get_max_angle()[source]
get_min_angle()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6747d0>]
set_angle_increment(angle_increment)[source]
set_extensiontype_(extensiontype_)[source]
set_max_angle(max_angle)[source]
set_min_angle(min_angle)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.b_factorSharpeningType(_brestore=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='b-factorSharpeningType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='b-factorSharpeningType')[source]
exportChildren(outfile, level, namespace_='', name_='b-factorSharpeningType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get__brestore()[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa010d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01110>]
set__brestore(_brestore)[source]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.background_masked_type(geometrical_shape=None, dimensions=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='background_masked_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='background_masked_type')[source]
exportChildren(outfile, level, namespace_='', name_='background_masked_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_dimensions()[source]
get_geometrical_shape()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fd90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fdd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fe10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fe50>]
set_details(details)[source]
set_dimensions(dimensions)[source]
set_geometrical_shape(geometrical_shape)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
validate_geometrical_shapeType(value)[source]
class emdbXMLTranslator.emdb_da.base_macromolecule_type(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Autogenerated unique identifier.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_macromolecule_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_macromolecule_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_macromolecule_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_chimera()[source]
get_details()[source]
get_extensiontype_()[source]
get_id()[source]
get_molecular_weight()[source]
get_mutant()[source]
get_name()[source]
get_natural_source()[source]
get_number_of_copies()[source]
get_oligomeric_state()[source]
get_recombinant_exp_flag()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8ed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8f10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af090>]
set_chimera(chimera)[source]
set_details(details)[source]
set_extensiontype_(extensiontype_)[source]
set_id(id)[source]
set_molecular_weight(molecular_weight)[source]
set_mutant(mutant)[source]
set_name(name)[source]
set_natural_source(natural_source)[source]
set_number_of_copies(number_of_copies)[source]
set_oligomeric_state(oligomeric_state)[source]
set_recombinant_exp_flag(recombinant_exp_flag)[source]
subclass = None
superclass = None
validate_pos_int_or_string_type(value)[source]
class emdbXMLTranslator.emdb_da.base_microscopy_type(id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Auto generated by application

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_microscopy_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_microscopy_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_microscopy_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_acceleration_voltage()[source]
get_alignment_procedure()[source]
get_c2_aperture_diameter()[source]
get_calibrated_defocus_max()[source]
get_calibrated_defocus_min()[source]
get_calibrated_magnification()[source]
get_cooling_holder_cryogen()[source]
get_date()[source]
get_details()[source]
get_electron_source()[source]
get_extensiontype_()[source]
get_id()[source]
get_illumination_mode()[source]
get_image_recording_list()[source]
get_imaging_mode()[source]
get_microscope()[source]
get_nominal_cs()[source]
get_nominal_defocus_max()[source]
get_nominal_defocus_min()[source]
get_nominal_magnification()[source]
get_software_list()[source]
get_specialist_optics()[source]
get_specimen_holder()[source]
get_specimen_holder_model()[source]
get_specimen_preparations()[source]
get_temperature()[source]
get_tilt_angle_max()[source]
get_tilt_angle_min()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efede10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efede50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efede90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efeded0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedf10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedf50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedf90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedfd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6740d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6741d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6742d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6743d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6744d0>]
set_acceleration_voltage(acceleration_voltage)[source]
set_alignment_procedure(alignment_procedure)[source]
set_c2_aperture_diameter(c2_aperture_diameter)[source]
set_calibrated_defocus_max(calibrated_defocus_max)[source]
set_calibrated_defocus_min(calibrated_defocus_min)[source]
set_calibrated_magnification(calibrated_magnification)[source]
set_cooling_holder_cryogen(cooling_holder_cryogen)[source]
set_date(date)[source]
set_details(details)[source]
set_electron_source(electron_source)[source]
set_extensiontype_(extensiontype_)[source]
set_id(id)[source]
set_illumination_mode(illumination_mode)[source]
set_image_recording_list(image_recording_list)[source]
set_imaging_mode(imaging_mode)[source]
set_microscope(microscope)[source]
set_nominal_cs(nominal_cs)[source]
set_nominal_defocus_max(nominal_defocus_max)[source]
set_nominal_defocus_min(nominal_defocus_min)[source]
set_nominal_magnification(nominal_magnification)[source]
set_software_list(software_list)[source]
set_specialist_optics(specialist_optics)[source]
set_specimen_holder(specimen_holder)[source]
set_specimen_holder_model(specimen_holder_model)[source]
set_specimen_preparations(specimen_preparations)[source]
set_temperature(temperature)[source]
set_tilt_angle_max(tilt_angle_max)[source]
set_tilt_angle_min(tilt_angle_min)[source]
subclass = None
superclass = None
validate_allowed_magnification(value)[source]
validate_cooling_holder_cryogenType(value)[source]
validate_electron_sourceType(value)[source]
validate_illumination_modeType(value)[source]
validate_imaging_modeType(value)[source]
validate_microscopeType(value)[source]
validate_specimen_holder_modelType(value)[source]
class emdbXMLTranslator.emdb_da.base_natural_source_type(database=None, organism=None, strain=None, synonym_organism=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_natural_source_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_natural_source_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_natural_source_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_database()[source]
get_extensiontype_()[source]
get_organism()[source]
get_strain()[source]
get_synonym_organism()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a84d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8550>]
set_database(database)[source]
set_extensiontype_(extensiontype_)[source]
set_organism(organism)[source]
set_strain(strain)[source]
set_synonym_organism(synonym_organism)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.base_preparation_type(id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Unique identifier. Autogenerated

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_preparation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_preparation_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_preparation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_buffer()[source]
get_concentration()[source]
get_details()[source]
get_extensiontype_()[source]
get_grid()[source]
get_id()[source]
get_shadowing()[source]
get_staining()[source]
get_sugar_embedding()[source]
get_vitrification()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efeda10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efeda50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efeda90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedb10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedb50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedb90>]
set_buffer(buffer)[source]
set_concentration(concentration)[source]
set_details(details)[source]
set_extensiontype_(extensiontype_)[source]
set_grid(grid)[source]
set_id(id)[source]
set_shadowing(shadowing)[source]
set_staining(staining)[source]
set_sugar_embedding(sugar_embedding)[source]
set_vitrification(vitrification)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.base_processing_type(id=None, image_recording_id=None, details=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_extensiontype_()[source]
get_id()[source]
get_image_recording_id()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67db10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67db50>]
set_details(details)[source]
set_extensiontype_(extensiontype_)[source]
set_id(id)[source]
set_image_recording_id(image_recording_id)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.base_supramolecule_type(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_supramolecule_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_supramolecule_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_supramolecule_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_category()[source]
get_details()[source]
get_extensiontype_()[source]
get_external_references()[source]
get_id()[source]
get_macromolecule_list()[source]
get_name()[source]
get_number_of_copies()[source]
get_oligomeric_state()[source]
get_parent()[source]
get_recombinant_exp_flag()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68de90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68ded0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68df10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68df50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68df90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dfd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6960d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696110>]
replace_external_references_at(index, value)[source]
set_category(category)[source]
set_details(details)[source]
set_extensiontype_(extensiontype_)[source]
set_external_references(external_references)[source]
set_id(id)[source]
set_macromolecule_list(macromolecule_list)[source]
set_name(name)[source]
set_number_of_copies(number_of_copies)[source]
set_oligomeric_state(oligomeric_state)[source]
set_parent(parent)[source]
set_recombinant_exp_flag(recombinant_exp_flag)[source]
subclass = None
superclass = None
validate_pos_int_or_string_type(value)[source]
class emdbXMLTranslator.emdb_da.base_type(help_text=None, warning_text=None, error_text=None, validation_rules=None, label=None, value=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_validation_rules(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='base_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='base_type')[source]
exportChildren(outfile, level, namespace_='', name_='base_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_error_text()[source]
get_extensiontype_()[source]
get_help_text()[source]
get_label()[source]
get_validation_rules()[source]
get_value()[source]
get_warning_text()[source]
hasContent_()[source]
insert_validation_rules_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed550>]
replace_validation_rules_at(index, value)[source]
set_error_text(error_text)[source]
set_extensiontype_(extensiontype_)[source]
set_help_text(help_text)[source]
set_label(label)[source]
set_validation_rules(validation_rules)[source]
set_value(value)[source]
set_warning_text(warning_text)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.basicType[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='basicType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='basicType')[source]
exportChildren(outfile, level, namespace_='', name_='basicType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.buffer_type(ph=None, component=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_component(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='buffer_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='buffer_type')[source]
exportChildren(outfile, level, namespace_='', name_='buffer_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_component()[source]
get_details()[source]
get_ph()[source]
hasContent_()[source]
insert_component_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed690>]
replace_component_at(index, value)[source]
set_component(component)[source]
set_details(details)[source]
set_ph(ph)[source]
subclass = None
superclass = None
validate_phType(value)[source]
class emdbXMLTranslator.emdb_da.c2_aperture_diameterType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='c2_aperture_diameterType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='c2_aperture_diameterType')[source]
exportChildren(outfile, level, namespace_='', name_='c2_aperture_diameterType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de8d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.calibrated_defocus_maxType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='calibrated_defocus_maxType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='calibrated_defocus_maxType')[source]
exportChildren(outfile, level, namespace_='', name_='calibrated_defocus_maxType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ded90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6dedd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.calibrated_defocus_minType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='calibrated_defocus_minType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='calibrated_defocus_minType')[source]
exportChildren(outfile, level, namespace_='', name_='calibrated_defocus_minType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6deb90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6debd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.camera_lengthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='camera_lengthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='camera_lengthType')[source]
exportChildren(outfile, level, namespace_='', name_='camera_lengthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0c10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.categoryType(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Currently we only support Gene Ontology.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='categoryType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='categoryType')[source]
exportChildren(outfile, level, namespace_='', name_='categoryType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7700d0>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.categoryType39(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Currently we only support Gene Ontology.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='categoryType39', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='categoryType39')[source]
exportChildren(outfile, level, namespace_='', name_='categoryType39', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7704d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770510>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.cell(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cell', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cell')[source]
exportChildren(outfile, level, namespace_='', name_='cell', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_natural_source()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15d10>]
set_natural_source(natural_source)[source]
subclass = None
superclass

alias of base_supramolecule_type

class emdbXMLTranslator.emdb_da.cellType(a=None, b=None, c=None, alpha=None, beta=None, gamma=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cellType')[source]
exportChildren(outfile, level, namespace_='', name_='cellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_a()[source]
get_alpha()[source]
get_b()[source]
get_beta()[source]
get_c()[source]
get_gamma()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7671d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767250>]
set_a(a)[source]
set_alpha(alpha)[source]
set_b(b)[source]
set_beta(beta)[source]
set_c(c)[source]
set_gamma(gamma)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.cell_angle_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cell_angle_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cell_angle_type')[source]
exportChildren(outfile, level, namespace_='', name_='cell_angle_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696ed0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.cell_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='cell_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='cell_type')[source]
exportChildren(outfile, level, namespace_='', name_='cell_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696dd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.chainType(id=None, residue_range=None, number_of_copies_in_final_model=None)[source]

Bases: emdbXMLTranslator.emdb_da.chain_model_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chainType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chainType')[source]
exportChildren(outfile, level, namespace_='', name_='chainType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_number_of_copies_in_final_model()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a710>]
set_number_of_copies_in_final_model(number_of_copies_in_final_model)[source]
subclass = None
superclass

alias of chain_model_type

class emdbXMLTranslator.emdb_da.chainType53(id=None, residue_range=None, number_of_copies_in_final_model=None)[source]

Bases: emdbXMLTranslator.emdb_da.chain_model_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chainType53', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chainType53')[source]
exportChildren(outfile, level, namespace_='', name_='chainType53', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_number_of_copies_in_final_model()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa013d0>]
set_number_of_copies_in_final_model(number_of_copies_in_final_model)[source]
subclass = None
superclass

alias of chain_model_type

class emdbXMLTranslator.emdb_da.chain_id_list(id=None, residue_range=None)[source]

Bases: emdbXMLTranslator.emdb_da.chain_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chain_id_list', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chain_id_list')[source]
exportChildren(outfile, level, namespace_='', name_='chain_id_list', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass

alias of chain_type

class emdbXMLTranslator.emdb_da.chain_model_type(id=None, residue_range=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.chain_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chain_model_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chain_model_type')[source]
exportChildren(outfile, level, namespace_='', name_='chain_model_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_extensiontype_()[source]
hasContent_()[source]
member_data_items_ = []
set_extensiontype_(extensiontype_)[source]
subclass = None
superclass

alias of chain_type

class emdbXMLTranslator.emdb_da.chain_type(id=None, residue_range=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_residue_range(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chain_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chain_type')[source]
exportChildren(outfile, level, namespace_='', name_='chain_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_extensiontype_()[source]
get_id()[source]
get_residue_range()[source]
hasContent_()[source]
insert_residue_range_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68db90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dbd0>]
replace_residue_range_at(index, value)[source]
set_extensiontype_(extensiontype_)[source]
set_id(id)[source]
set_residue_range(residue_range)[source]
subclass = None
superclass = None
validate_chain_pdb_id(value)[source]
validate_chain_pdb_id_patterns_ = [['^\\d|[A-Za-z]$']]
validate_residue_rangeType(value)[source]
validate_residue_rangeType_patterns_ = [['^\\d+-\\d+$']]
class emdbXMLTranslator.emdb_da.chamber_humidityType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chamber_humidityType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chamber_humidityType')[source]
exportChildren(outfile, level, namespace_='', name_='chamber_humidityType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d55d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.chamber_temperatureType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='chamber_temperatureType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='chamber_temperatureType')[source]
exportChildren(outfile, level, namespace_='', name_='chamber_temperatureType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d56d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5710>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.citation_listType(primary_citation=None, secondary_citation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_secondary_citation(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='citation_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='citation_listType')[source]
exportChildren(outfile, level, namespace_='', name_='citation_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_primary_citation()[source]
get_secondary_citation()[source]
hasContent_()[source]
insert_secondary_citation_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd0d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd110>]
replace_secondary_citation_at(index, value)[source]
set_primary_citation(primary_citation)[source]
set_secondary_citation(secondary_citation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.citation_list_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='citation_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='citation_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='citation_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.citation_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='citation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='citation_type')[source]
exportChildren(outfile, level, namespace_='', name_='citation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.classification_type(number_classes=None, average_number_members_per_class=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='classification_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='classification_type')[source]
exportChildren(outfile, level, namespace_='', name_='classification_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average_number_members_per_class()[source]
get_details()[source]
get_number_classes()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c32d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3390>]
set_average_number_members_per_class(average_number_members_per_class)[source]
set_details(details)[source]
set_number_classes(number_classes)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
validate_average_number_members_per_classType(value)[source]
class emdbXMLTranslator.emdb_da.code_type(superseded=None, supersedes=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

It is true, if the current status is ‘OBS’ and the entry has been replaced by newer entries. This is true if the current status is ‘REL’ and there are older entries that have been made obsoleted because of this one.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='code_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='code_type')[source]
exportChildren(outfile, level, namespace_='', name_='code_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_superseded()[source]
get_supersedes()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696890>]
set_superseded(superseded)[source]
set_supersedes(supersedes)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.coloured_gaussian[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='coloured_gaussian', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='coloured_gaussian')[source]
exportChildren(outfile, level, namespace_='', name_='coloured_gaussian', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.coma_freeType(residual_tilt=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='coma_freeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='coma_freeType')[source]
exportChildren(outfile, level, namespace_='', name_='coma_freeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_residual_tilt()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7690>]
set_residual_tilt(residual_tilt)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.complex(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, chimera=None, natural_source=None, recombinant_expression=None, molecular_weight=None, ribosome_details=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

add_natural_source(value)[source]
add_recombinant_expression(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='complex', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='complex')[source]
exportChildren(outfile, level, namespace_='', name_='complex', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_chimera()[source]
get_molecular_weight()[source]
get_natural_source()[source]
get_recombinant_expression()[source]
get_ribosome_details()[source]
hasContent_()[source]
insert_natural_source_at(index, value)[source]
insert_recombinant_expression_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa155d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15650>]
replace_natural_source_at(index, value)[source]
replace_recombinant_expression_at(index, value)[source]
set_chimera(chimera)[source]
set_molecular_weight(molecular_weight)[source]
set_natural_source(natural_source)[source]
set_recombinant_expression(recombinant_expression)[source]
set_ribosome_details(ribosome_details)[source]
subclass = None
superclass

alias of base_supramolecule_type

class emdbXMLTranslator.emdb_da.complex_type(chimera=None, id=None, name=None, category=None, parent=None, macromolecule_list=None, natural_source=None, recombinant_expression=None, molecular_weight=None, virus_shell=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_natural_source(value)[source]
add_recombinant_expression(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='complex_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='complex_type')[source]
exportChildren(outfile, level, namespace_='', name_='complex_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_category()[source]
get_chimera()[source]
get_details()[source]
get_id()[source]
get_macromolecule_list()[source]
get_molecular_weight()[source]
get_name()[source]
get_natural_source()[source]
get_parent()[source]
get_recombinant_expression()[source]
get_virus_shell()[source]
hasContent_()[source]
insert_natural_source_at(index, value)[source]
insert_recombinant_expression_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6961d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6962d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6963d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696450>]
replace_natural_source_at(index, value)[source]
replace_recombinant_expression_at(index, value)[source]
set_category(category)[source]
set_chimera(chimera)[source]
set_details(details)[source]
set_id(id)[source]
set_macromolecule_list(macromolecule_list)[source]
set_molecular_weight(molecular_weight)[source]
set_name(name)[source]
set_natural_source(natural_source)[source]
set_parent(parent)[source]
set_recombinant_expression(recombinant_expression)[source]
set_virus_shell(virus_shell)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.componentType(concentration=None, formula=None, name=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='componentType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='componentType')[source]
exportChildren(outfile, level, namespace_='', name_='componentType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_concentration()[source]
get_formula()[source]
get_name()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d53d0>]
set_concentration(concentration)[source]
set_formula(formula)[source]
set_name(name)[source]
subclass = None
superclass = None
validate_formulaType(value)[source]
validate_formulaType_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
class emdbXMLTranslator.emdb_da.concentrationType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

_emd_buffer_component.concentration_units

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='concentrationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='concentrationType')[source]
exportChildren(outfile, level, namespace_='', name_='concentrationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d54d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.concentrationType3(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='concentrationType3', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='concentrationType3')[source]
exportChildren(outfile, level, namespace_='', name_='concentrationType3', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d57d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5810>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.connectivityType(_n_link=None, _c_link=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='connectivityType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='connectivityType')[source]
exportChildren(outfile, level, namespace_='', name_='connectivityType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get__c_link()[source]
get__n_link()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01b50>]
set__c_link(_c_link)[source]
set__n_link(_n_link)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.contact_authorType(role=None, title=None, first_name=None, middle_name=None, last_name=None, organization=None, street=None, town_or_city=None, state_or_province=None, country=None, post_or_zip_code=None, email=None, telephone=None, fax=None, private=None)[source]

