Source code for MDAnalysis.coordinates.pdb.extensions

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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
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# Please cite your use of MDAnalysis in published work:
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# 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
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# pdb.extensions
# original file: edPDB.xpdb but only kept content needed for MDAnalysis
"""
Extensions to :mod:`Bio.PDB` --- :mod:`pdb.extensions`
======================================================

: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
http://github.com/orbeckst/GromacsWrapper/tree/master/edPDB/

Classes
-------

.. autoclass:: SloppyStructureBuilder
.. autoclass:: SloppyPDBIO

Functions
---------

.. autofunction:: get_structure
.. autofunction:: write_pdb
"""

import Bio.PDB
import Bio.PDB.StructureBuilder

import logging

logger = logging.getLogger('MDAnalysis.pdb.extensions')


[docs]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): Bio.PDB.StructureBuilder.StructureBuilder.__init__(self) self.max_resseq = -1 self.verbose = verbose def init_residue(self, resname, field, resseq, icode): """ Initiate a new Residue object. Arguments: 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) field = "H_" + resname 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) self.chain.add(residue) self.residue = residue
[docs]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 = "HETATM" else: record_type = "ATOM " name = atom.get_fullname() altloc = atom.get_altloc() x, y, z = atom.get_coord() bfactor = atom.get_bfactor() occupancy = atom.get_occupancy() 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())
[docs]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 :meth:`Bio.PDB.PDBParser.get_structure`. """ return sloppyparser.get_structure(pdbid, pdbfile)
[docs]def write_pdb(structure, filename, **kwargs): """Write Bio.PDB molecule *structure* to *filename*. :Arguments: *structure* Bio.PDB structure instance *filename* pdb file *selection* Bio.PDB.Selection """ selection = kwargs.pop('selection', None) io = SloppyPDBIO() # deals with resSeq > 9999 io.set_structure(structure) io.save(filename, select=selection)