Source code for PDBParser

## TEMPY is a Python library designed to help the user manipulate and analyse atomic structures and density maps from 3D EM. 
## Copyright (c) 2013 Daven Vasishtan,Irene Farabella, Arun Prasad Pandurangan, Harpal Sahota, Frank Alber and Maya Topf

#from ProtRep import *
# to use biopy and the possibility to use it with TEMPY
from ProtRep_Biopy import *
# to use normal
#from ProtRep_ire3 import *



class PDBParser:
    """A class to read PDB files either directly from the pdb or a structure instance from Biopython"""
    def __init__(self):
        pass

    @staticmethod
    def read_PDB_file(filename, hetatm=False, surface = False):
        """
        Read PDB file and create Structure instance based upon it.
           
        Argument:
        
            *filename*
                name of pdb file
            *hetatm*
                Boolean representing whether the PDB file contains hetatom.
            *surface*
                Boolean representing whether the PDB file contains surface accessibility data.
           """
        #need to fix hetatm and water here
        atomList = []
        footer = ''
        header = ''
        switch = False
        f = open(filename, 'r')
        for line in f.readlines():
            info = line.split()
            if info:
                if(info[0] == 'ATOM'):
                    switch = True
                    atomList.append(Atom(line, surface=surface))
                elif info[0] == 'TER' and len(atomList)!= 0:
                    atomList[-1].isTerm = True
                elif info[0][:6] == 'HETATM' and hetatm:
                    atomList.append(Atom(line, surface=surface))
                else:
                    if(switch):
                        footer += line
                    else:
                        header += line
        f.close()
        return Structure(atomList, filename=filename, header=header, footer=footer, surface=surface)

    @staticmethod
    def fetch_PDB(id, output_file):
        url = 'http://www.rcsb.org/pdb/files/%s.pdb' % id
        a = urllib.urlretrieve(url, output_file)
        return PDBParser.read_PDB_file(output_file)

   
#===============================================================================
#first function to use biopython here it is use directly the PDB file
#better to use the from structure
#         @staticmethod
#     def bio_to_TEMpy(filename,hetatm=False, surface = False):
#             #imported if and when the function is executed.
#             from Bio.PDB import PDBParser as PDBParserBiopy
#             atomList = []
#             hetatomList=[]
#             footer = ''
#             header = ''
#             pdb_code=filename.split("/")[-1]#use os.
#             p=PDBParserBiopy()#permissive default True
#             structure_id="%s" % pdb_code[:-4]
#             structure=p.get_structure(structure_id, filename)
#             residues = structure.get_residues()
#             for res in residues:
#                 hetfield=res.get_id()[0]
#                 if hetfield[0]=="H":
#                     for atom in res:
#                         BioPyAtom(atom)
#                         hetatomList.append(BioPyAtom(atom))
#                 if hetfield[0]=="W":
#                     for atom in res:
#                         BioPyAtom(atom)
#                         hetatomList.append(BioPyAtom(atom))
#                 else:
#                     for atom in res:
#                         BioPyAtom(atom)
#                         atomList.append(BioPyAtom(atom))
# #                     print "here",BioPyAtom(atom)
#             return BioPy_Structure(atomList, filename=filename, header=header, footer=footer, surface=surface)
#===============================================================================
    @staticmethod
    def bio_strcuture_to_TEMpy(filename,structure,hetatm=False, surface = False):
            #imported if and when the function is executed.
        """filename = name of pdb file
            hetatm = Boolean representing whether to add hetatm to the structure.Default and Raccomanded is False.
           surface = Boolean representing whether the PDB file contains surface accessibility data."""
           #NEED TO MAKE A RETURN AND LOOK AT THE CODE FOR hetatm=T. 
           #THERE IS A HETATM DEF FROM DAVEN add_het_atoms 
           #NEED TO CHECK IT
        from Bio.PDB import PDBParser as PDBParserBiopy
        atomList = []
        hetatomList=[]
        footer = ''
        header = ''
        pdb_code=filename.split("/")[-1]#use os.
        p=PDBParserBiopy()#permissive default True
        structure_id="%s" % pdb_code[:-4]
        structure=p.get_structure(structure_id, filename)
        residues = structure.get_residues()
        for res in residues:
            hetfield=res.get_id()[0]
            if hetfield[0]=="H":
                for atom in res:
                    BioPyAtom(atom)
                    hetatomList.append(BioPyAtom(atom))
            if hetfield[0]=="W":
                for atom in res:
                    BioPyAtom(atom)
                    hetatomList.append(BioPyAtom(atom))
            else:
                for atom in res:
                    BioPyAtom(atom)
                    atomList.append(BioPyAtom(atom))
        return BioPy_Structure(atomList, filename=filename, header=header, footer=footer, surface=surface)
    
    #===========================================================================
    # def convert_bio_atom_to_TEMpy(bio_atom):
    #     pass        
    #===========================================================================