# -*- 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
#
"""
CRD topology parser
===================
Read a list of atoms from a CHARMM CARD coordinate file (CRD) to build a basic topology.
Atom types and masses are guessed.
"""
from MDAnalysis.core.AtomGroup import Atom
from MDAnalysis.core.util import FORTRANReader
from MDAnalysis.topology.core import guess_atom_type, guess_atom_mass, guess_atom_charge
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')
[docs]def parse(filename):
"""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
:func:`MDAnalysis.topology.PSFParser.parse`.
"""
atoms = []
atom_serial = 0
with open(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])) == True:
extended = True
continue
elif line.split()[0] == line.split()[-1] and line.split()[0] != '*':
extended = False
continue
# anything else should be an atom
try:
if extended:
# 2I10,2X,A8,2X,A8,3F20.10,2X,A8,2X,A8,F20.10
serial,TotRes,resName,name,x,y,z,chainID,resSeq,tempFactor = extformat.read(line)
else:
# 2I5,1X,A4,1X,A4,3F10.5,1X,A4,1X,A4,F10.5
serial,TotRes,resName,name,x,y,z,chainID,resSeq,tempFactor = stdformat.read(line)
except:
print "Check CRD format at line %d: %s" % (linenum, line.rstrip())
raise #IOError("Check CRD format at line %d: %s" % (linenum, line.rstrip()))
atomtype = guess_atom_type(name)
mass = guess_atom_mass(name)
charge = guess_atom_charge(name)
atom_desc = Atom(atom_serial,name,atomtype,resName,TotRes,chainID,mass,charge)
atoms.append(atom_desc)
atom_serial += 1
structure = {}
structure["_atoms"] = atoms
# Other attributes are not read since they are not included in .crd files
other_attrs = ["_bonds" , "_angles" , "_dihe" , "_impr" , "_donors" , "_acceptors"]
for attr in other_attrs:
structure[attr] = []
return structure