Index

A

altTorsion() (in module Vector) anglar_sweep() (EnsembleGeneration.EnsembleGeneration method) arg() (Vector.Vector method)

axis_angle_to_euler() (in module Vector) axis_angle_to_matrix() (in module Vector)

B

BioPy_Residue (class in ProtRep_Biopy) BioPy_Structure (class in ProtRep_Biopy) BioPyAtom (class in ProtRep_Biopy) box_size() (EMMap.Map method)

break_into_segments() (ProtRep_Biopy.BioPy_Structure method) build_C_symmetric_model() (ProtRep_Biopy.BioPy_Structure method) build_C_symmetric_model_around_line() (ProtRep_Biopy.BioPy_Structure method) build_C_symmetric_model_using_map() (ProtRep_Biopy.BioPy_Structure method)

C

calculate_centre_of_mass() (ProtRep_Biopy.BioPy_Structure method) CCF() (ScoringFunctions.ScoringFunctions method) centre() (EMMap.Map method) chamfer_distance() (ScoringFunctions.ScoringFunctions method) change_init_position() (ProtRep_Biopy.BioPy_Structure method) (ProtRep_Biopy.BioPyAtom method) change_origin() (EMMap.Map method)

circular_sweep_with_fixed_spin() (EnsembleGeneration.EnsembleGeneration method) circular_sweep_with_tangential_spin() (EnsembleGeneration.EnsembleGeneration method) combine_SSE_structures() (ProtRep_Biopy.BioPy_Structure method) combine_structures() (ProtRep_Biopy.BioPy_Structure method) copy() (EMMap.Map method) (ProtRep_Biopy.BioPyAtom method) (ProtRep_Biopy.BioPy_Structure method) (Vector.Vector method) cross() (Vector.Vector method)

D

dist() (ProtRep_Biopy.BioPyAtom method) (Vector.Vector method) distance_from_init_position() (ProtRep_Biopy.BioPyAtom method)

dot() (Vector.Vector method)

E

EMMap (module) EnsembleGeneration (class in EnsembleGeneration) (module)

envelope_score() (ScoringFunctions.ScoringFunctions method) euler_to_matrix() (in module Vector)

F

fetch_mmCIF() (PDBParser.mmCIFParser static method) fetch_PDB() (PDBParser.PDBParser static method) find_same_atom() (ProtRep_Biopy.BioPy_Structure method)

fourier_filter() (EMMap.Map method) fourier_transform() (EMMap.Map method)

G

gaussian_blur() (StructureBlurrer.StructureBlurrer method) gaussian_blur_box() (StructureBlurrer.StructureBlurrer method) get_atom() (ProtRep_Biopy.BioPy_Structure method) get_atom_list() (ProtRep_Biopy.BioPy_Structure method) get_backbone() (ProtRep_Biopy.BioPy_Structure method) get_chain() (ProtRep_Biopy.BioPy_Structure method) get_chain_list() (ProtRep_Biopy.BioPy_Structure method) get_com() (EMMap.Map method) get_endian() (MapParser.MapParser static method) get_extreme_values() (ProtRep_Biopy.BioPy_Structure method) get_id_no() (ProtRep_Biopy.BioPyAtom method) get_line_between_points() (EMMap.Map method) get_mass() (ProtRep_Biopy.BioPyAtom method) get_max_threshold() (EMMap.Map method) get_min_threshold() (EMMap.Map method) get_name() (ProtRep_Biopy.BioPyAtom method) get_normal_vector() (EMMap.Map method) get_partial_DLSF() (ScoringFunctions.ScoringFunctions method) get_pos() (EMMap.Map method) get_pos_mass() (ProtRep_Biopy.BioPyAtom method)

get_pos_mass_list() (ProtRep_Biopy.BioPy_Structure method) get_pos_vector() (ProtRep_Biopy.BioPyAtom method) get_prot_mass_from_atoms() (ProtRep_Biopy.BioPy_Structure method) get_prot_mass_from_res() (ProtRep_Biopy.BioPy_Structure method) get_RB() (ProtRep_Biopy.BioPy_Structure method) get_res() (ProtRep_Biopy.BioPyAtom method) get_res_no() (ProtRep_Biopy.BioPyAtom method) get_residue() (ProtRep_Biopy.BioPy_Structure method) get_selection() (ProtRep_Biopy.BioPy_Structure method) get_selection_less_than() (ProtRep_Biopy.BioPy_Structure method) get_selection_more_than() (ProtRep_Biopy.BioPy_Structure method) get_significant_points() (EMMap.Map method) get_torsion_angles() (ProtRep_Biopy.BioPy_Structure method) get_vector_list() (ProtRep_Biopy.BioPy_Structure method) get_vectors() (EMMap.Map method) get_x() (ProtRep_Biopy.BioPyAtom method) get_y() (ProtRep_Biopy.BioPyAtom method) get_z() (ProtRep_Biopy.BioPyAtom method) getMap() (EMMap.Map method)

H

header_to_binary() (EMMap.Map method)

