def buildMapPdb2Sequence( sequence, filename_pdb, options, pdb_chain = ""):

    if not os.path.exists( filename_pdb ):
        return None, None
    
    structure = Scientific.IO.PDB.Structure( filename_pdb )
    
    map_pdb2seq = {}
    map_seq2pdb = {}
    
    for chain in structure.peptide_chains:

        if chain.chain_id == pdb_chain:
            
            ## align pdb sequence to sequence
            map_structure2seq = alignlib.makeAlignataVector()
            alignator = alignlib.makeFullDP( -10.0, -2.0 )

            ## build sequence of pdb file
            structure = ""
            
            for residue in chain.sequence():
                structure += AMINOACIDS[residue]

            ## align reference sequence to sequence of pdb file
            row = alignlib.makeSequence( structure )
            col = alignlib.makeSequence( sequence )
            alignator.Align(row, col, map_structure2seq)

            if options.loglevel >= 3:
                options.stdlog.write( "structure: %s\n" % structure )                
                options.stdlog.write( "sequence : %s\n" % sequence )
                options.stdlog.write( "alignment of structure to sequence:\n" )
                options.stdlog.write( alignlib.writePairAlignment( row, col, map_structure2seq ) + "\n" )
                
            # print alignlib.writeAlignataTable(map_structure2seq)

            residue_number = 0
            
            for residue in chain.residues:

                residue_number += 1
                
                mapped_residue = map_structure2seq.mapRowToCol(residue_number)
                
                if not mapped_residue:
                    if options.loglevel >= 3:
                        options.stdlog.write( "# skipped residue %s=%s %i\n" % (str(residue.number), residue.name, residue_number))
                    continue

                r = str(residue.number)
                map_pdb2seq[r] = mapped_residue
                map_seq2pdb[mapped_residue] = r
                
            return map_structure2seq, map_pdb2seq, map_seq2pdb, residue_number-1, str(chain.residues[0].number), str(chain.residues[-1].number), structure
Renders the stored list of breadcrumbs.
dataset/ETHPy150Open CGATOxford/cgat/legacy/PdbTools.py/buildMapPdb2Sequence--crossover with--dataset/ETHPy150Open django-erp/django-erp/djangoerp/core/templatetags/breadcrumbs.py/render_breadcrumbs