[Biopython-dev] [Bug 2943] New: MMCIFParser only handling a single model.

[bugzilla-daemon at portal.open-bio.org]

http://bugzilla.open-bio.org/show_bug.cgi?id=2943

           Summary: MMCIFParser only handling a single model.
           Product: Biopython
           Version: 1.52
          Platform: PC
        OS/Version: Windows XP
            Status: NEW
          Severity: normal
          Priority: P2
         Component: Main Distribution
        AssignedTo: biopython-dev at biopython.org
        ReportedBy: TallPaulInJax at yahoo.com


MMCIFParser as-written only handles a single model in a protein. Any protein
that has multiple modesl with repeating chains and residues will get an
exception since the residue ID will already exist. Please make the following
changes in MMCIFParser.py:

Change the __doc__ setting:
#Optional __DOC__ change if the new MMCIFlex is not used nor the changes
#to MMCIF2Dict based on the new MMCIFlex.
#Mod by Paul T. Bathen to reflect MMCIFlex built solely in Python
__doc__="mmCIF parser (implemented solely in Python, no lex/flex/C code
needed)" 

Regardles of the DOC changes:
Insert the following model_list line 
        occupancy_list=mmcif_dict["_atom_site.occupancy"]
        fieldname_list=mmcif_dict["_atom_site.group_PDB"]
        #Added by Paul T. Bathen Nov 2009
        model_list=mmcif_dict["_atom_site.pdbx_PDB_model_num"]
        try:

Make the following changes:
        #Modified by Paul T. Bathen Nov 2009: comment out this line
        #current_model_id=0
        structure_builder=self._structure_builder
        structure_builder.init_structure(structure_id)
        #Modified by Paul T. Bathen Nov 2009: comment out this line
        #structure_builder.init_model(current_model_id)
        structure_builder.init_seg(" ")
        #Added by Paul T. Bathen Nov 2009
        current_model_id = -1

Make the following changes in the for loop:
            #Note by Paul T. Bathen: should MMCIFParser include 
            #the HOH and WAT stmts in PDBParser immediately below?
            #if fieldname=="HETATM":
            #    if resname=="HOH" or resname=="WAT":
            #        hetero_flag="W"
            #    else:
            #        hetero_flag="H"

            if fieldname=="HETATM":
                hetatm_flag="H"
            else:
                hetatm_flag=" "

            #Added by Paul T. Bathen Nov 2009
            model_id = model_list[i]
            if current_model_id != model_id:
                current_model_id = model_id
                structure_builder.init_model(current_model_id)
            #end of addition

After these changes took place, and with the new MMCIFlex and MMCIF2Dict in
place, I was able to parse and test 2beg.cif and pdb2beg.ent and both parsed
with the same number of models, chains, and residues. 

Paul


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