Bases: emdbXMLTranslator.emdb_da.contact_details_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contact_authorType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contact_authorType')[source]
exportChildren(outfile, level, namespace_='', name_='contact_authorType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_private()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3c10>]
set_private(private)[source]
subclass = None
superclass

alias of contact_details_type

class emdbXMLTranslator.emdb_da.contact_details_type(role=None, title=None, first_name=None, middle_name=None, last_name=None, organization=None, street=None, town_or_city=None, state_or_province=None, country=None, post_or_zip_code=None, email=None, telephone=None, fax=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contact_details_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contact_details_type')[source]
exportChildren(outfile, level, namespace_='', name_='contact_details_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_country()[source]
get_email()[source]
get_extensiontype_()[source]
get_fax()[source]
get_first_name()[source]
get_last_name()[source]
get_middle_name()[source]
get_organization()[source]
get_post_or_zip_code()[source]
get_role()[source]
get_state_or_province()[source]
get_street()[source]
get_telephone()[source]
get_title()[source]
get_town_or_city()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f8bfed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f8bfdd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9de710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda8d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdaa10>]
set_country(country)[source]
set_email(email)[source]
set_extensiontype_(extensiontype_)[source]
set_fax(fax)[source]
set_first_name(first_name)[source]
set_last_name(last_name)[source]
set_middle_name(middle_name)[source]
set_organization(organization)[source]
set_post_or_zip_code(post_or_zip_code)[source]
set_role(role)[source]
set_state_or_province(state_or_province)[source]
set_street(street)[source]
set_telephone(telephone)[source]
set_title(title)[source]
set_town_or_city(town_or_city)[source]
subclass = None
superclass = None
validate_emailType(value)[source]
validate_emailType_patterns_ = [['^[A-Za-z0-9._%+-]+@[A-Za-z0-9.-]+\\.[A-Za-z]{2,4}$']]
validate_middle_nameType(value)[source]
validate_middle_nameType_patterns_ = [['^[A-Z]$']]
validate_roleType(value)[source]
validate_titleType(value)[source]
class emdbXMLTranslator.emdb_da.contourType(primary=None, level=None, source=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contourType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contourType')[source]
exportChildren(outfile, level, namespace_='', name_='contourType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_level()[source]
get_primary()[source]
get_source()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7676d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767710>]
set_level(level)[source]
set_primary(primary)[source]
set_source(source)[source]
subclass = None
superclass = None
validate_sourceType(value)[source]
class emdbXMLTranslator.emdb_da.contour_listType(contour=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_contour(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='contour_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='contour_listType')[source]
exportChildren(outfile, level, namespace_='', name_='contour_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_contour()[source]
hasContent_()[source]
insert_contour_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767590>]
replace_contour_at(index, value)[source]
set_contour(contour)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.coordinate_type(spatial_frequency=None, y=None, y_noise=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='coordinate_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='coordinate_type')[source]
exportChildren(outfile, level, namespace_='', name_='coordinate_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_spatial_frequency()[source]
get_y()[source]
get_y_noise()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d210>]
set_spatial_frequency(spatial_frequency)[source]
set_y(y)[source]
set_y_noise(y_noise)[source]
subclass = None
superclass = None
validate_yType(value)[source]
validate_y_noiseType(value)[source]
class emdbXMLTranslator.emdb_da.crossreferences_type(citation_list=None, emdb_list=None, pdb_list=None, auxiliary_link_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crossreferences_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crossreferences_type')[source]
exportChildren(outfile, level, namespace_='', name_='crossreferences_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_citation_list()[source]
get_emdb_list()[source]
get_pdb_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f908b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdaad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdab10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdab50>]
set_citation_list(citation_list)[source]
set_emdb_list(emdb_list)[source]
set_pdb_list(pdb_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.crystal_formationType(lipid_protein_ratio=None, lipid_mixture=None, instrument=None, atmosphere=None, temperature=None, time=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystal_formationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystal_formationType')[source]
exportChildren(outfile, level, namespace_='', name_='crystal_formationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_atmosphere()[source]
get_details()[source]
get_instrument()[source]
get_lipid_mixture()[source]
get_lipid_protein_ratio()[source]
get_temperature()[source]
get_time()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f93d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f94d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9550>]
set_atmosphere(atmosphere)[source]
set_details(details)[source]
set_instrument(instrument)[source]
set_lipid_mixture(lipid_mixture)[source]
set_lipid_protein_ratio(lipid_protein_ratio)[source]
set_temperature(temperature)[source]
set_time(time)[source]
subclass = None
superclass = None
validate_instrumentType48(value)[source]
class emdbXMLTranslator.emdb_da.crystal_formation_temperature_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystal_formation_temperature_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystal_formation_temperature_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystal_formation_temperature_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba590>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.crystal_formation_time_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystal_formation_time_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystal_formation_time_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystal_formation_time_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba690>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.crystal_parameters_type(unit_cell=None, plane_group=None, space_group=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystal_parameters_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystal_parameters_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystal_parameters_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_plane_group()[source]
get_space_group()[source]
get_unit_cell()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bae10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bae50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bae90>]
set_plane_group(plane_group)[source]
set_space_group(space_group)[source]
set_unit_cell(unit_cell)[source]
subclass = None
superclass = None
validate_plane_groupType(value)[source]
class emdbXMLTranslator.emdb_da.crystallography_microscopy_type(id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, camera_length=None, tilt_list=None, tilt_series=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_microscopy_type

add_tilt_series(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_microscopy_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_microscopy_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_microscopy_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_camera_length()[source]
get_tilt_list()[source]
get_tilt_series()[source]
hasContent_()[source]
insert_tilt_series_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6749d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674a50>]
replace_tilt_series_at(index, value)[source]
set_camera_length(camera_length)[source]
set_tilt_list(tilt_list)[source]
set_tilt_series(tilt_series)[source]
subclass = None
superclass

alias of base_microscopy_type

class emdbXMLTranslator.emdb_da.crystallography_preparation_type(id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, crystal_formation=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_preparation_type

TODO: add limits and units.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_preparation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_preparation_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_preparation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystal_formation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fcd0>]
set_crystal_formation(crystal_formation)[source]
subclass = None
superclass

alias of base_preparation_type

class emdbXMLTranslator.emdb_da.crystallography_processing_type(id=None, image_recording_id=None, details=None, final_reconstruction=None, crystal_parameters=None, startup_model=None, ctf_correction=None, molecular_replacement=None, lattice_distortion_correction=None, symmetry_determination=None, merging=None, crystallography_statistics=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_processing_type

add_startup_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystal_parameters()[source]
get_crystallography_statistics()[source]
get_ctf_correction()[source]
get_final_reconstruction()[source]
get_lattice_distortion_correction()[source]
get_merging()[source]
get_molecular_replacement()[source]
get_startup_model()[source]
get_symmetry_determination()[source]
hasContent_()[source]
insert_startup_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6852d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6853d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6854d0>]
replace_startup_model_at(index, value)[source]
set_crystal_parameters(crystal_parameters)[source]
set_crystallography_statistics(crystallography_statistics)[source]
set_ctf_correction(ctf_correction)[source]
set_final_reconstruction(final_reconstruction)[source]
set_lattice_distortion_correction(lattice_distortion_correction)[source]
set_merging(merging)[source]
set_molecular_replacement(molecular_replacement)[source]
set_startup_model(startup_model)[source]
set_symmetry_determination(symmetry_determination)[source]
subclass = None
superclass

alias of base_processing_type

class emdbXMLTranslator.emdb_da.crystallography_statistics_type(number_intensities_measured=None, number_structure_factors=None, fourier_space_coverage=None, r_sym=None, r_merge=None, overall_phase_error=None, overall_phase_residual=None, phase_error_rejection_criteria=None, high_resolution=None, shell_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_statistics_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_statistics_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_statistics_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_fourier_space_coverage()[source]
get_high_resolution()[source]
get_number_intensities_measured()[source]
get_number_structure_factors()[source]
get_overall_phase_error()[source]
get_overall_phase_residual()[source]
get_phase_error_rejection_criteria()[source]
get_r_merge()[source]
get_r_sym()[source]
get_shell_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baf50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baf90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bafd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c30d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c31d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3210>]
set_details(details)[source]
set_fourier_space_coverage(fourier_space_coverage)[source]
set_high_resolution(high_resolution)[source]
set_number_intensities_measured(number_intensities_measured)[source]
set_number_structure_factors(number_structure_factors)[source]
set_overall_phase_error(overall_phase_error)[source]
set_overall_phase_residual(overall_phase_residual)[source]
set_phase_error_rejection_criteria(phase_error_rejection_criteria)[source]
set_r_merge(r_merge)[source]
set_r_sym(r_sym)[source]
set_shell_list(shell_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.crystallography_tilt_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_tilt_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_tilt_type')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_tilt_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.crystallography_validation(parallel_resolution=None, perpendicular_resolution=None, number_observed_reflections=None, number_unique_reflections=None, weighted_phase_residual=None, weighted_r_factor=None, data_completeness=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='crystallography_validation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='crystallography_validation')[source]
exportChildren(outfile, level, namespace_='', name_='crystallography_validation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_data_completeness()[source]
get_number_observed_reflections()[source]
get_number_unique_reflections()[source]
get_parallel_resolution()[source]
get_perpendicular_resolution()[source]
get_weighted_phase_residual()[source]
get_weighted_r_factor()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d610>]
set_data_completeness(data_completeness)[source]
set_number_observed_reflections(number_observed_reflections)[source]
set_number_unique_reflections(number_unique_reflections)[source]
set_parallel_resolution(parallel_resolution)[source]
set_perpendicular_resolution(perpendicular_resolution)[source]
set_weighted_phase_residual(weighted_phase_residual)[source]
set_weighted_r_factor(weighted_r_factor)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.ctf_correction_type(phase_reversal=None, amplitude_correction=None, correction_operation=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ctf_correction_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ctf_correction_type')[source]
exportChildren(outfile, level, namespace_='', name_='ctf_correction_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_amplitude_correction()[source]
get_correction_operation()[source]
get_details()[source]
get_phase_reversal()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d4d0>]
set_amplitude_correction(amplitude_correction)[source]
set_correction_operation(correction_operation)[source]
set_details(details)[source]
set_phase_reversal(phase_reversal)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
validate_correction_operationType(value)[source]
class emdbXMLTranslator.emdb_da.data_completeness[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='data_completeness', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='data_completeness')[source]
exportChildren(outfile, level, namespace_='', name_='data_completeness', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.delta_phiType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='delta_phiType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='delta_phiType')[source]
exportChildren(outfile, level, namespace_='', name_='delta_phiType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa015d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.delta_zType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='delta_zType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='delta_zType')[source]
exportChildren(outfile, level, namespace_='', name_='delta_zType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa014d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.depthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='depthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='depthType')[source]
exportChildren(outfile, level, namespace_='', name_='depthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9ad0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.diameterType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='diameterType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='diameterType')[source]
exportChildren(outfile, level, namespace_='', name_='diameterType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767f90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.diameterType42(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='diameterType42', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='diameterType42')[source]
exportChildren(outfile, level, namespace_='', name_='diameterType42', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770990>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.diameterType74(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='diameterType74', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='diameterType74')[source]
exportChildren(outfile, level, namespace_='', name_='diameterType74', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a990>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.digitization_detailsType(scanner=None, dimensions=None, sampling_interval=None, frames_per_image=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='digitization_detailsType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='digitization_detailsType')[source]
exportChildren(outfile, level, namespace_='', name_='digitization_detailsType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_dimensions()[source]
get_frames_per_image()[source]
get_sampling_interval()[source]
get_scanner()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7ed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7f10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7f90>]
set_dimensions(dimensions)[source]
set_frames_per_image(frames_per_image)[source]
set_sampling_interval(sampling_interval)[source]
set_scanner(scanner)[source]
subclass = None
superclass = None
validate_scannerType(value)[source]
class emdbXMLTranslator.emdb_da.dimensionsType(width=None, height=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='dimensionsType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='dimensionsType')[source]
exportChildren(outfile, level, namespace_='', name_='dimensionsType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_height()[source]
get_width()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f00d0>]
set_height(height)[source]
set_width(width)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.dimensionsType49(radius=None, width=None, height=None, depth=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='dimensionsType49', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='dimensionsType49')[source]
exportChildren(outfile, level, namespace_='', name_='dimensionsType49', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_depth()[source]
get_height()[source]
get_radius()[source]
get_width()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f96d0>]
set_depth(depth)[source]
set_height(height)[source]
set_radius(radius)[source]
set_width(width)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.discrepancy_listType(discrepancy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_discrepancy(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='discrepancy_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='discrepancy_listType')[source]
exportChildren(outfile, level, namespace_='', name_='discrepancy_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy()[source]
hasContent_()[source]
insert_discrepancy_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01a10>]
replace_discrepancy_at(index, value)[source]
set_discrepancy(discrepancy)[source]
subclass = None
superclass = None
validate_discrepancyType(value)[source]
validate_discrepancyType_patterns_ = [['^[ARNDCEQGHILKMFPSTWYVUOBZJX]\\d+[ARNDCEQGHILKMFPSTWYVUOBZJX]$']]
class emdbXMLTranslator.emdb_da.discrepancy_listType57(discrepancy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_discrepancy(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='discrepancy_listType57', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='discrepancy_listType57')[source]
exportChildren(outfile, level, namespace_='', name_='discrepancy_listType57', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy()[source]
hasContent_()[source]
insert_discrepancy_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a110>]
replace_discrepancy_at(index, value)[source]
set_discrepancy(discrepancy)[source]
subclass = None
superclass = None
validate_discrepancyType58(value)[source]
validate_discrepancyType58_patterns_ = [['^[AGCTRYSWKMBDHVN\\.-]\\d+[AGCTRYSWKMBDHVN\\.-]$']]
class emdbXMLTranslator.emdb_da.discrepancy_listType62(discrepancy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_discrepancy(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='discrepancy_listType62', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='discrepancy_listType62')[source]
exportChildren(outfile, level, namespace_='', name_='discrepancy_listType62', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy()[source]
hasContent_()[source]
insert_discrepancy_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a450>]
replace_discrepancy_at(index, value)[source]
set_discrepancy(discrepancy)[source]
subclass = None
superclass = None
validate_discrepancyType63(value)[source]
validate_discrepancyType63_patterns_ = [['^[AGCURYSWKMBDHVN\\.-]\\d+[AGCURYSWKMBDHVN\\.-]$']]
class emdbXMLTranslator.emdb_da.discrepancy_listType79(discrepancy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_discrepancy(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='discrepancy_listType79', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='discrepancy_listType79')[source]
exportChildren(outfile, level, namespace_='', name_='discrepancy_listType79', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy()[source]
hasContent_()[source]
insert_discrepancy_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0acd0>]
replace_discrepancy_at(index, value)[source]
set_discrepancy(discrepancy)[source]
subclass = None
superclass = None
validate_discrepancyType80(value)[source]
validate_discrepancyType80_patterns_ = [['^[AGCTRYSWKMBDHVN\\.-]\\d+[AGCTRYSWKMBDHVN\\.-]$']]
class emdbXMLTranslator.emdb_da.dna(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, structure=None, synthetic_flag=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Is naturalExpression and recombinantExpression suitable for this component?

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='dna', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='dna')[source]
exportChildren(outfile, level, namespace_='', name_='dna', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_classification()[source]
get_sequence()[source]
get_structure()[source]
get_synthetic_flag()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af2d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af390>]
set_classification(classification)[source]
set_sequence(sequence)[source]
set_structure(structure)[source]
set_synthetic_flag(synthetic_flag)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_classificationType(value)[source]
class emdbXMLTranslator.emdb_da.em_label(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='em_label', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='em_label')[source]
exportChildren(outfile, level, namespace_='', name_='em_label', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_formula()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af990>]
set_formula(formula)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_formulaType73(value)[source]
validate_formulaType73_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
class emdbXMLTranslator.emdb_da.emdb_cross_reference_list_type(emdb_reference=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

List of related EMDB entries Maybe it can be combined with pdbReference into one datatype.

add_emdb_reference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='emdb_cross_reference_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='emdb_cross_reference_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='emdb_cross_reference_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_emdb_reference()[source]
hasContent_()[source]
insert_emdb_reference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdadd0>]
replace_emdb_reference_at(index, value)[source]
set_emdb_reference(emdb_reference)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.emdb_cross_reference_type(id=None, emdb_id=None, relationship=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

EMDB entries related to this entry

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='emdb_cross_reference_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='emdb_cross_reference_type')[source]
exportChildren(outfile, level, namespace_='', name_='emdb_cross_reference_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_emdb_id()[source]
get_id()[source]
get_relationship()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdac50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdac90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdacd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdad10>]
set_details(details)[source]
set_emdb_id(emdb_id)[source]
set_id(id)[source]
set_relationship(relationship)[source]
subclass = None
superclass = None
validate_emdb_id_type(value)[source]
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
class emdbXMLTranslator.emdb_da.energy_filterType(name=None, lower_energy_threshold=None, upper_energy_threshold=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='energy_filterType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='energy_filterType')[source]
exportChildren(outfile, level, namespace_='', name_='energy_filterType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_lower_energy_threshold()[source]
get_name()[source]
get_upper_energy_threshold()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdcd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdd10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdd50>]
set_lower_energy_threshold(lower_energy_threshold)[source]
set_name(name)[source]
set_upper_energy_threshold(upper_energy_threshold)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.entry_type(emdb_id=None, version=None, admin=None, crossreferences=None, sample=None, structure_determination_list=None, map=None, interpretation=None, validation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