L

laplace_CCF() (ScoringFunctions.ScoringFunctions method) laplace_filtered() (EMMap.Map method)

LSF() (ScoringFunctions.ScoringFunctions method)

M

make_atom_overlay_map() (StructureBlurrer.StructureBlurrer method) make_atom_overlay_map1() (StructureBlurrer.StructureBlurrer method) make_bin_map() (EMMap.Map method) make_clash_map() (EMMap.Map method) makeKDTree() (EMMap.Map method) Map (class in EMMap) map_grid_position() (ProtRep_Biopy.BioPyAtom method) map_randomise_position() (EMMap.Map method) map_rotate_by_axis_angle() (EMMap.Map method) map_size() (EMMap.Map method) mapComparison() (ScoringFunctions.ScoringFunctions method)

mapGridPosition() (StructureBlurrer.StructureBlurrer method) MapParser (class in MapParser) (module) matrix_transform() (EMMap.Map method) (ProtRep_Biopy.BioPyAtom method) (ProtRep_Biopy.BioPy_Structure method) (Vector.Vector method) max() (EMMap.Map method) mean() (EMMap.Map method) median() (EMMap.Map method) MI() (ScoringFunctions.ScoringFunctions method) min() (EMMap.Map method) mmCIFParser (class in PDBParser) mod() (Vector.Vector method)

N

no_of_chains() (ProtRep_Biopy.BioPy_Structure method) normal_vector_score() (ScoringFunctions.ScoringFunctions method)

normalise() (EMMap.Map method)

O

origin_change_maps() (EMMap.Map method)

P

PDBParser (class in PDBParser) (module) pixel_centre() (EMMap.Map method) protMap() (StructureBlurrer.StructureBlurrer method)

protMapBox() (EMMap.Map method) ProtRep_Biopy (module)

R

random_vector() (in module Vector) randomise_position() (EMMap.Map method) (ProtRep_Biopy.BioPy_Structure method) randomise_structs() (EnsembleGeneration.EnsembleGeneration method) read_mmCIF_file() (PDBParser.mmCIFParser static method) read_PDB_file() (PDBParser.PDBParser static method) readMRC() (MapParser.MapParser static method) readMRCHeader() (MapParser.MapParser static method) readSitus() (MapParser.MapParser static method) readXPLOR() (MapParser.MapParser static method) rename_chains() (ProtRep_Biopy.BioPy_Structure method) renumber_atoms() (ProtRep_Biopy.BioPy_Structure method) renumber_residues() (ProtRep_Biopy.BioPy_Structure method)

reorder_residues() (ProtRep_Biopy.BioPy_Structure method) represent_normal_vectors() (EMMap.Map method) resample_by_apix() (EMMap.Map method) resample_by_box_size() (EMMap.Map method) reset_position() (ProtRep_Biopy.BioPy_Structure method) (ProtRep_Biopy.BioPyAtom method) resize_map() (EMMap.Map method) reverse() (Vector.Vector method) RMSD_from_init_position() (ProtRep_Biopy.BioPy_Structure method) RMSD_from_same_structure() (ProtRep_Biopy.BioPy_Structure method) rotate_by_axis_angle() (EMMap.Map method) (ProtRep_Biopy.BioPy_Structure method) rotate_by_euler() (EMMap.Map method) (ProtRep_Biopy.BioPy_Structure method) rotate_by_matrix() (EMMap.Map method)

S

scale_map() (EMMap.Map method) SCCC() (ScoringFunctions.ScoringFunctions method) ScoringFunctions (class in ScoringFunctions) (module) set_x() (ProtRep_Biopy.BioPyAtom method) set_y() (ProtRep_Biopy.BioPyAtom method) set_z() (ProtRep_Biopy.BioPyAtom method)

shift_origin() (EMMap.Map method) spiral_sweep() (EnsembleGeneration.EnsembleGeneration method) split_into_chains() (ProtRep_Biopy.BioPy_Structure method) std() (EMMap.Map method) StructureBlurrer (class in StructureBlurrer) (module)

T

threshold_map() (EMMap.Map method) times() (Vector.Vector method) to_atom() (Vector.Vector method)

torsion() (in module Vector) TransformParser (class in TransformParser) (module) translate() (EMMap.Map method) (ProtRep_Biopy.BioPyAtom method) (ProtRep_Biopy.BioPy_Structure method) (Vector.Vector method)

U

unit() (Vector.Vector method)

update_header() (EMMap.Map method)

V

Vector (class in Vector) (module) vectorise() (ProtRep_Biopy.BioPy_Structure method)

vectorise_point() (EMMap.Map method)

W

write_to_MRC_file() (EMMap.Map method) write_to_PDB() (ProtRep_Biopy.BioPy_Structure method) (ProtRep_Biopy.BioPyAtom method)

writeTerm() (ProtRep_Biopy.BioPyAtom method)

X

x_origin() (EMMap.Map method)

x_size() (EMMap.Map method)

Y

y_origin() (EMMap.Map method)

y_size() (EMMap.Map method)

Z

z_origin() (EMMap.Map method)

z_size() (EMMap.Map method)