# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
# MDAnalysis --- http://mdanalysis.googlecode.com
# Copyright (c) 2006-2011 Naveen Michaud-Agrawal,
#               Elizabeth J. Denning, Oliver Beckstein,
#               and contributors (see website for details)
# Released under the GNU Public Licence, v2 or any higher version
# Please cite your use of MDAnalysis in published work:
#     N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and
#     O. Beckstein. MDAnalysis: A Toolkit for the Analysis of
#     Molecular Dynamics Simulations. J. Comput. Chem. 32 (2011), 2319--2327,
#     doi:10.1002/jcc.21787
# pdb.extensions
# original file: edPDB.xpdb but only kept content needed for MDAnalysis
:mod:`pdb.extensions` -- Extensions to :mod:`Bio.PDB`
:Author:  Oliver Beckstein
:Year:    2009
:License: Biopython
Extension to :mod:`Bio.PDB` to handle large pdb files.
Partly published on http://biopython.org/wiki/Reading_large_PDB_files
and more code at
Module content
.. autoclass:: SloppyStructureBuilder
.. autoclass:: SloppyPDBIO
.. autofunction:: get_structure
.. autofunction:: write_pdb
import Bio.PDB
import Bio.PDB.StructureBuilder
import logging
logger = logging.getLogger('MDAnalysis.pdb.extensions')
class SloppyStructureBuilder(Bio.PDB.StructureBuilder.StructureBuilder):
    """Cope with resSeq < 10,000 limitation by just incrementing internally.
    Solves the follwing problem with :class:`Bio.PDB.StructureBuilder.StructureBuilder`:
    Q: What's wrong here??
       Some atoms or residues will be missing in the data structure.
       WARNING: Residue (' ', 8954, ' ') redefined at line 74803.
       PDBConstructionException: Blank altlocs in duplicate residue SOL (' ', 8954, ' ') at line 74803.
    A: resSeq only goes to 9999 --> goes back to 0 (PDB format is not really good here)
    .. warning::  H and W records are probably not handled yet (don't have examples to test)
    def __init__(self,verbose=False):
        self.max_resseq = -1
        self.verbose = verbose
    def init_residue(self, resname, field, resseq, icode):
        Initiate a new Residue object.
        o resname - string, e.g. "ASN"
        o field - hetero flag, "W" for waters, "H" for
            hetero residues, otherwise blanc.
        o resseq - int, sequence identifier
        o icode - string, insertion code
        if field!=" ":
            if field=="H":
                # The hetero field consists of H_ + the residue name (e.g. H_FUC)
        res_id=(field, resseq, icode)
        if resseq > self.max_resseq:
            self.max_resseq  = resseq
        if field==" ":
            fudged_resseq = False
            while (self.chain.has_id(res_id) or resseq == 0):
                # There already is a residue with the id (field, resseq, icode).
                # resseq == 0 catches already wrapped residue numbers which do not
                # trigger the has_id() test.
                # Be sloppy and just increment...
                # (This code will not leave gaps in resids... I think)
                # XXX: shouldn't we also do this for hetero atoms and water??
                self.max_resseq += 1
                resseq = self.max_resseq
                res_id = (field, resseq, icode)    # use max_resseq!
                fudged_resseq = True
            if fudged_resseq and self.verbose:
                logger.debug("Residues are wrapping (Residue ('%s', %i, '%s') at line %i)."
                             % (field, resseq, icode, self.line_counter) +
                             ".... assigning new resid %d.\n" % self.max_resseq)
        residue=Bio.PDB.Residue.Residue(res_id, resname, self.segid)
class SloppyPDBIO(Bio.PDB.PDBIO):
    """PDBIO class that can deal with large pdb files as used in MD simulations.
    - resSeq simply wrap and are printed modulo 10,000.
    - atom numbers wrap at 99,999 and are printed modulo 100,000
    # directly copied from PDBIO.py
    # (has to be copied because of the package layout it is not externally accessible)
    _ATOM_FORMAT_STRING="%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n"
    def _get_atom_line(self, atom, hetfield, segid, atom_number, resname,
        resseq, icode, chain_id, element="  ", charge="  "):
        Returns an ATOM PDB string that is guaranteed to fit into the ATOM format.
        - Resid (resseq) is wrapped (modulo 10,000) to fit into %4i (4I) format
        - Atom number (atom_number) is wrapped (modulo 100,000) to fit into %4i (4I) format
        if hetfield!=" ":
            record_type="ATOM  "
        x, y, z=atom.get_coord()
        args=(record_type, atom_number % 100000, name, altloc, resname, chain_id,
            resseq % 10000, icode, x, y, z, occupancy, bfactor, segid,
            element, charge)
        return self._ATOM_FORMAT_STRING % args
sloppyparser = Bio.PDB.PDBParser(PERMISSIVE=True,structure_builder=SloppyStructureBuilder())
def get_structure(pdbfile,pdbid='system'):
    """Read the *pdbfilename*  and return a Bio.PDB structure.
    This function ignores duplicate atom numbers and resids from the
    file and simply increments them.
    .. Note::
       The call signature is reversed compared to the one of
    return sloppyparser.get_structure(pdbid,pdbfile)
def write_pdb(structure, filename, **kwargs):
    """Write Bio.PDB molecule *structure* to *filename*.
         Bio.PDB structure instance
         pdb file
    selection = kwargs.pop('selection', None)
    io = SloppyPDBIO()     # deals with resSeq > 9999
    io.save(filename, select=selection)