For example: EMD-1001The XML schema version that validates the header file. This attribute should contain a default value: the current schema version.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='entry_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='entry_type')[source]
exportChildren(outfile, level, namespace_='', name_='entry_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_admin()[source]
get_crossreferences()[source]
get_emdb_id()[source]
get_interpretation()[source]
get_map()[source]
get_sample()[source]
get_structure_determination_list()[source]
get_validation()[source]
get_version()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f908cd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9de5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f8bf9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efd1ed0>]
set_admin(admin)[source]
set_crossreferences(crossreferences)[source]
set_emdb_id(emdb_id)[source]
set_interpretation(interpretation)[source]
set_map(map)[source]
set_sample(sample)[source]
set_structure_determination_list(structure_determination_list)[source]
set_validation(validation)[source]
set_version(version)[source]
subclass = None
superclass = None
validate_emdb_id_type(value)[source]
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
class emdbXMLTranslator.emdb_da.experimentalType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

kDa/nm is for helices.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='experimentalType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='experimentalType')[source]
exportChildren(outfile, level, namespace_='', name_='experimentalType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa016d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7703d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770410>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType45(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType45', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType45')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType45', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f91d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9210>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType47(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType47', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType47')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType47', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f92d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9310>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType54(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType54', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType54')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType54', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01ed0>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType59(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType59', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType59')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType59', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a250>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType64(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType64', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType64')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType64', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a590>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType68(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType68', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType68')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType68', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a690>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType70(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType70', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType70')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType70', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a790>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType72(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType72', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType72')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType72', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a890>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.external_referencesType81(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='external_referencesType81', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='external_referencesType81')[source]
exportChildren(outfile, level, namespace_='', name_='external_referencesType81', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0add0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0ae10>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.extractionType(number_tomograms=None, number_subtomograms=None, reference_model=None, method=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='extractionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='extractionType')[source]
exportChildren(outfile, level, namespace_='', name_='extractionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_method()[source]
get_number_subtomograms()[source]
get_number_tomograms()[source]
get_reference_model()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7443d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7444d0>]
set_details(details)[source]
set_method(method)[source]
set_number_subtomograms(number_subtomograms)[source]
set_number_tomograms(number_tomograms)[source]
set_reference_model(reference_model)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.extractionType13(number_tomograms=None, number_subtomograms=None, reference_model=None, method=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='extractionType13', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='extractionType13')[source]
exportChildren(outfile, level, namespace_='', name_='extractionType13', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_method()[source]
get_number_subtomograms()[source]
get_number_tomograms()[source]
get_reference_model()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7550d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755190>]
set_details(details)[source]
set_method(method)[source]
set_number_subtomograms(number_subtomograms)[source]
set_number_tomograms(number_tomograms)[source]
set_reference_model(reference_model)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_current_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_current_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_current_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_current_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba090>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_dose_rate_type(units='ions/nm^2/s', valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_dose_rate_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_dose_rate_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_dose_rate_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba190>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_duration_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_duration_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_duration_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_duration_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba290>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_final_thickness_type(units='nm', valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_final_thickness_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_final_thickness_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_final_thickness_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba490>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_initial_thickness_type(units='nm', valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_initial_thickness_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_initial_thickness_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_initial_thickness_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba390>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fib_voltage_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fib_voltage_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fib_voltage_type')[source]
exportChildren(outfile, level, namespace_='', name_='fib_voltage_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6aff10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6aff50>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fiducial_marker_type(fiducial_type=None, manufacturer=None, diameter=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fiducial_marker_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fiducial_marker_type')[source]
exportChildren(outfile, level, namespace_='', name_='fiducial_marker_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_diameter()[source]
get_fiducial_type()[source]
get_manufacturer()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afcd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afd10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afd50>]
set_diameter(diameter)[source]
set_fiducial_type(fiducial_type)[source]
set_manufacturer(manufacturer)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.fiducial_markers_listType(fiducial_marker=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_fiducial_marker(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fiducial_markers_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fiducial_markers_listType')[source]
exportChildren(outfile, level, namespace_='', name_='fiducial_markers_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fiducial_marker()[source]
hasContent_()[source]
insert_fiducial_marker_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5e90>]
replace_fiducial_marker_at(index, value)[source]
set_fiducial_marker(fiducial_marker)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.figure_listType(figure=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_figure(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='figure_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='figure_listType')[source]
exportChildren(outfile, level, namespace_='', name_='figure_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_figure()[source]
hasContent_()[source]
insert_figure_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770b50>]
replace_figure_at(index, value)[source]
set_figure(figure)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.figure_type(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='figure_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='figure_type')[source]
exportChildren(outfile, level, namespace_='', name_='figure_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d2d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d310>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
validate_fileType(value)[source]
validate_fileType_patterns_ = [['^emd_\\d{4,}.+$']]
class emdbXMLTranslator.emdb_da.film[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='film', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='film')[source]
exportChildren(outfile, level, namespace_='', name_='film', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.film_or_detector_modelType(category=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='film_or_detector_modelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='film_or_detector_modelType')[source]
exportChildren(outfile, level, namespace_='', name_='film_or_detector_modelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_category()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7e10>]
set_category(category)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.film_thicknessType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='film_thicknessType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='film_thicknessType')[source]
exportChildren(outfile, level, namespace_='', name_='film_thicknessType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0f90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.film_type(id=None, film_material=None, film_topology=None, film_thickness=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='film_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='film_type')[source]
exportChildren(outfile, level, namespace_='', name_='film_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_film_material()[source]
get_film_thickness()[source]
get_film_topology()[source]
get_id()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d0d0>]
set_film_material(film_material)[source]
set_film_thickness(film_thickness)[source]
set_film_topology(film_topology)[source]
set_id(id)[source]
subclass = None
superclass = None
validate_film_topologyType(value)[source]
class emdbXMLTranslator.emdb_da.final_modelType(access_code=None, chain=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_chain(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='final_modelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='final_modelType')[source]
exportChildren(outfile, level, namespace_='', name_='final_modelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_access_code()[source]
get_chain()[source]
get_details()[source]
hasContent_()[source]
insert_chain_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a850>]
replace_chain_at(index, value)[source]
set_access_code(access_code)[source]
set_chain(chain)[source]
set_details(details)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.final_multi_reference_alignmentType(number_reference_projections=None, merit_function=None, angular_sampling=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='final_multi_reference_alignmentType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType')[source]
exportChildren(outfile, level, namespace_='', name_='final_multi_reference_alignmentType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angular_sampling()[source]
get_details()[source]
get_merit_function()[source]
get_number_reference_projections()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7440d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7441d0>]
set_angular_sampling(angular_sampling)[source]
set_details(details)[source]
set_merit_function(merit_function)[source]
set_number_reference_projections(number_reference_projections)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.final_multi_reference_alignmentType10(number_reference_projections=None, merit_function=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='final_multi_reference_alignmentType10', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType10')[source]
exportChildren(outfile, level, namespace_='', name_='final_multi_reference_alignmentType10', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_merit_function()[source]
get_number_reference_projections()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7445d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744650>]
set_details(details)[source]
set_merit_function(merit_function)[source]
set_number_reference_projections(number_reference_projections)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.final_multi_reference_alignmentType11(number_reference_projections=None, merit_function=None, angular_sampling=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='final_multi_reference_alignmentType11', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType11')[source]
exportChildren(outfile, level, namespace_='', name_='final_multi_reference_alignmentType11', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angular_sampling()[source]
get_details()[source]
get_merit_function()[source]
get_number_reference_projections()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cd50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cd90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cdd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74ce10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74ce50>]
set_angular_sampling(angular_sampling)[source]
set_details(details)[source]
set_merit_function(merit_function)[source]
set_number_reference_projections(number_reference_projections)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.final_multi_reference_alignmentType14(number_reference_projections=None, merit_function=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='final_multi_reference_alignmentType14', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='final_multi_reference_alignmentType14')[source]
exportChildren(outfile, level, namespace_='', name_='final_multi_reference_alignmentType14', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_merit_function()[source]
get_number_reference_projections()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7552d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755310>]
set_details(details)[source]
set_merit_function(merit_function)[source]
set_number_reference_projections(number_reference_projections)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.focused_ion_beamType(instrument=None, ion=None, voltage=None, current=None, dose_rate=None, duration=None, temperature=None, initial_thickness=None, final_thickness=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='focused_ion_beamType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='focused_ion_beamType')[source]
exportChildren(outfile, level, namespace_='', name_='focused_ion_beamType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_current()[source]
get_details()[source]
get_dose_rate()[source]
get_duration()[source]
get_final_thickness()[source]
get_initial_thickness()[source]
get_instrument()[source]
get_ion()[source]
get_temperature()[source]
get_voltage()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de5d0>]
set_current(current)[source]
set_details(details)[source]
set_dose_rate(dose_rate)[source]
set_duration(duration)[source]
set_final_thickness(final_thickness)[source]
set_initial_thickness(initial_thickness)[source]
set_instrument(instrument)[source]
set_ion(ion)[source]
set_temperature(temperature)[source]
set_voltage(voltage)[source]
subclass = None
superclass = None
validate_instrumentType6(value)[source]
validate_ionType(value)[source]
class emdbXMLTranslator.emdb_da.fsc_curve(file=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='fsc_curve', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='fsc_curve')[source]
exportChildren(outfile, level, namespace_='', name_='fsc_curve', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d1d0>]
set_details(details)[source]
set_file(file)[source]
subclass = None
superclass = None
validate_fileType33(value)[source]
validate_fileType33_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
class emdbXMLTranslator.emdb_da.glow_dischargeType(glow_discharge_params=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='glow_dischargeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='glow_dischargeType')[source]
exportChildren(outfile, level, namespace_='', name_='glow_dischargeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_glow_discharge_params()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd9d0>]
set_glow_discharge_params(glow_discharge_params)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.glow_discharge_params_type(time=None, atmosphere=None, pressure=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='glow_discharge_params_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='glow_discharge_params_type')[source]
exportChildren(outfile, level, namespace_='', name_='glow_discharge_params_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_atmosphere()[source]
get_pressure()[source]
get_time()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe58d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5910>]
set_atmosphere(atmosphere)[source]
set_pressure(pressure)[source]
set_time(time)[source]
subclass = None
superclass = None
validate_atmosphereType(value)[source]
class emdbXMLTranslator.emdb_da.grant_reference_type(funding_body=None, code=None, country=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='grant_reference_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='grant_reference_type')[source]
exportChildren(outfile, level, namespace_='', name_='grant_reference_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_code()[source]
get_country()[source]
get_funding_body()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68da50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68da90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dad0>]
set_code(code)[source]
set_country(country)[source]
set_funding_body(funding_body)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.grant_supportType(grant_reference=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_grant_reference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='grant_supportType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='grant_supportType')[source]
exportChildren(outfile, level, namespace_='', name_='grant_supportType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_grant_reference()[source]
hasContent_()[source]
insert_grant_reference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3b10>]
replace_grant_reference_at(index, value)[source]
set_grant_reference(grant_reference)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.grid_type(model=None, material=None, mesh=None, support_film=None, glow_discharge=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_support_film(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='grid_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='grid_type')[source]
exportChildren(outfile, level, namespace_='', name_='grid_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_glow_discharge()[source]
get_material()[source]
get_mesh()[source]
get_model()[source]
get_support_film()[source]
hasContent_()[source]
insert_support_film_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe56d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe57d0>]
replace_support_film_at(index, value)[source]
set_details(details)[source]
set_glow_discharge(glow_discharge)[source]
set_material(material)[source]
set_mesh(mesh)[source]
set_model(model)[source]
set_support_film(support_film)[source]
subclass = None
superclass = None
validate_materialType(value)[source]
validate_modelType(value)[source]
class emdbXMLTranslator.emdb_da.half_map_listType(half_map=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_half_map(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='half_map_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='half_map_listType')[source]
exportChildren(outfile, level, namespace_='', name_='half_map_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_half_map()[source]
hasContent_()[source]
insert_half_map_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f90d0>]
replace_half_map_at(index, value)[source]
set_half_map(half_map)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.hard_validation_regexpType(_error_text=None, regexp=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='hard_validation_regexpType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='hard_validation_regexpType')[source]
exportChildren(outfile, level, namespace_='', name_='hard_validation_regexpType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get__error_text()[source]
get_regexp()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5290>]
set__error_text(_error_text)[source]
set_regexp(regexp)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.heightType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='heightType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='heightType')[source]
exportChildren(outfile, level, namespace_='', name_='heightType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f02d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.heightType51(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='heightType51', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='heightType51')[source]
exportChildren(outfile, level, namespace_='', name_='heightType51', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f99d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.helical_parameters_type(delta_z=None, delta_phi=None, axial_symmetry=None, hand=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helical_parameters_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helical_parameters_type')[source]
exportChildren(outfile, level, namespace_='', name_='helical_parameters_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_axial_symmetry()[source]
get_delta_phi()[source]
get_delta_z()[source]
get_hand()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a89d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8a10>]
set_axial_symmetry(axial_symmetry)[source]
set_delta_phi(delta_phi)[source]
set_delta_z(delta_z)[source]
set_hand(hand)[source]
subclass = None
superclass = None
validate_axial_symmetryType(value)[source]
validate_axial_symmetryType_patterns_ = [['^[C|D][1-9][0-9]*$']]
validate_handType(value)[source]
class emdbXMLTranslator.emdb_da.helical_processing_type(id=None, image_recording_id=None, details=None, final_reconstruction=None, ctf_correction=None, segment_selection=None, refinement=None, startup_model=None, layer_lines=None, initial_angle_assignment=None, final_angle_assignment=None, crystal_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_processing_type

add_segment_selection(value)[source]
add_startup_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helical_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helical_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='helical_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystal_parameters()[source]
get_ctf_correction()[source]
get_final_angle_assignment()[source]
get_final_reconstruction()[source]
get_initial_angle_assignment()[source]
get_layer_lines()[source]
get_refinement()[source]
get_segment_selection()[source]
get_startup_model()[source]
hasContent_()[source]
insert_segment_selection_at(index, value)[source]
insert_startup_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6855d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6856d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685790>]
replace_segment_selection_at(index, value)[source]
replace_startup_model_at(index, value)[source]
set_crystal_parameters(crystal_parameters)[source]
set_ctf_correction(ctf_correction)[source]
set_final_angle_assignment(final_angle_assignment)[source]
set_final_reconstruction(final_reconstruction)[source]
set_initial_angle_assignment(initial_angle_assignment)[source]
set_layer_lines(layer_lines)[source]
set_refinement(refinement)[source]
set_segment_selection(segment_selection)[source]
set_startup_model(startup_model)[source]
subclass = None
superclass

alias of base_processing_type

class emdbXMLTranslator.emdb_da.helix_lengthType(min=None, max=None, average=None, software_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helix_lengthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helix_lengthType')[source]
exportChildren(outfile, level, namespace_='', name_='helix_lengthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average()[source]
get_max()[source]
get_min()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74ca10>]
set_average(average)[source]
set_max(max)[source]
set_min(min)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.helix_lengthType30(min=None, max=None, average=None, software_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='helix_lengthType30', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='helix_lengthType30')[source]
exportChildren(outfile, level, namespace_='', name_='helix_lengthType30', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average()[source]
get_max()[source]
get_min()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f650>]
set_average(average)[source]
set_max(max)[source]
set_min(min)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.high_frequency_cutoffType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_frequency_cutoffType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_frequency_cutoffType')[source]
exportChildren(outfile, level, namespace_='', name_='high_frequency_cutoffType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9e90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.high_pressure_freezingType(instrument=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_pressure_freezingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_pressure_freezingType')[source]
exportChildren(outfile, level, namespace_='', name_='high_pressure_freezingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_instrument()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5fd0>]
set_details(details)[source]
set_instrument(instrument)[source]
subclass = None
superclass = None
validate_instrumentType5(value)[source]
class emdbXMLTranslator.emdb_da.high_resolutionType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_resolutionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_resolutionType')[source]
exportChildren(outfile, level, namespace_='', name_='high_resolutionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744ad0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.high_resolutionType18(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_resolutionType18', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_resolutionType18')[source]
exportChildren(outfile, level, namespace_='', name_='high_resolutionType18', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755790>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.high_resolutionType82(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_resolutionType82', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_resolutionType82')[source]
exportChildren(outfile, level, namespace_='', name_='high_resolutionType82', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0aed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0af10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.high_resolutionType83(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='high_resolutionType83', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='high_resolutionType83')[source]
exportChildren(outfile, level, namespace_='', name_='high_resolutionType83', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15390>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.image_recordingType(id=None, film_or_detector_model=None, detector_mode=None, digitization_details=None, number_grids_imaged=None, number_real_images=None, number_diffraction_images=None, average_exposure_time=None, average_electron_dose_per_image=None, detector_distance=None, details=None, od_range=None, bits_per_pixel=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='image_recordingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='image_recordingType')[source]
exportChildren(outfile, level, namespace_='', name_='image_recordingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average_electron_dose_per_image()[source]
get_average_exposure_time()[source]
get_bits_per_pixel()[source]
get_details()[source]
get_detector_distance()[source]
get_detector_mode()[source]
get_digitization_details()[source]
get_film_or_detector_model()[source]
get_id()[source]
get_number_diffraction_images()[source]
get_number_grids_imaged()[source]
get_number_real_images()[source]
get_od_range()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7a50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7ad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7b50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7b90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7c10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7c50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7cd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7d10>]
set_average_electron_dose_per_image(average_electron_dose_per_image)[source]
set_average_exposure_time(average_exposure_time)[source]
set_bits_per_pixel(bits_per_pixel)[source]
set_details(details)[source]
set_detector_distance(detector_distance)[source]
set_detector_mode(detector_mode)[source]
set_digitization_details(digitization_details)[source]
set_film_or_detector_model(film_or_detector_model)[source]
set_id(id)[source]
set_number_diffraction_images(number_diffraction_images)[source]
set_number_grids_imaged(number_grids_imaged)[source]
set_number_real_images(number_real_images)[source]
set_od_range(od_range)[source]
subclass = None
superclass = None
validate_detector_modeType(value)[source]
class emdbXMLTranslator.emdb_da.image_recording_listType(image_recording=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_image_recording(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='image_recording_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='image_recording_listType')[source]
exportChildren(outfile, level, namespace_='', name_='image_recording_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_image_recording()[source]
hasContent_()[source]
insert_image_recording_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7910>]
replace_image_recording_at(index, value)[source]
set_image_recording(image_recording)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.image_recording_type(film=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Images may have been recorded on different detectors

