Source code for MDAnalysis.topology.CRDParser

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# MDAnalysis --- http://www.MDAnalysis.org
# Copyright (c) 2006-2015 Naveen Michaud-Agrawal, Elizabeth J. Denning, Oliver Beckstein
# and contributors (see AUTHORS for the full list)
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# 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
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"""
CRD topology parser
===================

Read a list of atoms from a CHARMM CARD coordinate file (CRD) to build a basic topology.

Atom types, charges and masses are guessed.

Classes
-------

.. autoclass:: CRDParser
   :members:
   :inherited-members:

"""
from __future__ import absolute_import

from ..core.AtomGroup import Atom
from ..lib.util import openany, FORTRANReader
from .core import guess_atom_type, guess_atom_mass, guess_atom_charge
from .base import TopologyReader


[docs]class CRDParser(TopologyReader): """Parse a CHARMM CARD coordinate file for topology information."""
[docs] def parse(self): """Parse CRD file *filename* and return the dict `structure`. Only reads the list of atoms. :Returns: MDAnalysis internal *structure* dict .. SeeAlso:: The *structure* dict is defined in `MDAnalysis.topology` """ extformat = FORTRANReader('2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10') stdformat = FORTRANReader('2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5') atoms = [] atom_serial = 0 with openany(self.filename) as crd: for linenum, line in enumerate(crd): # reading header if line.split()[0] == '*': continue elif line.split()[-1] == 'EXT' and bool(int(line.split()[0])) is True: r = extformat continue elif line.split()[0] == line.split()[-1] and line.split()[0] != '*': r = stdformat continue # anything else should be an atom try: serial, TotRes, resName, name, x, y, z, chainID, resSeq, tempFactor = r.read(line) except: raise ValueError("Check CRD format at line {0}: {1}" "".format(linenum, line.rstrip())) atomtype = guess_atom_type(name) mass = guess_atom_mass(name) charge = guess_atom_charge(name) atoms.append(Atom(atom_serial, name, atomtype, resName, TotRes, chainID, mass, charge, universe=self._u)) atom_serial += 1 structure = {} structure['atoms'] = atoms return structure