add_film(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='image_recording_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='image_recording_type')[source]
exportChildren(outfile, level, namespace_='', name_='image_recording_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_film()[source]
hasContent_()[source]
insert_film_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674b90>]
replace_film_at(index, value)[source]
set_film(film)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.in_plane_rotation[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='in_plane_rotation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='in_plane_rotation')[source]
exportChildren(outfile, level, namespace_='', name_='in_plane_rotation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.in_plane_translation[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='in_plane_translation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='in_plane_translation')[source]
exportChildren(outfile, level, namespace_='', name_='in_plane_translation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.indexingType(software_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='indexingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='indexingType')[source]
exportChildren(outfile, level, namespace_='', name_='indexingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74cc50>]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.indexingType31(software_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='indexingType31', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='indexingType31')[source]
exportChildren(outfile, level, namespace_='', name_='indexingType31', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f710>]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.initial_modelType(access_code=None, chain=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_chain(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='initial_modelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='initial_modelType')[source]
exportChildren(outfile, level, namespace_='', name_='initial_modelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_access_code()[source]
get_chain()[source]
get_details()[source]
hasContent_()[source]
insert_chain_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a650>]
replace_chain_at(index, value)[source]
set_access_code(access_code)[source]
set_chain(chain)[source]
set_details(details)[source]
subclass = None
superclass = None
validate_access_codeType(value)[source]
validate_access_codeType_patterns_ = [['^\\d[\\dA-Za-z]{3}$'], ['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.integer_vector_map_type(col=None, row=None, sec=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='integer_vector_map_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='integer_vector_map_type')[source]
exportChildren(outfile, level, namespace_='', name_='integer_vector_map_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_col()[source]
get_row()[source]
get_sec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f050>]
set_col(col)[source]
set_row(row)[source]
set_sec(sec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.interpretation_type(modelling_list=None, figure_list=None, segmentation_list=None, slices_list=None, additional_map_list=None, half_map_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='interpretation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='interpretation_type')[source]
exportChildren(outfile, level, namespace_='', name_='interpretation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_additional_map_list()[source]
get_figure_list()[source]
get_half_map_list()[source]
get_modelling_list()[source]
get_segmentation_list()[source]
get_slices_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6965d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696650>]
set_additional_map_list(additional_map_list)[source]
set_figure_list(figure_list)[source]
set_half_map_list(half_map_list)[source]
set_modelling_list(modelling_list)[source]
set_segmentation_list(segmentation_list)[source]
set_slices_list(slices_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.journal_citation(published=None, author=None, editor=None, title=None, journal=None, journal_abbreviation=None, country=None, issue=None, volume=None, first_page=None, last_page=None, year=None, language=None, external_references=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_author(value)[source]
add_editor(value)[source]
add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='journal_citation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='journal_citation')[source]
exportChildren(outfile, level, namespace_='', name_='journal_citation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_author()[source]
get_country()[source]
get_details()[source]
get_editor()[source]
get_external_references()[source]
get_first_page()[source]
get_issue()[source]
get_journal()[source]
get_journal_abbreviation()[source]
get_language()[source]
get_last_page()[source]
get_published()[source]
get_title()[source]
get_volume()[source]
get_year()[source]
hasContent_()[source]
insert_author_at(index, value)[source]
insert_editor_at(index, value)[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f6d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f8d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f990>]
replace_author_at(index, value)[source]
replace_editor_at(index, value)[source]
replace_external_references_at(index, value)[source]
set_author(author)[source]
set_country(country)[source]
set_details(details)[source]
set_editor(editor)[source]
set_external_references(external_references)[source]
set_first_page(first_page)[source]
set_issue(issue)[source]
set_journal(journal)[source]
set_journal_abbreviation(journal_abbreviation)[source]
set_language(language)[source]
set_last_page(last_page)[source]
set_published(published)[source]
set_title(title)[source]
set_volume(volume)[source]
set_year(year)[source]
subclass = None
superclass = None
validate_journal_abbreviationType(value)[source]
validate_journal_abbreviationType_patterns_ = [['^[A-Z][a-z]*\\.?( [A-Z][a-z]+\\.?)*$']]
validate_page_type(value)[source]
validate_yearType46(value)[source]
class emdbXMLTranslator.emdb_da.key_datesType(deposition=None, header_release=None, map_release=None, obsolete=None, update=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='key_datesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='key_datesType')[source]
exportChildren(outfile, level, namespace_='', name_='key_datesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_deposition()[source]
get_header_release()[source]
get_map_release()[source]
get_obsolete()[source]
get_update()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c37d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3850>]
set_deposition(deposition)[source]
set_header_release(header_release)[source]
set_map_release(map_release)[source]
set_obsolete(obsolete)[source]
set_update(update)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.lattice_distortion_correctionType(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='lattice_distortion_correctionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='lattice_distortion_correctionType')[source]
exportChildren(outfile, level, namespace_='', name_='lattice_distortion_correctionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744cd0>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.lattice_distortion_correctionType20(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='lattice_distortion_correctionType20', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='lattice_distortion_correctionType20')[source]
exportChildren(outfile, level, namespace_='', name_='lattice_distortion_correctionType20', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755990>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.layer_lines(file=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='layer_lines', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='layer_lines')[source]
exportChildren(outfile, level, namespace_='', name_='layer_lines', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d290>]
set_file(file)[source]
subclass = None
superclass = None
validate_fileType34(value)[source]
validate_fileType34_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
class emdbXMLTranslator.emdb_da.layer_linesType(number_helices=None, helix_length=None, straightening=None, indexing=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='layer_linesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='layer_linesType')[source]
exportChildren(outfile, level, namespace_='', name_='layer_linesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helix_length()[source]
get_indexing()[source]
get_number_helices()[source]
get_straightening()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c810>]
set_helix_length(helix_length)[source]
set_indexing(indexing)[source]
set_number_helices(number_helices)[source]
set_straightening(straightening)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.layer_linesType29(number_helices=None, helix_length=None, straightening=None, indexing=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='layer_linesType29', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='layer_linesType29')[source]
exportChildren(outfile, level, namespace_='', name_='layer_linesType29', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helix_length()[source]
get_indexing()[source]
get_number_helices()[source]
get_straightening()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f4d0>]
set_helix_length(helix_length)[source]
set_indexing(indexing)[source]
set_number_helices(number_helices)[source]
set_straightening(straightening)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.legacyType(astigmatism=None, electron_beam_tilt_params=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='legacyType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='legacyType')[source]
exportChildren(outfile, level, namespace_='', name_='legacyType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_astigmatism()[source]
get_electron_beam_tilt_params()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7850>]
set_astigmatism(astigmatism)[source]
set_electron_beam_tilt_params(electron_beam_tilt_params)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.ligand(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None, external_references=None, recombinant_expression=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Is naturalExpression and recombinantExpression suitable for this component?

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ligand', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ligand')[source]
exportChildren(outfile, level, namespace_='', name_='ligand', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_external_references()[source]
get_formula()[source]
get_natural_source()[source]
get_recombinant_expression()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af8d0>]
replace_external_references_at(index, value)[source]
set_external_references(external_references)[source]
set_formula(formula)[source]
set_natural_source(natural_source)[source]
set_recombinant_expression(recombinant_expression)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_formulaType71(value)[source]
validate_formulaType71_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
class emdbXMLTranslator.emdb_da.lipid(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, formula=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Is naturalExpression and recombinantExpression suitable for this component?

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='lipid', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='lipid')[source]
exportChildren(outfile, level, namespace_='', name_='lipid', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_external_references()[source]
get_formula()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af750>]
replace_external_references_at(index, value)[source]
set_external_references(external_references)[source]
set_formula(formula)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_formulaType69(value)[source]
validate_formulaType69_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
class emdbXMLTranslator.emdb_da.low_frequency_cutoffType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='low_frequency_cutoffType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='low_frequency_cutoffType')[source]
exportChildren(outfile, level, namespace_='', name_='low_frequency_cutoffType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9d50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9d90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.low_resolutionType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='low_resolutionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='low_resolutionType')[source]
exportChildren(outfile, level, namespace_='', name_='low_resolutionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744b90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744bd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.low_resolutionType19(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='low_resolutionType19', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='low_resolutionType19')[source]
exportChildren(outfile, level, namespace_='', name_='low_resolutionType19', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755890>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.low_resolutionType84(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='low_resolutionType84', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='low_resolutionType84')[source]
exportChildren(outfile, level, namespace_='', name_='low_resolutionType84', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15490>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.lower_energy_thresholdType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='lower_energy_thresholdType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='lower_energy_thresholdType')[source]
exportChildren(outfile, level, namespace_='', name_='lower_energy_thresholdType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cde10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cde50>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.macromoleculeType(id=None, number_of_copies=None, oligomeric_state=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='macromoleculeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='macromoleculeType')[source]
exportChildren(outfile, level, namespace_='', name_='macromoleculeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_id()[source]
get_number_of_copies()[source]
get_oligomeric_state()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7702d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770310>]
set_id(id)[source]
set_number_of_copies(number_of_copies)[source]
set_oligomeric_state(oligomeric_state)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.macromolecule_listType(macromolecule=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_macromolecule(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='macromolecule_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='macromolecule_listType')[source]
exportChildren(outfile, level, namespace_='', name_='macromolecule_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_macromolecule()[source]
hasContent_()[source]
insert_macromolecule_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770190>]
replace_macromolecule_at(index, value)[source]
set_macromolecule(macromolecule)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.macromolecule_listType40(macromolecule_id=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_macromolecule_id(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='macromolecule_listType40', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='macromolecule_listType40')[source]
exportChildren(outfile, level, namespace_='', name_='macromolecule_listType40', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_macromolecule_id()[source]
hasContent_()[source]
insert_macromolecule_id_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7705d0>]
replace_macromolecule_id_at(index, value)[source]
set_macromolecule_id(macromolecule_id)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.macromolecule_list_type(macromolecule=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_macromolecule(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='macromolecule_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='macromolecule_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='macromolecule_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_macromolecule()[source]
hasContent_()[source]
insert_macromolecule_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696b90>]
replace_macromolecule_at(index, value)[source]
set_macromolecule(macromolecule)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.macromolecules_and_complexes_type(macromolecule_id=None, complex_id=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Depending on the problem, one can either reference the sample on the macromolecule level or the complex level.

add_complex_id(value)[source]
add_macromolecule_id(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='macromolecules_and_complexes_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='macromolecules_and_complexes_type')[source]
exportChildren(outfile, level, namespace_='', name_='macromolecules_and_complexes_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_complex_id()[source]
get_macromolecule_id()[source]
hasContent_()[source]
insert_complex_id_at(index, value)[source]
insert_macromolecule_id_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dd90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68ddd0>]
replace_complex_id_at(index, value)[source]
replace_macromolecule_id_at(index, value)[source]
set_complex_id(complex_id)[source]
set_macromolecule_id(macromolecule_id)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.map_statistics_type(minimum=None, maximum=None, average=None, std=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='map_statistics_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='map_statistics_type')[source]
exportChildren(outfile, level, namespace_='', name_='map_statistics_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_average()[source]
get_maximum()[source]
get_minimum()[source]
get_std()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afa50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afa90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afb10>]
set_average(average)[source]
set_maximum(maximum)[source]
set_minimum(minimum)[source]
set_std(std)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.map_type(size_kbytes=None, format=None, file=None, symmetry=None, data_type=None, dimensions=None, origin=None, spacing=None, cell=None, axis_order=None, statistics=None, pixel_spacing=None, contour_list=None, label=None, annotation_details=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='map_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='map_type')[source]
exportChildren(outfile, level, namespace_='', name_='map_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_annotation_details()[source]
get_axis_order()[source]
get_cell()[source]
get_contour_list()[source]
get_data_type()[source]
get_details()[source]
get_dimensions()[source]
get_file()[source]
get_format()[source]
get_label()[source]
get_origin()[source]
get_pixel_spacing()[source]
get_size_kbytes()[source]
get_spacing()[source]
get_statistics()[source]
get_symmetry()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685c10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685c50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685cd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685d10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685d50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685ed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685f10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685f90>]
set_annotation_details(annotation_details)[source]
set_axis_order(axis_order)[source]
set_cell(cell)[source]
set_contour_list(contour_list)[source]
set_data_type(data_type)[source]
set_details(details)[source]
set_dimensions(dimensions)[source]
set_file(file)[source]
set_format(format)[source]
set_label(label)[source]
set_origin(origin)[source]
set_pixel_spacing(pixel_spacing)[source]
set_size_kbytes(size_kbytes)[source]
set_spacing(spacing)[source]
set_statistics(statistics)[source]
set_symmetry(symmetry)[source]
subclass = None
superclass = None
validate_fileType32(value)[source]
validate_fileType32_patterns_ = [['^emd_\\d{4,}([A-Za-z0-9_]*).map(.gz|)$']]
validate_map_data_type(value)[source]
class emdbXMLTranslator.emdb_da.max[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='max', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='max')[source]
exportChildren(outfile, level, namespace_='', name_='max', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.max_angleType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='max_angleType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='max_angleType')[source]
exportChildren(outfile, level, namespace_='', name_='max_angleType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f07d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.maximum_likelihood_type(parameters=None, noise_model=None, software_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='maximum_likelihood_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='maximum_likelihood_type')[source]
exportChildren(outfile, level, namespace_='', name_='maximum_likelihood_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_noise_model()[source]
get_parameters()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67da10>]
set_noise_model(noise_model)[source]
set_parameters(parameters)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.mergingType(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mergingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mergingType')[source]
exportChildren(outfile, level, namespace_='', name_='mergingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744ed0>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.mergingType22(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='mergingType22', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='mergingType22')[source]
exportChildren(outfile, level, namespace_='', name_='mergingType22', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755b50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755b90>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.microscopy_listType(microscopy=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_microscopy(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='microscopy_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='microscopy_listType')[source]
exportChildren(outfile, level, namespace_='', name_='microscopy_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_microscopy()[source]
hasContent_()[source]
insert_microscopy_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd7d0>]
replace_microscopy_at(index, value)[source]
set_microscopy(microscopy)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.min[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='min', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='min')[source]
exportChildren(outfile, level, namespace_='', name_='min', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.min_angleType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='min_angleType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='min_angleType')[source]
exportChildren(outfile, level, namespace_='', name_='min_angleType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f06d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.model_heterogeneityType(number_classes=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='model_heterogeneityType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='model_heterogeneityType')[source]
exportChildren(outfile, level, namespace_='', name_='model_heterogeneityType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_number_classes()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73acd0>]
set_number_classes(number_classes)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.model_type(access_code=None, chain=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_chain(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='model_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='model_type')[source]
exportChildren(outfile, level, namespace_='', name_='model_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_access_code()[source]
get_chain()[source]
hasContent_()[source]
insert_chain_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a87d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8810>]
replace_chain_at(index, value)[source]
set_access_code(access_code)[source]
set_chain(chain)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.modelling_listType(modelling=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_modelling(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='modelling_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='modelling_listType')[source]
exportChildren(outfile, level, namespace_='', name_='modelling_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_modelling()[source]
hasContent_()[source]
insert_modelling_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770a50>]
replace_modelling_at(index, value)[source]
set_modelling(modelling)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.modelling_type(initial_model=None, final_model=None, refinement_protocol=None, software_list=None, details=None, target_criteria=None, refinement_space=None, overall_bvalue=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_initial_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='modelling_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='modelling_type')[source]
exportChildren(outfile, level, namespace_='', name_='modelling_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_final_model()[source]
get_initial_model()[source]
get_overall_bvalue()[source]
get_refinement_protocol()[source]
get_refinement_space()[source]
get_software_list()[source]
get_target_criteria()[source]
hasContent_()[source]
insert_initial_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67d8d0>]
replace_initial_model_at(index, value)[source]
set_details(details)[source]
set_final_model(final_model)[source]
set_initial_model(initial_model)[source]
set_overall_bvalue(overall_bvalue)[source]
set_refinement_protocol(refinement_protocol)[source]
set_refinement_space(refinement_space)[source]
set_software_list(software_list)[source]
set_target_criteria(target_criteria)[source]
subclass = None
superclass = None
validate_refinement_protocolType(value)[source]
class emdbXMLTranslator.emdb_da.molecular_replacementType(starting_model=None, resolution_range=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_starting_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='molecular_replacementType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='molecular_replacementType')[source]
exportChildren(outfile, level, namespace_='', name_='molecular_replacementType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_resolution_range()[source]
get_software_list()[source]
get_starting_model()[source]
hasContent_()[source]
insert_starting_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7447d0>]
replace_starting_model_at(index, value)[source]
set_details(details)[source]
set_resolution_range(resolution_range)[source]
set_software_list(software_list)[source]
set_starting_model(starting_model)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.molecular_replacementType15(starting_model=None, resolution_range=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_starting_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='molecular_replacementType15', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='molecular_replacementType15')[source]
exportChildren(outfile, level, namespace_='', name_='molecular_replacementType15', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_resolution_range()[source]
get_software_list()[source]
get_starting_model()[source]
hasContent_()[source]
insert_starting_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7553d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755490>]
replace_starting_model_at(index, value)[source]
set_details(details)[source]
set_resolution_range(resolution_range)[source]
set_software_list(software_list)[source]
set_starting_model(starting_model)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.molecular_weightType(units=None, theoretical=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

kDa/nm is for helices.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='molecular_weightType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='molecular_weightType')[source]
exportChildren(outfile, level, namespace_='', name_='molecular_weightType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_theoretical()[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7706d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770750>]
set_theoretical(theoretical)[source]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.molecular_weight_type(experimental=None, theoretical=None, method=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='molecular_weight_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='molecular_weight_type')[source]
exportChildren(outfile, level, namespace_='', name_='molecular_weight_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_experimental()[source]
get_method()[source]
get_theoretical()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8c10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8c50>]
set_experimental(experimental)[source]
set_method(method)[source]
set_theoretical(theoretical)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.molecule_id[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='molecule_id', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='molecule_id')[source]
exportChildren(outfile, level, namespace_='', name_='molecule_id', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.name_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='name_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='name_type')[source]
exportChildren(outfile, level, namespace_='', name_='name_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.natural_hostType(database=None, organism=None, strain=None, synonym_organism=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_hostType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_hostType')[source]
exportChildren(outfile, level, namespace_='', name_='natural_hostType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.natural_sourceType(database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_sourceType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_sourceType')[source]
exportChildren(outfile, level, namespace_='', name_='natural_sourceType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_organ()[source]
get_tissue()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767890>]
set_cell(cell)[source]
set_organ(organ)[source]
set_tissue(tissue)[source]
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.natural_sourceType36(database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_sourceType36', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_sourceType36')[source]
exportChildren(outfile, level, namespace_='', name_='natural_sourceType36', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_organ()[source]
get_tissue()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7679d0>]
set_cell(cell)[source]
set_organ(organ)[source]
set_tissue(tissue)[source]
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.natural_sourceType37(database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_sourceType37', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_sourceType37')[source]
exportChildren(outfile, level, namespace_='', name_='natural_sourceType37', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_organ()[source]
get_tissue()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767ad0>]
set_organ(organ)[source]
set_tissue(tissue)[source]
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.natural_sourceType38(database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None, organelle=None, cellular_location=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_sourceType38', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_sourceType38')[source]
exportChildren(outfile, level, namespace_='', name_='natural_sourceType38', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_cellular_location()[source]
get_organ()[source]
get_organelle()[source]
get_tissue()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767b90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767c10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767c50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767c90>]
set_cell(cell)[source]
set_cellular_location(cellular_location)[source]
set_organ(organ)[source]
set_organelle(organelle)[source]
set_tissue(tissue)[source]
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.natural_source_type(database=None, organism=None, strain=None, synonym_organism=None, organ=None, tissue=None, cell=None, organelle=None, cellular_location=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_natural_source_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='natural_source_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='natural_source_type')[source]
exportChildren(outfile, level, namespace_='', name_='natural_source_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_cellular_location()[source]
get_organ()[source]
get_organelle()[source]
get_tissue()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a86d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8710>]
set_cell(cell)[source]
set_cellular_location(cellular_location)[source]
set_organ(organ)[source]
set_organelle(organelle)[source]
set_tissue(tissue)[source]
subclass = None
superclass

alias of base_natural_source_type

class emdbXMLTranslator.emdb_da.noise_modelType(white_gaussian=None, coloured_gaussian=None, other=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='noise_modelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='noise_modelType')[source]
exportChildren(outfile, level, namespace_='', name_='noise_modelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_coloured_gaussian()[source]
get_other()[source]
get_white_gaussian()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73ae50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73ae90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73aed0>]
set_coloured_gaussian(coloured_gaussian)[source]
set_other(other)[source]
set_white_gaussian(white_gaussian)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.nominal_csType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='nominal_csType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='nominal_csType')[source]
exportChildren(outfile, level, namespace_='', name_='nominal_csType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de9d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.nominal_defocus_maxType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='nominal_defocus_maxType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='nominal_defocus_maxType')[source]
exportChildren(outfile, level, namespace_='', name_='nominal_defocus_maxType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6dec90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6decd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.nominal_defocus_minType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='nominal_defocus_minType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='nominal_defocus_minType')[source]
exportChildren(outfile, level, namespace_='', name_='nominal_defocus_minType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6dea90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6dead0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.non_journal_citation(published=None, author=None, editor=None, book_title=None, thesis_title=None, book_chapter_title=None, volume=None, publisher=None, publication_location=None, country=None, first_page=None, last_page=None, year=None, language=None, external_references=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_author(value)[source]
add_editor(value)[source]
add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='non_journal_citation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='non_journal_citation')[source]
exportChildren(outfile, level, namespace_='', name_='non_journal_citation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_author()[source]
get_book_chapter_title()[source]
get_book_title()[source]
get_country()[source]
get_details()[source]
get_editor()[source]
get_external_references()[source]
get_first_page()[source]
get_language()[source]
get_last_page()[source]
get_publication_location()[source]
get_published()[source]
get_publisher()[source]
get_thesis_title()[source]
get_volume()[source]
get_year()[source]
hasContent_()[source]
insert_author_at(index, value)[source]
insert_editor_at(index, value)[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f2d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69f550>]
replace_author_at(index, value)[source]
replace_editor_at(index, value)[source]
replace_external_references_at(index, value)[source]
set_author(author)[source]
set_book_chapter_title(book_chapter_title)[source]
set_book_title(book_title)[source]
set_country(country)[source]
set_details(details)[source]
set_editor(editor)[source]
set_external_references(external_references)[source]
set_first_page(first_page)[source]
set_language(language)[source]
set_last_page(last_page)[source]
set_publication_location(publication_location)[source]
set_published(published)[source]
set_publisher(publisher)[source]
set_thesis_title(thesis_title)[source]
set_volume(volume)[source]
set_year(year)[source]
subclass = None
superclass = None
validate_page_type(value)[source]
validate_publication_locationType(value)[source]
validate_publication_locationType_patterns_ = [['^[\\w -]+(, [\\w -]+)*$']]
validate_yearType(value)[source]
class emdbXMLTranslator.emdb_da.noneType[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='noneType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='noneType')[source]
exportChildren(outfile, level, namespace_='', name_='noneType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.number_classes[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='number_classes', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='number_classes')[source]
exportChildren(outfile, level, namespace_='', name_='number_classes', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.number_helices[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='number_helices', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='number_helices')[source]
exportChildren(outfile, level, namespace_='', name_='number_helices', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.number_observed_reflections[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='number_observed_reflections', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='number_observed_reflections')[source]
exportChildren(outfile, level, namespace_='', name_='number_observed_reflections', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.number_unique_reflections[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='number_unique_reflections', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='number_unique_reflections')[source]
exportChildren(outfile, level, namespace_='', name_='number_unique_reflections', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.obsolete_listType(entry=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_entry(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='obsolete_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='obsolete_listType')[source]
exportChildren(outfile, level, namespace_='', name_='obsolete_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_entry()[source]
hasContent_()[source]
insert_entry_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3910>]
replace_entry_at(index, value)[source]
set_entry(entry)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.organelle_or_cellular_component(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None, molecular_weight=None, recombinant_expression=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='organelle_or_cellular_component', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='organelle_or_cellular_component')[source]
exportChildren(outfile, level, namespace_='', name_='organelle_or_cellular_component', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_molecular_weight()[source]
get_natural_source()[source]
get_recombinant_expression()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15b50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15b90>]
set_molecular_weight(molecular_weight)[source]
set_natural_source(natural_source)[source]
set_recombinant_expression(recombinant_expression)[source]
subclass = None
superclass

alias of base_supramolecule_type

class emdbXMLTranslator.emdb_da.organism_type(ncbi=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='organism_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='organism_type')[source]
exportChildren(outfile, level, namespace_='', name_='organism_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ncbi()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a83d0>]
set_ncbi(ncbi)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.organizationType(type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='organizationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='organizationType')[source]
exportChildren(outfile, level, namespace_='', name_='organizationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3fd0>]
set_type(type_)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.originType(col=None, row=None, sec=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='originType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='originType')[source]
exportChildren(outfile, level, namespace_='', name_='originType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_col()[source]
get_row()[source]
get_sec()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fe50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fe90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fed0>]
set_col(col)[source]
set_row(row)[source]
set_sec(sec)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.orthogonal_tiltType(software_list=None, number_images=None, tilt_angle1=None, tilt_angle2=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='orthogonal_tiltType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='orthogonal_tiltType')[source]
exportChildren(outfile, level, namespace_='', name_='orthogonal_tiltType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_number_images()[source]
get_software_list()[source]
get_tilt_angle1()[source]
get_tilt_angle2()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fa90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fb10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fb50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fb90>]
set_details(details)[source]
set_number_images(number_images)[source]
set_software_list(software_list)[source]
set_tilt_angle1(tilt_angle1)[source]
set_tilt_angle2(tilt_angle2)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.osmium_ferricyanide[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='osmium_ferricyanide', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='osmium_ferricyanide')[source]
exportChildren(outfile, level, namespace_='', name_='osmium_ferricyanide', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.osmium_tetroxide[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='osmium_tetroxide', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='osmium_tetroxide')[source]
exportChildren(outfile, level, namespace_='', name_='osmium_tetroxide', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.other[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='other', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='other')[source]
exportChildren(outfile, level, namespace_='', name_='other', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.otherType[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='otherType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='otherType')[source]
exportChildren(outfile, level, namespace_='', name_='otherType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.otherType52(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='otherType52', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='otherType52')[source]
exportChildren(outfile, level, namespace_='', name_='otherType52', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa012d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01310>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.other_macromolecule(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, recombinant_expression=None, structure=None, synthetic_flag=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Use to cater for cyclic-pseudo-peptide, other, peptide nucleic acid and polydeoxyribonucleotide/polyribonucleotide hybrid categories. Most items are optional and there is no checking done

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='other_macromolecule', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='other_macromolecule')[source]
exportChildren(outfile, level, namespace_='', name_='other_macromolecule', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_classification()[source]
get_recombinant_expression()[source]
get_sequence()[source]
get_structure()[source]
get_synthetic_flag()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baa10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baa50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baa90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6baad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bab10>]
set_classification(classification)[source]
set_recombinant_expression(recombinant_expression)[source]
set_sequence(sequence)[source]
set_structure(structure)[source]
set_synthetic_flag(synthetic_flag)[source]
subclass = None
superclass

alias of base_macromolecule_type

class emdbXMLTranslator.emdb_da.out_of_plane_rotation[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='out_of_plane_rotation', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='out_of_plane_rotation')[source]
exportChildren(outfile, level, namespace_='', name_='out_of_plane_rotation', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.parallel_resolution[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='parallel_resolution', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='parallel_resolution')[source]
exportChildren(outfile, level, namespace_='', name_='parallel_resolution', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.parametersType(in_plane_translation=None, in_plane_rotation=None, out_of_plane_rotation=None, model_heterogeneity=None, other=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='parametersType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='parametersType')[source]
exportChildren(outfile, level, namespace_='', name_='parametersType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_in_plane_rotation()[source]
get_in_plane_translation()[source]
get_model_heterogeneity()[source]
get_other()[source]
get_out_of_plane_rotation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a9d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73aa10>]
set_in_plane_rotation(in_plane_rotation)[source]
set_in_plane_translation(in_plane_translation)[source]
set_model_heterogeneity(model_heterogeneity)[source]
set_other(other)[source]
set_out_of_plane_rotation(out_of_plane_rotation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.particle_selection_type(number_particles_selected=None, reference_model=None, method=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='particle_selection_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='particle_selection_type')[source]
exportChildren(outfile, level, namespace_='', name_='particle_selection_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_method()[source]
get_number_particles_selected()[source]
get_reference_model()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe54d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe55d0>]
set_details(details)[source]
set_method(method)[source]
set_number_particles_selected(number_particles_selected)[source]
set_reference_model(reference_model)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.pdb_cross_reference_list_type(pdb_reference=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

List of related PDB entries

add_pdb_reference(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pdb_cross_reference_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pdb_cross_reference_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='pdb_cross_reference_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_pdb_reference()[source]
hasContent_()[source]
insert_pdb_reference_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5050>]
replace_pdb_reference_at(index, value)[source]
set_pdb_reference(pdb_reference)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.pdb_cross_reference_type(id=None, pdb_id=None, relationship=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

PDB entries related to this entry. The chainID list can be used to specify which specific chains are related to this map.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pdb_cross_reference_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pdb_cross_reference_type')[source]
exportChildren(outfile, level, namespace_='', name_='pdb_cross_reference_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_id()[source]
get_pdb_id()[source]
get_relationship()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdae90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdaed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdaf10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efdaf50>]
set_details(details)[source]
set_id(id)[source]
set_pdb_id(pdb_id)[source]
set_relationship(relationship)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.pdb_model_type(pdb_id=None, chain_id_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pdb_model_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pdb_model_type')[source]
exportChildren(outfile, level, namespace_='', name_='pdb_model_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_chain_id_list()[source]
get_pdb_id()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dc90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68dcd0>]
set_chain_id_list(chain_id_list)[source]
set_pdb_id(pdb_id)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.perpendicular_resolution[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='perpendicular_resolution', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='perpendicular_resolution')[source]
exportChildren(outfile, level, namespace_='', name_='perpendicular_resolution', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.phase_reversalType(anisotropic=None, correction_space=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='phase_reversalType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='phase_reversalType')[source]
exportChildren(outfile, level, namespace_='', name_='phase_reversalType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_anisotropic()[source]
get_correction_space()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a1d0>]
set_anisotropic(anisotropic)[source]
set_correction_space(correction_space)[source]
subclass = None
superclass = None
validate_correction_space_type(value)[source]
class emdbXMLTranslator.emdb_da.phophotungstic_acid[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='phophotungstic_acid', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='phophotungstic_acid')[source]
exportChildren(outfile, level, namespace_='', name_='phophotungstic_acid', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.pixel_spacingType(x=None, y=None, z=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pixel_spacingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pixel_spacingType')[source]
exportChildren(outfile, level, namespace_='', name_='pixel_spacingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_x()[source]
get_y()[source]
get_z()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7674d0>]
set_x(x)[source]
set_y(y)[source]
set_z(z)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.pixel_spacing_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pixel_spacing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pixel_spacing_type')[source]
exportChildren(outfile, level, namespace_='', name_='pixel_spacing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afbd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afc10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.pressureType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='pressureType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='pressureType')[source]
exportChildren(outfile, level, namespace_='', name_='pressureType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdbd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdc10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.primary_citationType(citation_type=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='primary_citationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='primary_citationType')[source]
exportChildren(outfile, level, namespace_='', name_='primary_citationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_citation_type()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd1d0>]
set_citation_type(citation_type)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.projection_matching_processingType(number_reference_projections=None, merit_function=None, angular_sampling=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='projection_matching_processingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='projection_matching_processingType')[source]
exportChildren(outfile, level, namespace_='', name_='projection_matching_processingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angular_sampling()[source]
get_merit_function()[source]
get_number_reference_projections()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a410>]
set_angular_sampling(angular_sampling)[source]
set_merit_function(merit_function)[source]
set_number_reference_projections(number_reference_projections)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.protein_or_peptide(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, recombinant_expression=None, enantiomer=None, sequence=None, ec_number=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

add_ec_number(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='protein_or_peptide', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='protein_or_peptide')[source]
exportChildren(outfile, level, namespace_='', name_='protein_or_peptide', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ec_number()[source]
get_enantiomer()[source]
get_recombinant_expression()[source]
get_sequence()[source]
hasContent_()[source]
insert_ec_number_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af210>]
replace_ec_number_at(index, value)[source]
set_ec_number(ec_number)[source]
set_enantiomer(enantiomer)[source]
set_recombinant_expression(recombinant_expression)[source]
set_sequence(sequence)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_ec_numberType(value)[source]
validate_ec_numberType_patterns_ = [['^EC \\d+(\\.\\d+){3}$']]
validate_enantiomerType(value)[source]
class emdbXMLTranslator.emdb_da.radiusType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='radiusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='radiusType')[source]
exportChildren(outfile, level, namespace_='', name_='radiusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f97d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.random_conical_tiltType(number_images=None, tilt_angle=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='random_conical_tiltType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='random_conical_tiltType')[source]
exportChildren(outfile, level, namespace_='', name_='random_conical_tiltType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_number_images()[source]
get_software_list()[source]
get_tilt_angle()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f8d0>]
set_details(details)[source]
set_number_images(number_images)[source]
set_software_list(software_list)[source]
set_tilt_angle(tilt_angle)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.recombinant_source_type(database=None, organism=None, strain=None, cell=None, plasmid=None, synonym_organism=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='recombinant_source_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='recombinant_source_type')[source]
exportChildren(outfile, level, namespace_='', name_='recombinant_source_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cell()[source]
get_database()[source]
get_organism()[source]
get_plasmid()[source]
get_strain()[source]
get_synonym_organism()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a81d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a82d0>]
set_cell(cell)[source]
set_database(database)[source]
set_organism(organism)[source]
set_plasmid(plasmid)[source]
set_strain(strain)[source]
set_synonym_organism(synonym_organism)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.reconstruction_filtering_type(background_masked=None, spatial_filtering=None, sharpening=None, b_factorSharpening=None, other=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='reconstruction_filtering_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='reconstruction_filtering_type')[source]
exportChildren(outfile, level, namespace_='', name_='reconstruction_filtering_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_b_factorSharpening()[source]
get_background_masked()[source]
get_other()[source]
get_sharpening()[source]
get_spatial_filtering()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69ff10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69ff50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69ff90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69ffd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8050>]
set_b_factorSharpening(b_factorSharpening)[source]
set_background_masked(background_masked)[source]
set_other(other)[source]
set_sharpening(sharpening)[source]
set_spatial_filtering(spatial_filtering)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.reconstruction_type(number_images_used=None, number_classes_used=None, applied_symmetry=None, algorithm=None, resolution=None, resolution_method=None, reconstruction_filtering=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='reconstruction_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='reconstruction_type')[source]
exportChildren(outfile, level, namespace_='', name_='reconstruction_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_algorithm()[source]
get_applied_symmetry()[source]
get_details()[source]
get_number_classes_used()[source]
get_number_images_used()[source]
get_reconstruction_filtering()[source]
get_resolution()[source]
get_resolution_method()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674d10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674d50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674e90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674ed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674f10>]
set_algorithm(algorithm)[source]
set_applied_symmetry(applied_symmetry)[source]
set_details(details)[source]
set_number_classes_used(number_classes_used)[source]
set_number_images_used(number_images_used)[source]
set_reconstruction_filtering(reconstruction_filtering)[source]
set_resolution(resolution)[source]
set_resolution_method(resolution_method)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
validate_reconstruction_algorithm_type(value)[source]
validate_resolution_methodType(value)[source]
class emdbXMLTranslator.emdb_da.refinementType(startup_model=None, starting_symmetry=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_starting_symmetry(value)[source]
add_startup_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='refinementType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='refinementType')[source]
exportChildren(outfile, level, namespace_='', name_='refinementType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
get_starting_symmetry()[source]
get_startup_model()[source]
hasContent_()[source]
insert_starting_symmetry_at(index, value)[source]
insert_startup_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c510>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c590>]
replace_starting_symmetry_at(index, value)[source]
replace_startup_model_at(index, value)[source]
set_details(details)[source]
set_software_list(software_list)[source]
set_starting_symmetry(starting_symmetry)[source]
set_startup_model(startup_model)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.refinementType27(startup_model=None, starting_symmetry=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_starting_symmetry(value)[source]
add_startup_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='refinementType27', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='refinementType27')[source]
exportChildren(outfile, level, namespace_='', name_='refinementType27', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
get_starting_symmetry()[source]
get_startup_model()[source]
hasContent_()[source]
insert_starting_symmetry_at(index, value)[source]
insert_startup_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f250>]
replace_starting_symmetry_at(index, value)[source]
replace_startup_model_at(index, value)[source]
set_details(details)[source]
set_software_list(software_list)[source]
set_starting_symmetry(starting_symmetry)[source]
set_startup_model(startup_model)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.regexp_string(help_text=None, string=None, validation_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='regexp_string', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='regexp_string')[source]
exportChildren(outfile, level, namespace_='', name_='regexp_string', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_help_text()[source]
get_string()[source]
get_validation_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed210>]
set_help_text(help_text)[source]
set_string(string)[source]
set_validation_list(validation_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.relationshipType(in_frame=None, other=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='relationshipType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='relationshipType')[source]
exportChildren(outfile, level, namespace_='', name_='relationshipType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_in_frame()[source]
get_other()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd510>]
set_in_frame(in_frame)[source]
set_other(other)[source]
subclass = None
superclass = None
validate_in_frameType(value)[source]
class emdbXMLTranslator.emdb_da.relationshipType1(in_frame=None, other=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='relationshipType1', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='relationshipType1')[source]
exportChildren(outfile, level, namespace_='', name_='relationshipType1', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_in_frame()[source]
get_other()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd610>]
set_in_frame(in_frame)[source]
set_other(other)[source]
subclass = None
superclass = None
validate_in_frameType2(value)[source]
class emdbXMLTranslator.emdb_da.resolutionType(units=None, type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='resolutionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='resolutionType')[source]
exportChildren(outfile, level, namespace_='', name_='resolutionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
gds_format_float(input_data, input_name='')[source]
get_type()[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0e50>]
set_type(type_)[source]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.resolutionType75(units=None, type_=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='resolutionType75', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='resolutionType75')[source]
exportChildren(outfile, level, namespace_='', name_='resolutionType75', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_type()[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0aa50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0aa90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0aad0>]
set_type(type_)[source]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.resolution_rangeType(high_resolution=None, low_resolution=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='resolution_rangeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='resolution_rangeType')[source]
exportChildren(outfile, level, namespace_='', name_='resolution_rangeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_high_resolution()[source]
get_low_resolution()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7449d0>]
set_high_resolution(high_resolution)[source]
set_low_resolution(low_resolution)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.resolution_rangeType17(high_resolution=None, low_resolution=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='resolution_rangeType17', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='resolution_rangeType17')[source]
exportChildren(outfile, level, namespace_='', name_='resolution_rangeType17', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_high_resolution()[source]
get_low_resolution()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755690>]
set_high_resolution(high_resolution)[source]
set_low_resolution(low_resolution)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.results_type[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='results_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='results_type')[source]
exportChildren(outfile, level, namespace_='', name_='results_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.rna(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, sequence=None, classification=None, structure=None, synthetic_flag=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Is naturalExpression and recombinantExpression suitable for this component?

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='rna', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='rna')[source]
exportChildren(outfile, level, namespace_='', name_='rna', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_classification()[source]
get_sequence()[source]
get_structure()[source]
get_synthetic_flag()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af4d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af510>]
set_classification(classification)[source]
set_sequence(sequence)[source]
set_structure(structure)[source]
set_synthetic_flag(synthetic_flag)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_classificationType65(value)[source]
class emdbXMLTranslator.emdb_da.saccharide(mutant=None, chimera=None, id=None, name=None, natural_source=None, molecular_weight=None, details=None, number_of_copies=None, oligomeric_state=None, recombinant_exp_flag=None, enantiomer=None, formula=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_macromolecule_type

Is naturalExpression and recombinantExpression suitable for this component?

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='saccharide', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='saccharide')[source]
exportChildren(outfile, level, namespace_='', name_='saccharide', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_enantiomer()[source]
get_external_references()[source]
get_formula()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af5d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af610>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6af650>]
replace_external_references_at(index, value)[source]
set_enantiomer(enantiomer)[source]
set_external_references(external_references)[source]
set_formula(formula)[source]
subclass = None
superclass

alias of base_macromolecule_type

validate_enantiomerType66(value)[source]
validate_formulaType67(value)[source]
validate_formulaType67_patterns_ = [['^([\\[\\]\\(\\)]*[A-Z][a-z]?[\\+\\-\\d/\\[\\]\\(\\)]*)+$']]
class emdbXMLTranslator.emdb_da.sample(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None, number_unique_components=None, molecular_weight=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

Deprecated (2014-10-21)

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sample', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sample')[source]
exportChildren(outfile, level, namespace_='', name_='sample', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_molecular_weight()[source]
get_natural_source()[source]
get_number_unique_components()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15e50>]
set_molecular_weight(molecular_weight)[source]
set_natural_source(natural_source)[source]
set_number_unique_components(number_unique_components)[source]
subclass = None
superclass

alias of base_supramolecule_type

class emdbXMLTranslator.emdb_da.sample_type(name=None, supramolecule_list=None, macromolecule_list=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sample_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sample_type')[source]
exportChildren(outfile, level, namespace_='', name_='sample_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_macromolecule_list()[source]
get_name()[source]
get_supramolecule_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe53d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5410>]
set_macromolecule_list(macromolecule_list)[source]
set_name(name)[source]
set_supramolecule_list(supramolecule_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.sampling_intervalType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sampling_intervalType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sampling_intervalType')[source]
exportChildren(outfile, level, namespace_='', name_='sampling_intervalType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0390>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f03d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.sci_name_type(synonym=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Deprecated (2014/11/12)

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sci_name_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sci_name_type')[source]
exportChildren(outfile, level, namespace_='', name_='sci_name_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_synonym()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8ad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8b10>]
set_synonym(synonym)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.secondary_citationType(citation_type=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='secondary_citationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='secondary_citationType')[source]
exportChildren(outfile, level, namespace_='', name_='secondary_citationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_citation_type()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd2d0>]
set_citation_type(citation_type)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.sectioningType(ultramicrotomy=None, focused_ion_beam=None, other_sectioning=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sectioningType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sectioningType')[source]
exportChildren(outfile, level, namespace_='', name_='sectioningType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_focused_ion_beam()[source]
get_other_sectioning()[source]
get_ultramicrotomy()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de0d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de150>]
set_focused_ion_beam(focused_ion_beam)[source]
set_other_sectioning(other_sectioning)[source]
set_ultramicrotomy(ultramicrotomy)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_lengthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_lengthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_lengthType')[source]
exportChildren(outfile, level, namespace_='', name_='segment_lengthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c1d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c210>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_lengthType24(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_lengthType24', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_lengthType24')[source]
exportChildren(outfile, level, namespace_='', name_='segment_lengthType24', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755e90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_overlapType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_overlapType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_overlapType')[source]
exportChildren(outfile, level, namespace_='', name_='segment_overlapType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c2d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c310>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_overlapType25(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_overlapType25', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_overlapType25')[source]
exportChildren(outfile, level, namespace_='', name_='segment_overlapType25', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755f90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_selectionType(number_segments=None, segment_length=None, segment_overlap=None, total_filament_length=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_selectionType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_selectionType')[source]
exportChildren(outfile, level, namespace_='', name_='segment_selectionType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_number_segments()[source]
get_segment_length()[source]
get_segment_overlap()[source]
get_software_list()[source]
get_total_filament_length()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c0d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c110>]
set_details(details)[source]
set_number_segments(number_segments)[source]
set_segment_length(segment_length)[source]
set_segment_overlap(segment_overlap)[source]
set_software_list(software_list)[source]
set_total_filament_length(total_filament_length)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segment_selectionType23(number_segments=None, segment_length=None, segment_overlap=None, total_filament_length=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segment_selectionType23', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segment_selectionType23')[source]
exportChildren(outfile, level, namespace_='', name_='segment_selectionType23', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_number_segments()[source]
get_segment_length()[source]
get_segment_overlap()[source]
get_software_list()[source]
get_total_filament_length()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755c50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755cd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755d10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755d50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755d90>]
set_details(details)[source]
set_number_segments(number_segments)[source]
set_segment_length(segment_length)[source]
set_segment_overlap(segment_overlap)[source]
set_software_list(software_list)[source]
set_total_filament_length(total_filament_length)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.segmentationType(file=None, details=None, mask_details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segmentationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segmentationType')[source]
exportChildren(outfile, level, namespace_='', name_='segmentationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_file()[source]
get_mask_details()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770d50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770dd0>]
set_details(details)[source]
set_file(file)[source]
set_mask_details(mask_details)[source]
subclass = None
superclass = None
validate_fileType43(value)[source]
validate_fileType43_patterns_ = [['^emd_\\d{4,}_seg.xml$']]
class emdbXMLTranslator.emdb_da.segmentation_listType(segmentation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_segmentation(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='segmentation_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='segmentation_listType')[source]
exportChildren(outfile, level, namespace_='', name_='segmentation_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_segmentation()[source]
hasContent_()[source]
insert_segmentation_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770c50>]
replace_segmentation_at(index, value)[source]
set_segmentation(segmentation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.sequenceType(string=None, discrepancy_list=None, connectivity=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sequenceType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sequenceType')[source]
exportChildren(outfile, level, namespace_='', name_='sequenceType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_connectivity()[source]
get_discrepancy_list()[source]
get_external_references()[source]
get_string()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa018d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01950>]
replace_external_references_at(index, value)[source]
set_connectivity(connectivity)[source]
set_discrepancy_list(discrepancy_list)[source]
set_external_references(external_references)[source]
set_string(string)[source]
subclass = None
superclass = None
validate_stringType(value)[source]
validate_stringType_patterns_ = [['^[ ARNDCEQGHILKMFPSTWYVUOBZJX]+$']]
class emdbXMLTranslator.emdb_da.sequenceType55(string=None, discrepancy_list=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sequenceType55', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sequenceType55')[source]
exportChildren(outfile, level, namespace_='', name_='sequenceType55', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy_list()[source]
get_external_references()[source]
get_string()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a050>]
replace_external_references_at(index, value)[source]
set_discrepancy_list(discrepancy_list)[source]
set_external_references(external_references)[source]
set_string(string)[source]
subclass = None
superclass = None
validate_stringType56(value)[source]
validate_stringType56_patterns_ = [['^[ ACGTRYSWKMBDHVN\\.-]+$']]
class emdbXMLTranslator.emdb_da.sequenceType60(string=None, discrepancy_list=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sequenceType60', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sequenceType60')[source]
exportChildren(outfile, level, namespace_='', name_='sequenceType60', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy_list()[source]
get_external_references()[source]
get_string()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a350>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0a390>]
replace_external_references_at(index, value)[source]
set_discrepancy_list(discrepancy_list)[source]
set_external_references(external_references)[source]
set_string(string)[source]
subclass = None
superclass = None
validate_stringType61(value)[source]
validate_stringType61_patterns_ = [['^[ ACGURYSWKMBDHVN\\.-]+$']]
class emdbXMLTranslator.emdb_da.sequenceType77(string=None, discrepancy_list=None, external_references=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_external_references(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sequenceType77', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sequenceType77')[source]
exportChildren(outfile, level, namespace_='', name_='sequenceType77', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_discrepancy_list()[source]
get_external_references()[source]
get_string()[source]
hasContent_()[source]
insert_external_references_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0ab90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0abd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0ac10>]
replace_external_references_at(index, value)[source]
set_discrepancy_list(discrepancy_list)[source]
set_external_references(external_references)[source]
set_string(string)[source]
subclass = None
superclass = None
validate_stringType78(value)[source]
class emdbXMLTranslator.emdb_da.shadowingType(material=None, angle=None, thickness=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='shadowingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='shadowingType')[source]
exportChildren(outfile, level, namespace_='', name_='shadowingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angle()[source]
get_details()[source]
get_material()[source]
get_thickness()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5b50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5b90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5bd0>]
set_angle(angle)[source]
set_details(details)[source]
set_material(material)[source]
set_thickness(thickness)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.sharpeningType(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sharpeningType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sharpeningType')[source]
exportChildren(outfile, level, namespace_='', name_='sharpeningType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9f90>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.shellType(id=None, high_resolution=None, low_resolution=None, number_structure_factors=None, phase_residual=None, fourier_space_coverage=None, multiplicity=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='shellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='shellType')[source]
exportChildren(outfile, level, namespace_='', name_='shellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_fourier_space_coverage()[source]
get_high_resolution()[source]
get_id()[source]
get_low_resolution()[source]
get_multiplicity()[source]
get_number_structure_factors()[source]
get_phase_residual()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa151d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15290>]
set_fourier_space_coverage(fourier_space_coverage)[source]
set_high_resolution(high_resolution)[source]
set_id(id)[source]
set_low_resolution(low_resolution)[source]
set_multiplicity(multiplicity)[source]
set_number_structure_factors(number_structure_factors)[source]
set_phase_residual(phase_residual)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.shell_listType(shell=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_shell(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='shell_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='shell_listType')[source]
exportChildren(outfile, level, namespace_='', name_='shell_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_shell()[source]
hasContent_()[source]
insert_shell_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa0afd0>]
replace_shell_at(index, value)[source]
set_shell(shell)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.singleparticle_processing_type(id=None, image_recording_id=None, details=None, particle_selection=None, ctf_correction=None, startup_model=None, initial_angle_assignment=None, final_reconstruction=None, final_angle_assignment=None, final_multi_reference_alignment=None, final_two_d_classification=None, final_three_d_classification=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_processing_type

add_particle_selection(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='singleparticle_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='singleparticle_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='singleparticle_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ctf_correction()[source]
get_final_angle_assignment()[source]
get_final_multi_reference_alignment()[source]
get_final_reconstruction()[source]
get_final_three_d_classification()[source]
get_final_two_d_classification()[source]
get_initial_angle_assignment()[source]
get_particle_selection()[source]
get_startup_model()[source]
hasContent_()[source]
insert_particle_selection_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dc10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dc50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dc90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dcd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dd10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dd50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dd90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67ddd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67de10>]
replace_particle_selection_at(index, value)[source]
set_ctf_correction(ctf_correction)[source]
set_final_angle_assignment(final_angle_assignment)[source]
set_final_multi_reference_alignment(final_multi_reference_alignment)[source]
set_final_reconstruction(final_reconstruction)[source]
set_final_three_d_classification(final_three_d_classification)[source]
set_final_two_d_classification(final_two_d_classification)[source]
set_initial_angle_assignment(initial_angle_assignment)[source]
set_particle_selection(particle_selection)[source]
set_startup_model(startup_model)[source]
subclass = None
superclass

alias of base_processing_type

class emdbXMLTranslator.emdb_da.sitesType(deposition=None, last_processing=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sitesType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sitesType')[source]
exportChildren(outfile, level, namespace_='', name_='sitesType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_deposition()[source]
get_last_processing()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3650>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3690>]
set_deposition(deposition)[source]
set_last_processing(last_processing)[source]
subclass = None
superclass = None
validate_depositionType(value)[source]
validate_last_processingType(value)[source]
class emdbXMLTranslator.emdb_da.slices_listType(slice=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_slice(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='slices_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='slices_listType')[source]
exportChildren(outfile, level, namespace_='', name_='slices_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_slice()[source]
hasContent_()[source]
insert_slice_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770e90>]
replace_slice_at(index, value)[source]
set_slice(slice)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.soft_validation_regexpType(warning_text=None, regexp=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='soft_validation_regexpType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='soft_validation_regexpType')[source]
exportChildren(outfile, level, namespace_='', name_='soft_validation_regexpType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_regexp()[source]
get_warning_text()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5190>]
set_regexp(regexp)[source]
set_warning_text(warning_text)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.software_list_type(software=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_software(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='software_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='software_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='software_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_software()[source]
hasContent_()[source]
insert_software_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696710>]
replace_software_at(index, value)[source]
set_software(software)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.software_type(name=None, version=None, processing_details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='software_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='software_type')[source]
exportChildren(outfile, level, namespace_='', name_='software_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_name()[source]
get_processing_details()[source]
get_version()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fa50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fa90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fad0>]
set_name(name)[source]
set_processing_details(processing_details)[source]
set_version(version)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.spacingType(x=None, y=None, z=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='spacingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='spacingType')[source]
exportChildren(outfile, level, namespace_='', name_='spacingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_x()[source]
get_y()[source]
get_z()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75ff90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75ffd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767050>]
set_x(x)[source]
set_y(y)[source]
set_z(z)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.spatial_filteringType(low_frequency_cutoff=None, high_frequency_cutoff=None, filter_function=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='spatial_filteringType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='spatial_filteringType')[source]
exportChildren(outfile, level, namespace_='', name_='spatial_filteringType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_filter_function()[source]
get_high_frequency_cutoff()[source]
get_low_frequency_cutoff()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9b90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9bd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9c10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9c50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9c90>]
set_details(details)[source]
set_filter_function(filter_function)[source]
set_high_frequency_cutoff(high_frequency_cutoff)[source]
set_low_frequency_cutoff(low_frequency_cutoff)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.spatial_frequencyType(valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='spatial_frequencyType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='spatial_frequencyType')[source]
exportChildren(outfile, level, namespace_='', name_='spatial_frequencyType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f73a090>]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.specialist_optics_type(phase_plate=None, sph_aberration_corrector=None, chr_aberration_corrector=None, energy_filter=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='specialist_optics_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='specialist_optics_type')[source]
exportChildren(outfile, level, namespace_='', name_='specialist_optics_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_chr_aberration_corrector()[source]
get_energy_filter()[source]
get_phase_plate()[source]
get_sph_aberration_corrector()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5f50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5f90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5fd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed050>]
set_chr_aberration_corrector(chr_aberration_corrector)[source]
set_energy_filter(energy_filter)[source]
set_phase_plate(phase_plate)[source]
set_sph_aberration_corrector(sph_aberration_corrector)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.specimen_preparation_listType(specimen_preparation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_specimen_preparation(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='specimen_preparation_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='specimen_preparation_listType')[source]
exportChildren(outfile, level, namespace_='', name_='specimen_preparation_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_specimen_preparation()[source]
hasContent_()[source]
insert_specimen_preparation_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd6d0>]
replace_specimen_preparation_at(index, value)[source]
set_specimen_preparation(specimen_preparation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.specimen_preparationsType(specimen_preparation_id=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_specimen_preparation_id(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='specimen_preparationsType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='specimen_preparationsType')[source]
exportChildren(outfile, level, namespace_='', name_='specimen_preparationsType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_specimen_preparation_id()[source]
hasContent_()[source]
insert_specimen_preparation_id_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de690>]
replace_specimen_preparation_id_at(index, value)[source]
set_specimen_preparation_id(specimen_preparation_id)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.stain_type(ammonium_molybdate=None, uranyl_acetate=None, uranyl_formate=None, phophotungstic_acid=None, osmium_tetroxide=None, osmium_ferricyanide=None, auro_glucothionate=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='stain_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='stain_type')[source]
exportChildren(outfile, level, namespace_='', name_='stain_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ammonium_molybdate()[source]
get_auro_glucothionate()[source]
get_osmium_ferricyanide()[source]
get_osmium_tetroxide()[source]
get_phophotungstic_acid()[source]
get_uranyl_acetate()[source]
get_uranyl_formate()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe59d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5a50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5ad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5b10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5b50>]
set_ammonium_molybdate(ammonium_molybdate)[source]
set_auro_glucothionate(auro_glucothionate)[source]
set_osmium_ferricyanide(osmium_ferricyanide)[source]
set_osmium_tetroxide(osmium_tetroxide)[source]
set_phophotungstic_acid(phophotungstic_acid)[source]
set_uranyl_acetate(uranyl_acetate)[source]
set_uranyl_formate(uranyl_formate)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.stainingType(type_=None, material=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='stainingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='stainingType')[source]
exportChildren(outfile, level, namespace_='', name_='stainingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_material()[source]
get_type()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d58d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5950>]
set_details(details)[source]
set_material(material)[source]
set_type(type_)[source]
subclass = None
superclass = None
validate_typeType(value)[source]
class emdbXMLTranslator.emdb_da.starting_map_type(random_conical_tilt=None, orthogonal_tilt=None, emdb_id=None, pdb_model=None, insilico_model=None, other=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_pdb_model(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='starting_map_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='starting_map_type')[source]
exportChildren(outfile, level, namespace_='', name_='starting_map_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_emdb_id()[source]
get_insilico_model()[source]
get_orthogonal_tilt()[source]
get_other()[source]
get_pdb_model()[source]
get_random_conical_tilt()[source]
hasContent_()[source]
insert_pdb_model_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6859d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685a50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685a90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685ad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685b10>]
replace_pdb_model_at(index, value)[source]
set_details(details)[source]
set_emdb_id(emdb_id)[source]
set_insilico_model(insilico_model)[source]
set_orthogonal_tilt(orthogonal_tilt)[source]
set_other(other)[source]
set_pdb_model(pdb_model)[source]
set_random_conical_tilt(random_conical_tilt)[source]
subclass = None
superclass = None
validate_emdb_id_type(value)[source]
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
class emdbXMLTranslator.emdb_da.starting_modelType(access_code=None, chain=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_chain(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='starting_modelType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='starting_modelType')[source]
exportChildren(outfile, level, namespace_='', name_='starting_modelType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_access_code()[source]
get_chain()[source]
hasContent_()[source]
insert_chain_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f7448d0>]
replace_chain_at(index, value)[source]
set_access_code(access_code)[source]
set_chain(chain)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.starting_modelType16(access_code=None, chain=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_chain(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='starting_modelType16', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='starting_modelType16')[source]
exportChildren(outfile, level, namespace_='', name_='starting_modelType16', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_access_code()[source]
get_chain()[source]
hasContent_()[source]
insert_chain_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755590>]
replace_chain_at(index, value)[source]
set_access_code(access_code)[source]
set_chain(chain)[source]
subclass = None
superclass = None
validate_pdb_code_type(value)[source]
validate_pdb_code_type_patterns_ = [['^\\d[\\dA-Za-z]{3}$']]
class emdbXMLTranslator.emdb_da.starting_symmetryType(helical_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='starting_symmetryType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='starting_symmetryType')[source]
exportChildren(outfile, level, namespace_='', name_='starting_symmetryType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helical_parameters()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c650>]
set_helical_parameters(helical_parameters)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.starting_symmetryType28(helical_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='starting_symmetryType28', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='starting_symmetryType28')[source]
exportChildren(outfile, level, namespace_='', name_='starting_symmetryType28', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_helical_parameters()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f310>]
set_helical_parameters(helical_parameters)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.statusType(date=None, code=None, processing_site=None, annotator=None, details=None, id=None)[source]

Bases: emdbXMLTranslator.emdb_da.version_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='statusType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='statusType')[source]
exportChildren(outfile, level, namespace_='', name_='statusType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_id()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3dd0>]
set_id(id)[source]
subclass = None
superclass

alias of version_type

class emdbXMLTranslator.emdb_da.status_type(date=None, code=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='status_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='status_type')[source]
exportChildren(outfile, level, namespace_='', name_='status_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_code()[source]
get_date()[source]
get_details()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda550>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda590>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda5d0>]
set_code(code)[source]
set_date(date)[source]
set_details(details)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.string_type(help_text=None, warning_text=None, error_text=None, validation_rules=None, label=None, value=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='string_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='string_type')[source]
exportChildren(outfile, level, namespace_='', name_='string_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass

alias of base_type

class emdbXMLTranslator.emdb_da.string_validation_type(regular_expression=None, enum=None, controlled_vocabulary_link=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_enum(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='string_validation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='string_validation_type')[source]
exportChildren(outfile, level, namespace_='', name_='string_validation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_enum()[source]
get_regular_expression()[source]
hasContent_()[source]
insert_enum_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed2d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed310>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed350>]
replace_enum_at(index, value)[source]
set_enum(enum)[source]
set_regular_expression(regular_expression)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.structure_determination_listType(structure_determination=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_structure_determination(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='structure_determination_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='structure_determination_listType')[source]
exportChildren(outfile, level, namespace_='', name_='structure_determination_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_structure_determination()[source]
hasContent_()[source]
insert_structure_determination_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3450>]
replace_structure_determination_at(index, value)[source]
set_structure_determination(structure_determination)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.structure_determination_type(id=None, method=None, aggregation_state=None, macromolecules_and_complexes=None, specimen_preparation_list=None, microscopy_list=None, image_processing=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Unique identifier that will allow the DA system to be refactored in terms of experiments rather than maps. Can be autogenerated unless user wants to specify a previously existing one.

add_image_processing(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='structure_determination_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='structure_determination_type')[source]
exportChildren(outfile, level, namespace_='', name_='structure_determination_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_aggregation_state()[source]
get_id()[source]
get_image_processing()[source]
get_macromolecules_and_complexes()[source]
get_method()[source]
get_microscopy_list()[source]
get_specimen_preparation_list()[source]
hasContent_()[source]
insert_image_processing_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe51d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe5290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efe52d0>]
replace_image_processing_at(index, value)[source]
set_aggregation_state(aggregation_state)[source]
set_id(id)[source]
set_image_processing(image_processing)[source]
set_macromolecules_and_complexes(macromolecules_and_complexes)[source]
set_method(method)[source]
set_microscopy_list(microscopy_list)[source]
set_specimen_preparation_list(specimen_preparation_list)[source]
subclass = None
superclass = None
validate_aggregation_stateType(value)[source]
validate_methodType(value)[source]
class emdbXMLTranslator.emdb_da.structure_factors(file=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='structure_factors', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='structure_factors')[source]
exportChildren(outfile, level, namespace_='', name_='structure_factors', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_file()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d390>]
set_file(file)[source]
subclass = None
superclass = None
validate_fileType35(value)[source]
validate_fileType35_patterns_ = [['^emd_\\d{4,}_fsc.xml$']]
class emdbXMLTranslator.emdb_da.subtomogram_averaging_processing_type(id=None, image_recording_id=None, details=None, final_reconstruction=None, extraction=None, ctf_correction=None, final_multi_reference_alignment=None, final_three_d_classification=None, final_angle_assignment=None, crystal_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_processing_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='subtomogram_averaging_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='subtomogram_averaging_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='subtomogram_averaging_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystal_parameters()[source]
get_ctf_correction()[source]
get_extraction()[source]
get_final_angle_assignment()[source]
get_final_multi_reference_alignment()[source]
get_final_reconstruction()[source]
get_final_three_d_classification()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67ded0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67df10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67df50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67df90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f67dfd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685090>]
set_crystal_parameters(crystal_parameters)[source]
set_ctf_correction(ctf_correction)[source]
set_extraction(extraction)[source]
set_final_angle_assignment(final_angle_assignment)[source]
set_final_multi_reference_alignment(final_multi_reference_alignment)[source]
set_final_reconstruction(final_reconstruction)[source]
set_final_three_d_classification(final_three_d_classification)[source]
subclass = None
superclass

alias of base_processing_type

class emdbXMLTranslator.emdb_da.subtomogram_reconstruction_type(number_subtomograms_used=None, applied_symmetry=None, number_classes_used=None, algorithm=None, resolution=None, resolution_method=None, reconstruction_filtering=None, software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='subtomogram_reconstruction_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='subtomogram_reconstruction_type')[source]
exportChildren(outfile, level, namespace_='', name_='subtomogram_reconstruction_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_algorithm()[source]
get_applied_symmetry()[source]
get_details()[source]
get_number_classes_used()[source]
get_number_subtomograms_used()[source]
get_reconstruction_filtering()[source]
get_resolution()[source]
get_resolution_method()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba8d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6ba950>]
set_algorithm(algorithm)[source]
set_applied_symmetry(applied_symmetry)[source]
set_details(details)[source]
set_number_classes_used(number_classes_used)[source]
set_number_subtomograms_used(number_subtomograms_used)[source]
set_reconstruction_filtering(reconstruction_filtering)[source]
set_resolution(resolution)[source]
set_resolution_method(resolution_method)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
validate_reconstruction_algorithm_type(value)[source]
validate_resolution_methodType76(value)[source]
class emdbXMLTranslator.emdb_da.sugar_embeddingType(material=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='sugar_embeddingType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='sugar_embeddingType')[source]
exportChildren(outfile, level, namespace_='', name_='sugar_embeddingType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_material()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5a50>]
set_details(details)[source]
set_material(material)[source]
subclass = None
superclass = None
validate_materialType4(value)[source]
class emdbXMLTranslator.emdb_da.superseded_by_listType(entry=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_entry(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='superseded_by_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='superseded_by_listType')[source]
exportChildren(outfile, level, namespace_='', name_='superseded_by_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_entry()[source]
hasContent_()[source]
insert_entry_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3a10>]
replace_entry_at(index, value)[source]
set_entry(entry)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.supersedes_type(date=None, entry=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='supersedes_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='supersedes_type')[source]
exportChildren(outfile, level, namespace_='', name_='supersedes_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_date()[source]
get_details()[source]
get_entry()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda690>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda6d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda710>]
set_date(date)[source]
set_details(details)[source]
set_entry(entry)[source]
subclass = None
superclass = None
validate_emdb_id_type(value)[source]
validate_emdb_id_type_patterns_ = [['^EMD-\\d{4,}$']]
class emdbXMLTranslator.emdb_da.supramolecule_listType(supramolecule=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_supramolecule(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='supramolecule_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='supramolecule_listType')[source]
exportChildren(outfile, level, namespace_='', name_='supramolecule_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_supramolecule()[source]
hasContent_()[source]
insert_supramolecule_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cd8d0>]
replace_supramolecule_at(index, value)[source]
set_supramolecule(supramolecule)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.symmetry_determinationType(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='symmetry_determinationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='symmetry_determinationType')[source]
exportChildren(outfile, level, namespace_='', name_='symmetry_determinationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f744dd0>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.symmetry_determinationType21(software_list=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='symmetry_determinationType21', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='symmetry_determinationType21')[source]
exportChildren(outfile, level, namespace_='', name_='symmetry_determinationType21', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755a50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f755a90>]
set_details(details)[source]
set_software_list(software_list)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.telephone_number_type(country=None, area=None, local=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='telephone_number_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='telephone_number_type')[source]
exportChildren(outfile, level, namespace_='', name_='telephone_number_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_area()[source]
get_country()[source]
get_local()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fb90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fbd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f69fc10>]
set_area(area)[source]
set_country(country)[source]
set_local(local)[source]
subclass = None
superclass = None
validate_areaType(value)[source]
validate_areaType_patterns_ = [['^\\d{2,5}$']]
validate_countryType(value)[source]
validate_countryType_patterns_ = [['^\\d{1,3}$']]
validate_localType(value)[source]
validate_localType_patterns_ = [['^\\d+( ext. \\d+)?$']]
class emdbXMLTranslator.emdb_da.temperatureType(temperature_min=None, temperature_max=None, temperature_average=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='temperatureType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='temperatureType')[source]
exportChildren(outfile, level, namespace_='', name_='temperatureType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_temperature_average()[source]
get_temperature_max()[source]
get_temperature_min()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6dee90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6deed0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6def10>]
set_temperature_average(temperature_average)[source]
set_temperature_max(temperature_max)[source]
set_temperature_min(temperature_min)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.temperature_averageType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='temperature_averageType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='temperature_averageType')[source]
exportChildren(outfile, level, namespace_='', name_='temperature_averageType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7250>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.temperature_maxType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='temperature_maxType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='temperature_maxType')[source]
exportChildren(outfile, level, namespace_='', name_='temperature_maxType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7110>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7150>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.temperature_minType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='temperature_minType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='temperature_minType')[source]
exportChildren(outfile, level, namespace_='', name_='temperature_minType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6defd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6e7050>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.temperature_type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='temperature_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='temperature_type')[source]
exportChildren(outfile, level, namespace_='', name_='temperature_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696c90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f696cd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.theoreticalType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

kDa/nm is for helices.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='theoreticalType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='theoreticalType')[source]
exportChildren(outfile, level, namespace_='', name_='theoreticalType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa01790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa017d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.thicknessType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='thicknessType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='thicknessType')[source]
exportChildren(outfile, level, namespace_='', name_='thicknessType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5d90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5dd0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_angle1Type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_angle1Type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_angle1Type')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_angle1Type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fc50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fc90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_angle2Type(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_angle2Type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_angle2Type')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_angle2Type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fd50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75fd90>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_angleType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_angleType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_angleType')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_angleType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f9d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_angle_max[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Deprecated (2014/11/14)SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_angle_max', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_angle_max')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_angle_max', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_angle_min[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

Deprecated (2014/11/14)SHOULD NOT BE USED FOR TOMOGRAPHY - only for compatibility purposes with v1.9!! Use tomography microscopy instead. Angle is assumed in degrees

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_angle_min', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_angle_min')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_angle_min', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tilt_listType(angle=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_angle(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_listType')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_angle()[source]
hasContent_()[source]
insert_angle_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0cd0>]
replace_angle_at(index, value)[source]
set_angle(angle)[source]
subclass = None
superclass = None
validate_angleType7(value)[source]
class emdbXMLTranslator.emdb_da.tilt_series_type(axis1=None, axis2=None, axis_rotation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tilt_series_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tilt_series_type')[source]
exportChildren(outfile, level, namespace_='', name_='tilt_series_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_axis1()[source]
get_axis2()[source]
get_axis_rotation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6748d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674910>]
set_axis1(axis1)[source]
set_axis2(axis2)[source]
set_axis_rotation(axis_rotation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.timeType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='timeType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='timeType')[source]
exportChildren(outfile, level, namespace_='', name_='timeType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdad0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdb10>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.tissue(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, natural_source=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tissue', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tissue')[source]
exportChildren(outfile, level, namespace_='', name_='tissue', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_natural_source()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15c50>]
set_natural_source(natural_source)[source]
subclass = None
superclass

alias of base_supramolecule_type

class emdbXMLTranslator.emdb_da.tomography_microscopy_type(id=None, specimen_preparations=None, microscope=None, illumination_mode=None, imaging_mode=None, electron_source=None, acceleration_voltage=None, c2_aperture_diameter=None, nominal_cs=None, nominal_defocus_min=None, calibrated_defocus_min=None, nominal_defocus_max=None, calibrated_defocus_max=None, nominal_magnification=None, calibrated_magnification=None, specimen_holder_model=None, cooling_holder_cryogen=None, temperature=None, alignment_procedure=None, specialist_optics=None, software_list=None, details=None, date=None, image_recording_list=None, specimen_holder=None, tilt_angle_min=None, tilt_angle_max=None, tilt_series=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_microscopy_type

add_tilt_series(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tomography_microscopy_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tomography_microscopy_type')[source]
exportChildren(outfile, level, namespace_='', name_='tomography_microscopy_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_tilt_series()[source]
hasContent_()[source]
insert_tilt_series_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f674690>]
replace_tilt_series_at(index, value)[source]
set_tilt_series(tilt_series)[source]
subclass = None
superclass

alias of base_microscopy_type

class emdbXMLTranslator.emdb_da.tomography_preparation_type(id=None, concentration=None, buffer=None, staining=None, sugar_embedding=None, shadowing=None, grid=None, vitrification=None, details=None, fiducial_markers_list=None, high_pressure_freezing=None, embedding_material=None, cryo_protectant=None, sectioning=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_preparation_type

TODO: add limits and units.

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tomography_preparation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tomography_preparation_type')[source]
exportChildren(outfile, level, namespace_='', name_='tomography_preparation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_cryo_protectant()[source]
get_embedding_material()[source]
get_fiducial_markers_list()[source]
get_high_pressure_freezing()[source]
get_sectioning()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedc50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedc90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedcd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedd10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efedd50>]
set_cryo_protectant(cryo_protectant)[source]
set_embedding_material(embedding_material)[source]
set_fiducial_markers_list(fiducial_markers_list)[source]
set_high_pressure_freezing(high_pressure_freezing)[source]
set_sectioning(sectioning)[source]
subclass = None
superclass

alias of base_preparation_type

class emdbXMLTranslator.emdb_da.tomography_processing_type(id=None, image_recording_id=None, details=None, final_reconstruction=None, series_aligment_software_list=None, ctf_correction=None, crystal_parameters=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_processing_type

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='tomography_processing_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='tomography_processing_type')[source]
exportChildren(outfile, level, namespace_='', name_='tomography_processing_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystal_parameters()[source]
get_ctf_correction()[source]
get_final_reconstruction()[source]
get_series_aligment_software_list()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685150>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6851d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f685210>]
set_crystal_parameters(crystal_parameters)[source]
set_ctf_correction(ctf_correction)[source]
set_final_reconstruction(final_reconstruction)[source]
set_series_aligment_software_list(series_aligment_software_list)[source]
subclass = None
superclass

alias of base_processing_type

class emdbXMLTranslator.emdb_da.total_filament_lengthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='total_filament_lengthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='total_filament_lengthType')[source]
exportChildren(outfile, level, namespace_='', name_='total_filament_lengthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f74c410>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.total_filament_lengthType26(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='total_filament_lengthType26', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='total_filament_lengthType26')[source]
exportChildren(outfile, level, namespace_='', name_='total_filament_lengthType26', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f75f0d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.ultramicrotomyType(instrument=None, temperature=None, final_thickness=None, details=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ultramicrotomyType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ultramicrotomyType')[source]
exportChildren(outfile, level, namespace_='', name_='ultramicrotomyType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_details()[source]
get_final_thickness()[source]
get_instrument()[source]
get_temperature()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de210>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de250>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de290>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6de2d0>]
set_details(details)[source]
set_final_thickness(final_thickness)[source]
set_instrument(instrument)[source]
set_temperature(temperature)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.ultramicrotomy_final_thickness_type(units='nm', valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='ultramicrotomy_final_thickness_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='ultramicrotomy_final_thickness_type')[source]
exportChildren(outfile, level, namespace_='', name_='ultramicrotomy_final_thickness_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afe10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6afe50>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.unit_cell_type(a=None, b=None, c=None, c_sampling_length=None, gamma=None, alpha=None, beta=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='unit_cell_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='unit_cell_type')[source]
exportChildren(outfile, level, namespace_='', name_='unit_cell_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_a()[source]
get_alpha()[source]
get_b()[source]
get_beta()[source]
get_c()[source]
get_c_sampling_length()[source]
get_gamma()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6babd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bac10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bac50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bac90>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bacd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bad10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6bad50>]
set_a(a)[source]
set_alpha(alpha)[source]
set_b(b)[source]
set_beta(beta)[source]
set_c(c)[source]
set_c_sampling_length(c_sampling_length)[source]
set_gamma(gamma)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.upper_energy_thresholdType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='upper_energy_thresholdType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='upper_energy_thresholdType')[source]
exportChildren(outfile, level, namespace_='', name_='upper_energy_thresholdType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdf10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6cdf50>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.uranyl_acetate[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='uranyl_acetate', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='uranyl_acetate')[source]
exportChildren(outfile, level, namespace_='', name_='uranyl_acetate', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.uranyl_formate[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='uranyl_formate', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='uranyl_formate')[source]
exportChildren(outfile, level, namespace_='', name_='uranyl_formate', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.validationType(validation_type=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_validation_type(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='validationType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='validationType')[source]
exportChildren(outfile, level, namespace_='', name_='validationType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_validation_type()[source]
hasContent_()[source]
insert_validation_type_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6c3550>]
replace_validation_type_at(index, value)[source]
set_validation_type(validation_type)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.validation_listType(soft_validation_regexp=None, hard_validation_regexp=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_hard_validation_regexp(value)[source]
add_soft_validation_regexp(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='validation_listType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='validation_listType')[source]
exportChildren(outfile, level, namespace_='', name_='validation_listType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_hard_validation_regexp()[source]
get_soft_validation_regexp()[source]
hasContent_()[source]
insert_hard_validation_regexp_at(index, value)[source]
insert_soft_validation_regexp_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5050>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6d5090>]
replace_hard_validation_regexp_at(index, value)[source]
replace_soft_validation_regexp_at(index, value)[source]
set_hard_validation_regexp(hard_validation_regexp)[source]
set_soft_validation_regexp(soft_validation_regexp)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.validation_type(fsc_curve=None, crystallography_validation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='validation_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='validation_type')[source]
exportChildren(outfile, level, namespace_='', name_='validation_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_crystallography_validation()[source]
get_fsc_curve()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d090>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f68d0d0>]
set_crystallography_validation(crystallography_validation)[source]
set_fsc_curve(fsc_curve)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.version_list_type(status=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

add_status(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='version_list_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='version_list_type')[source]
exportChildren(outfile, level, namespace_='', name_='version_list_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_status()[source]
hasContent_()[source]
insert_status_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda310>]
replace_status_at(index, value)[source]
set_status(status)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.version_type(date=None, code=None, processing_site=None, annotator=None, details=None, extensiontype_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='version_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='version_type')[source]
exportChildren(outfile, level, namespace_='', name_='version_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_annotator()[source]
get_code()[source]
get_date()[source]
get_details()[source]
get_extensiontype_()[source]
get_processing_site()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda3d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda410>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda450>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda490>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efda4d0>]
set_annotator(annotator)[source]
set_code(code)[source]
set_date(date)[source]
set_details(details)[source]
set_extensiontype_(extensiontype_)[source]
set_processing_site(processing_site)[source]
subclass = None
superclass = None
validate_dateType(value)[source]
validate_processing_siteType(value)[source]
class emdbXMLTranslator.emdb_da.virus(id=None, name=None, category=None, parent=None, macromolecule_list=None, details=None, number_of_copies=None, oligomeric_state=None, external_references=None, recombinant_exp_flag=None, sci_species_name=None, sci_species_strain=None, natural_host=None, host_system=None, molecular_weight=None, virus_shell=None, virus_type=None, virus_isolate=None, virus_enveloped=None, virus_empty=None, syn_species_name=None, sci_species_serotype=None, sci_species_serocomplex=None, sci_species_subspecies=None)[source]

Bases: emdbXMLTranslator.emdb_da.base_supramolecule_type

add_natural_host(value)[source]
add_virus_shell(value)[source]
build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='virus', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='virus')[source]
exportChildren(outfile, level, namespace_='', name_='virus', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_host_system()[source]
get_molecular_weight()[source]
get_natural_host()[source]
get_sci_species_name()[source]
get_sci_species_serocomplex()[source]
get_sci_species_serotype()[source]
get_sci_species_strain()[source]
get_sci_species_subspecies()[source]
get_syn_species_name()[source]
get_virus_empty()[source]
get_virus_enveloped()[source]
get_virus_isolate()[source]
get_virus_shell()[source]
get_virus_type()[source]
hasContent_()[source]
insert_natural_host_at(index, value)[source]
insert_virus_shell_at(index, value)[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15710>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa157d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa158d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15910>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15950>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15990>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa159d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15a10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10fa15a50>]
replace_natural_host_at(index, value)[source]
replace_virus_shell_at(index, value)[source]
set_host_system(host_system)[source]
set_molecular_weight(molecular_weight)[source]
set_natural_host(natural_host)[source]
set_sci_species_name(sci_species_name)[source]
set_sci_species_serocomplex(sci_species_serocomplex)[source]
set_sci_species_serotype(sci_species_serotype)[source]
set_sci_species_strain(sci_species_strain)[source]
set_sci_species_subspecies(sci_species_subspecies)[source]
set_syn_species_name(syn_species_name)[source]
set_virus_empty(virus_empty)[source]
set_virus_enveloped(virus_enveloped)[source]
set_virus_isolate(virus_isolate)[source]
set_virus_shell(virus_shell)[source]
set_virus_type(virus_type)[source]
subclass = None
superclass

alias of base_supramolecule_type

validate_virus_isolateType(value)[source]
validate_virus_typeType(value)[source]
class emdbXMLTranslator.emdb_da.virus_shellType(id=None, name=None, diameter=None, triangulation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='virus_shellType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='virus_shellType')[source]
exportChildren(outfile, level, namespace_='', name_='virus_shellType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_diameter()[source]
get_id()[source]
get_name()[source]
get_triangulation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767dd0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767e10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767e50>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f767e90>]
set_diameter(diameter)[source]
set_id(id)[source]
set_name(name)[source]
set_triangulation(triangulation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.virus_shellType41(name=None, diameter=None, triangulation=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='virus_shellType41', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='virus_shellType41')[source]
exportChildren(outfile, level, namespace_='', name_='virus_shellType41', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_diameter()[source]
get_name()[source]
get_triangulation()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f770890>]
set_diameter(diameter)[source]
set_name(name)[source]
set_triangulation(triangulation)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.virus_species_name_type(ncbi=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='virus_species_name_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='virus_species_name_type')[source]
exportChildren(outfile, level, namespace_='', name_='virus_species_name_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_ncbi()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8d10>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6a8d50>]
set_ncbi(ncbi)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.vitrification_type(cryogen_name=None, chamber_humidity=None, chamber_temperature=None, instrument=None, details=None, timed_resolved_state=None, method=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='vitrification_type', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='vitrification_type')[source]
exportChildren(outfile, level, namespace_='', name_='vitrification_type', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_chamber_humidity()[source]
get_chamber_temperature()[source]
get_cryogen_name()[source]
get_details()[source]
get_instrument()[source]
get_method()[source]
get_timed_resolved_state()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed750>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed790>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed7d0>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed810>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed850>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10efed8d0>]
set_chamber_humidity(chamber_humidity)[source]
set_chamber_temperature(chamber_temperature)[source]
set_cryogen_name(cryogen_name)[source]
set_details(details)[source]
set_instrument(instrument)[source]
set_method(method)[source]
set_timed_resolved_state(timed_resolved_state)[source]
subclass = None
superclass = None
validate_cryogen_nameType(value)[source]
validate_instrumentType(value)[source]
class emdbXMLTranslator.emdb_da.weighted_phase_residual[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='weighted_phase_residual', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='weighted_phase_residual')[source]
exportChildren(outfile, level, namespace_='', name_='weighted_phase_residual', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.weighted_r_factor[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='weighted_r_factor', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='weighted_r_factor')[source]
exportChildren(outfile, level, namespace_='', name_='weighted_r_factor', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.white_gaussian[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='white_gaussian', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='white_gaussian')[source]
exportChildren(outfile, level, namespace_='', name_='white_gaussian', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.widthType(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='widthType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='widthType')[source]
exportChildren(outfile, level, namespace_='', name_='widthType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f0190>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f6f01d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.widthType50(units=None, valueOf_=None)[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='widthType50', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='widthType50')[source]
exportChildren(outfile, level, namespace_='', name_='widthType50', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
get_units()[source]
get_valueOf_()[source]
hasContent_()[source]
member_data_items_ = [<emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f9890>, <emdbXMLTranslator.emdb_da.MemberSpec_ object at 0x10f9f98d0>]
set_units(units)[source]
set_valueOf_(valueOf_)[source]
subclass = None
superclass = None
class emdbXMLTranslator.emdb_da.zemlin_tableauType[source]

Bases: emdbXMLTranslator.emdb_da.GeneratedsSuper

build(node)[source]
buildAttributes(node, attrs, already_processed)[source]
buildChildren(child_, node, nodeName_, fromsubclass_=False)[source]
export(outfile, level, namespace_='', name_='zemlin_tableauType', namespacedef_='', pretty_print=True)[source]
exportAttributes(outfile, level, already_processed, namespace_='', name_='zemlin_tableauType')[source]
exportChildren(outfile, level, namespace_='', name_='zemlin_tableauType', fromsubclass_=False, pretty_print=True)[source]
static factory(*args_, **kwargs_)[source]
hasContent_()[source]
member_data_items_ = []
subclass = None
superclass = None

emdbXMLTranslator.emdb_settings module

emdb_settings.py

Global settings for project wrapped as a class to confine namespace

TODO:

Version history:

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

class emdbXMLTranslator.emdb_settings.emdb_settings[source]
archiveHeaderTemplate = '/data/emstaging/EMD-*/header/emd-*.xml'
diffDir = '/data/emdb_diff'
emdb19To19Dir = '/data/emdb19_to_19'
emdb20Dir = '/data/emdb20'
emdb20To19Dir = '/data/emdb20_to_19'
header20Template = '/data/emdb20/emd-*.xml'
log_format = '%(asctime)s [%(levelname)s] %(name)s: %(message)s'
log_level = 20

emdbXMLTranslator.emdb_user_methods module

class emdbXMLTranslator.emdb_user_methods.MethodSpec(name='', source='', class_names='', class_names_compiled=None)[source]

Bases: object

get_class_names()[source]
get_class_names_compiled()[source]
get_interpolated_source(values_dict)[source]

Get the method source code, interpolating values from values_dict into it. The source returned by this method is inserted into the generated class.

get_name()[source]
get_source()[source]
match_name(class_name)[source]

Match against the name of the class currently being generated. If this method returns True, the method will be inserted in

the generated class.
set_class_names(class_names)[source]
set_class_names_compiled(class_names_compiled)[source]
set_name(name)[source]
set_source(source)[source]
show()[source]
emdbXMLTranslator.emdb_user_methods.main()[source]
emdbXMLTranslator.emdb_user_methods.test()[source]

emdbXMLTranslator.emdb_xml_translate module

emdb_xml_translate.py

Convert EMDB XML files from one schema version to another.

TODO:

Version history: 0.1, 2014-09-23, Ardan Patwardhan: Only conversion between v1.9 and v2.0 is supported 0.2, 2015-11-06, Ardan Patwardhan: 1) Uses regenerated emdb_da.py and emdb_19.py

  1. 2.0 -> 1.9: Refactored and simplified supplement section, fitting section that were giving errors
  2. 2.0 -> 1.9: image_recording is now a list
  3. 2.0 -> 1.9: processing_site is now handled correctly
  4. Refactored code to a class structure, and introduced Constants class
  5. Fixed code for tomography microscopy tilt
  6. 2.0 -> 1.9: helical reconstructions will always be transferred as single particle to avoid loss of data
  7. 2.0 -> 1.9: code for alignment has been commented out - the schema needs to support astigmatism and electron beam tilt for backward compatibility
  8. 2.0 -> 1.9: Sample component ID - this is now a simple counter to avoid issues with identical IDs for supramolecule and macromolecule components
  9. 2.0 -> 1.9: Assume full overlap for related EMDB entries if no relationship is speficied
0.3, 2015-11-11, Ardan Patwardhan: 1) 1.9 -> 2.0: Updated image recording section to handle list
  1. Error with slices fixed (tested on emd-1011.xml)
  2. 1.9 -> 2.0: alignment code commented out - support needs to be added to 2.0 schema
  3. 1.9 -> 2.0: updated handling of helical parameters (tested on emd-1052.xml)
  4. 1.9 -> 2.0: updated set_two_d_crystal_parameters to set_crystal_parameters
  5. 1.9 -> 2.0: nucleic acid DNA/RNA is now transferred as other_macromolecule. Support needs to be added to other_macromolecule for structure, synthetic_flag. Example: emd-1128.xml
  6. 1.9 -> 2.0: improved handling of cases where there are multiple imaging and image acquisition elements (example: emd-1534.xml)
  7. Use extension types for microscopy and defined constants for using them
  8. 2.0 -> 1.9: Num sample components - handles situations where sample component is or is not defined
0.4, 2015-11-12, Ardan Patwardhan: 1) 2.0 -> 1.9: overallBValue is float - fixed
  1. 1.9 <-> 2.0: improved handling of cases with multiple detectors and microscopes (emd-2845.xml)
  2. 1.9 and 2.0 have different formats for EMDB accession code - this is now handled correctly
0.5, 2015-11-26, Ardan Patwardhan 1) re-enabled support for astigmatism and beam tilt following schema changes
  1. added support for DNA/RNA hybrid macromolecules
  2. 2.0: capitalized some enumerations to conform to new schema, cleaned up other enumerations
  3. added support for external references for supramolecules
  4. 1.9 <-> 2.0: fixed support for eulerAngleDetails (from 1.9)
  5. 1.9 <-> 2.0: added support for legacy item replaceExistingEntry (from 1.9; e.g., emd-1010.xml
  6. 2.0 -> 1.9: reinstated support for helical reconstructions that was commented out in v0.2
  7. 2.0 -> 1.9: fixed translation to crystalGrowDetails
  8. 2.0 -> 1.9: fixed bug with reconstruction>algorithm - ‘helical:’ is no longer written out
  9. Figuresets and masksets will now only be written out of they have content
  10. 1.9 -> 2.0: if the ncbi for strain is not specified it will now be ignored (previously it because UNKNOWN by default)
  11. 1.9 -> 2.0: best effort is made to map PDB chains in cases where no PDB code has been specified.
  12. Num sample components is now propagated back and forth without taking into account the actual number
  13. 1.9 <-> 2.0: implemented support for 3D crystal symmetry and added crystal parameters and crystal symmetry support to tomogram, subtomogram and helical categories
  14. 1.9 <-> 2.0: added support for helical symmetry to all methods
  15. 1.9 <-> 2.0: improved handling of eulerAngleDetails
  16. Support added for the following but commented out for now: When converting from 2.0 -> 1.9, the PDB ID is prefixed to Chain ID (for chains) because the relationships are decoupled in v1.9
  17. Fixed issues with transfer of number of class averages, updated EMDB DA schema so that 2D and 3D classification use same type
0.6, 2015-12-14, Ardan Patwardhan 1) updated schema and updated emdb_da.py; changes match 0.9 of cifEMDBTranslator
  1. changes helical and singleParticle tags for reconstruction to avoid dangling text in reconstruction when going 2.0->1.9
  2. 2.0 -> 1.9: fitting PDBs - reverted to outputting chains as PDBID_CHAINID to make them unique
  3. 1.9 <-> 2.0: transfer supersededByList
  4. 1.9 <-> 2.0: use version history to store the 1.9 status @prior attribute info
  5. 0 contour levels were not being written out because of a generateDS bug - this has been fixed in generateDS
  6. 2.0 -> 1.0: ctf correction info was only being written out for the first reconstruction - this has now been corrected

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

class emdbXMLTranslator.emdb_xml_translate.EMDBXMLTranslator[source]

Class for translating EMDB files 2.0 <-> 1.9

class Constants[source]

There are many constants in use for the translation. They have been collected here for ease of use.

EMDB_DUMMY_CODE = 'EMD-0000'
EMDB_PAT = <_sre.SRE_Pattern object at 0x117c3b6c0>
EMDB_PREFIX = 'EMD-'
EMM_EC = 'electronCrystallography'
EMM_HEL = 'helical'
EMM_SP = 'singleParticle'
EMM_STOM = 'subtomogramAveraging'
EMM_TOM = 'tomography'
EM_DATE_FORMAT = '%d-%b-%Y'
EM_SAMPLE_ID = 1000
EM_UNIDENTIFIED_TAXID = 32644
EUL_ANG_END_TAG = '{/eulerAngleDetails}'
EUL_ANG_PAT = <_sre.SRE_Pattern object at 0x7f9e40c11b10>
EUL_ANG_START_TAG = '{eulerAngleDetails}'
EXT_BASE_MICROSCOPY_TYPE = 'base_microscopy_type'
EXT_BASE_PREPARATION_TYPE = 'base_preparation_type'
EXT_CRYSTALLOGRAPHY_MICROSCOPY_TYPE = 'crystallography_microscopy_type'
EXT_CRYSTALLOGRAPHY_PREPARATION_TYPE = 'crystallography_preparation_type'
EXT_TOMOGRAPHY_MICROSCOPY_TYPE = 'tomography_microscopy_type'
EXT_TOMOGRAPHY_PREPARATION_TYPE = 'tomography_preparation_type'
HEL_SP_PAT = <_sre.SRE_Pattern object at 0x7f9e459cda90>
HEL_TAG = '{helical/}'
PDB_CHAIN_PAT = <_sre.SRE_Pattern object at 0x7f9e459cb260>
SP_TAG = '{singleParticle/}'
STS_HOLD1 = 'HOLD1'
STS_HPUB = 'HPUB'
STS_OBS = 'OBS'
STS_REL = 'REL'
U_ANG = u'\u212b'
U_ANGA = 'A'
U_DEG = 'deg'
U_DEGF = 'degrees'
U_EL_A2 = 'e/A**2'
U_FIB_DOSE_RATE = 'ions/nm^2/s'
U_KDA_NM = 'kDa/nm'
U_KEL = 'K'
U_KVOLT = 'kV'
U_MCRN = 'microns'
U_MDA = 'MDa'
U_MG_ML = 'mg/mL'
U_MM = 'mm'
U_NM = 'nm'
U_PAMP = 'pA'
U_SEC = 's'
EMDBXMLTranslator.checkSet(getX, setX, transform=None)[source]

Call setX only if getX does not return None

Parameters: @param getX: getter function that must return value @param setX: setter function @param transform: Apply transform(x) before calling setter function

EMDBXMLTranslator.formatEMDBCode(codeIn, numberOnly=False)[source]

Format code so that it is either in the form EMD-XXXX or just XXXX

Parameters: @param codeIn: string representing EMDB code in some legal format, e.g. emd-xxxx, EMD-xxxx or xxxx @param numberOnly: Boolean if true - return only xxxx otherwise return EMD-xxxx @return: EMDB accession code in specified format

EMDBXMLTranslator.setValueAndUnits(getter, setter, constructor, units=None, transform=None)[source]

There are several elements that take a value and have an units attribute. This function makes it easier to copy over these elements

Parameters: @param getter: Getter function to get (value,units) @param setter: Setter function to set (value,units) @param constructor: Constructor for object that takes (units, valueOf_) as params @param units: If this is not None then set units based on this otherwise transfer value @param transform: Apply transform(x) before calling setter function

EMDBXMLTranslator.setWarningLevel(level)[source]

Set the level of logging warnings. 0 = no warnings, 3 = max warnings, 1 = default

Parameters @param level: warning level 0 -> 3

EMDBXMLTranslator.translate_1_9_to_1_9(inputFile, outputFile)[source]

Convert input file from 1.9 to 1.9 schema. This gets tags into the same ordering as other >1.9 converters.

Parameters: @param inputFile: Name of input file @param outputFile: Name of output file

EMDBXMLTranslator.translate_1_9_to_2_0(inputFile, outputFile)[source]

Convert input file from 1.9 to 2.0 schema

Parameters: @param inputFile: Name of input file @param outputFile: Name of output file

EMDBXMLTranslator.translate_2_0_to_1_9(inputFile, outputFile)[source]

Convert input file from 2.0 to 1.9 schema

Parameters: @param inputFile: Name of input file @param outputFile: Name of output file

EMDBXMLTranslator.warn(level, msg)[source]

Log a warning message but take into account the warningLevel

Parameters: @param level: only messages with level >= warningLevel are printed @param msg: warning message

emdbXMLTranslator.emdb_xml_translate.main()[source]

Convert EMDB XML files from one schema version to another

emdbXMLTranslator.process_all_19_19 module

process_all_19_19.py

Wrapper script for emdb_xml_translate.py for converting v 1.9 files in EMDB to v1.9. The only reason for doing this is that it puts elements in a canonical order that makes comparison with 1.9 -> 2.0 -> 1.9 translation easier.

TODO:

Version history: 0.2, 2015-11-12, Ardan Patwardhan: Minor changes associated with moving file to new project structure 0.3, 2015-11-18, Ardan Patwardhan: Adding mechanism to exclude empty tags which should make comparison easier

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

emdbXMLTranslator.process_all_19_19.main()[source]

Convert all EMDB XML 1.9 header files to canonical XML 1.9 files. This makes comparison with output from round-trip conversion (1.9 -> 2.0 -> 1.9) easier.

emdbXMLTranslator.process_all_19_19.process_all_19_19(filePathTemplate, outDir)[source]

Take a v1.9 file and read and write it using emdb_xml_translate.py to put it in a canonical form. Some post processing is also done to remove empty tags etc

Parameters: @param filePathTemplate: Regular expression that is passed to a glob function to extract a list of input files @param outDir: The canonical files will be written to this directory

emdbXMLTranslator.process_all_19_20 module

process_all_19_20.py

Wrapper script for emdb_xml_translate.py for converting v 1.9 files in EMDB to v2.0.

TODO:

Version history:

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

emdbXMLTranslator.process_all_19_20.main()[source]

Convert all EMDB XML 1.9 header files to XML 2.0 files

emdbXMLTranslator.process_all_19_20.process_all_19_20(filePathTemplate, outDir)[source]

emdbXMLTranslator.process_all_20_19 module

process_all_20_19.py

Wrapper script for emdb_xml_translate.py for converting v 2.0 files in EMDB to v1.9.

TODO:

Version history:

Copyright [2014-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

emdbXMLTranslator.process_all_20_19.main()[source]

Convert all EMDB XML 2.0 header files to XML 1.9 files

emdbXMLTranslator.process_all_20_19.process_all_20_19(filePathTemplate, outDir)[source]

emdbXMLTranslator.translator_test module

unittest.py

Test that the translator is working

TODO: 1) Should discover files in data/cif

Version history: 0.1, 2015-11-11, Ardan Patwardhan: Define tests for 1.9 > 2.0 and 2.0 > 1.9 0.2, 2016-01-06, Ardan Patwardhan: Added tests for emdb_[19|20]_to_json.py

Copyright [2015-2016] EMBL - European Bioinformatics Institute Licensed under the Apache License, Version 2.0 (the “License”); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an “AS IS” BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

class emdbXMLTranslator.translator_test.TestTranslator(methodName='runTest')[source]

Bases: unittest.case.TestCase

Run the translator on a bunch of example files

inputXML19Dir = 'data/input/v1.9'
inputXML20Dir = 'data/input/v2.0'
outputJSON19Dir = 'data/output/json/v1.9'
outputJSON20Dir = 'data/output/json/v2.0'
outputXML19Dir = 'data/output/v1.9'
outputXML20Dir = 'data/output/v2.0'
roundtrip19Dir = 'data/output/roundtrip_v1.9'
setUp()[source]
test_19_to_20()[source]

Test conversion of files in the data/input/v1.9 directory from v1.9 to v2.0, and then back to v1.9

test_19_to_json()[source]

Test conversion of files in data/input/v1.9 directory to jsons in data/output/v2.0

test_20_to_19()[source]

Test conversion of files in the data/input/v2.0 directory from v2.0 to v1.9

test_20_to_json()[source]

Test conversion of files in data/input/v2.0 directory to jsons in data/output/v1.9

Module contents