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# MDAnalysis --- https://www.mdanalysis.org
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# Please cite your use of MDAnalysis in published work:
#
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
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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
#
"""
PSF topology parser
===================
Reads a CHARMM/NAMD/XPLOR PSF_ file to build the system. The topology will
contain atom IDs, segids, residue IDs, residue names, atom names, atom types,
charges and masses. Bonds, angles, dihedrals and impropers are also read from
the file.
It reads both standard and extended ("EXT") PSF formats and can also parse NAMD
space-separated "PSF" file variants.
.. _PSF: http://www.charmm.org/documentation/c35b1/struct.html
Classes
-------
.. autoclass:: PSFParser
:members:
:inherited-members:
"""
import logging
import functools
from math import ceil
import numpy as np
from ..lib.util import openany, atoi
from .base import TopologyReaderBase, squash_by, change_squash
from ..core.topologyattrs import (
Atomids,
Atomnames,
Atomtypes,
Masses,
Charges,
Resids,
Resnums,
Resnames,
Segids,
Bonds,
Angles,
Dihedrals,
Impropers
)
from ..core.topology import Topology
logger = logging.getLogger("MDAnalysis.topology.PSF")
[docs]class PSFParser(TopologyReaderBase):
"""Read topology information from a CHARMM/NAMD/XPLOR PSF_ file.
Creates a Topology with the following Attributes:
- ids
- names
- types
- masses
- charges
- resids
- resnames
- segids
- bonds
- angles
- dihedrals
- impropers
.. _PSF: http://www.charmm.org/documentation/c35b1/struct.html
.. versionchanged:: 2.8.0
PSFParser now reads string resids and converts them to integers.
"""
format = 'PSF'
[docs] def parse(self, **kwargs):
"""Parse PSF file into Topology
Returns
-------
MDAnalysis *Topology* object
"""
# Open and check psf validity
with openany(self.filename) as psffile:
header = next(psffile)
if not header.startswith("PSF"):
err = ("{0} is not valid PSF file (header = {1})"
"".format(self.filename, header))
logger.error(err)
raise ValueError(err)
header_flags = header[3:].split()
if "NAMD" in header_flags:
self._format = "NAMD" # NAMD/VMD
elif "EXT" in header_flags:
self._format = "EXTENDED" # CHARMM
else:
self._format = "STANDARD" # CHARMM
next(psffile)
title = next(psffile).split()
if not (title[1] == "!NTITLE"):
err = "{0} is not a valid PSF file".format(self.filename)
logger.error(err)
raise ValueError(err)
# psfremarks = [psffile.next() for i in range(int(title[0]))]
for _ in range(int(title[0])):
next(psffile)
logger.debug("PSF file {0}: format {1}"
"".format(self.filename, self._format))
# Atoms first and mandatory
top = self._parse_sec(
psffile, ('NATOM', 1, 1, self._parseatoms))
# Then possibly other sections
sections = (
#("atoms", ("NATOM", 1, 1, self._parseatoms)),
(Bonds, ("NBOND", 2, 4, self._parsesection)),
(Angles, ("NTHETA", 3, 3, self._parsesection)),
(Dihedrals, ("NPHI", 4, 2, self._parsesection)),
(Impropers, ("NIMPHI", 4, 2, self._parsesection)),
#("donors", ("NDON", 2, 4, self._parsesection)),
#("acceptors", ("NACC", 2, 4, self._parsesection))
)
try:
for attr, info in sections:
next(psffile)
top.add_TopologyAttr(
attr(self._parse_sec(psffile, info)))
except StopIteration:
# Reached the end of the file before we expected
for attr in (Bonds, Angles, Dihedrals, Impropers):
if not hasattr(top, attr.attrname):
top.add_TopologyAttr(attr([]))
return top
def _parse_sec(self, psffile, section_info):
"""Parse a single section of the PSF
Returns
-------
A list of Attributes from this section
"""
desc, atoms_per, per_line, parsefunc = section_info
header = next(psffile)
while header.strip() == "":
header = next(psffile)
header = header.split()
# Get the number
num = float(header[0])
sect_type = header[1].strip('!:')
# Make sure the section type matches the desc
if not sect_type == desc:
err = ("Expected section {0} but found {1}"
"".format(desc, sect_type))
logger.error(err)
raise ValueError(err)
# Now figure out how many lines to read
numlines = int(ceil(num/per_line))
psffile_next = functools.partial(next, psffile)
return parsefunc(psffile_next, atoms_per, numlines)
def _parseatoms(self, lines, atoms_per, numlines):
"""Parses atom section in a Charmm PSF file.
Normal (standard) and extended (EXT) PSF format are
supported. CHEQ is supported in the sense that CHEQ data is simply
ignored.
CHARMM Format from ``source/psffres.src``:
CHEQ::
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I),ECH(I),EHA(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8,2G14.6)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8,2G14.6)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8,2G14.6) XPLOR
no CHEQ::
II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I)
standard format:
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,I4,1X,2G14.6,I8)
(I8,1X,A4,1X,A4,1X,A4,1X,A4,1X,A4,1X,2G14.6,I8) XPLOR
expanded format EXT:
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,I4,1X,2G14.6,I8)
(I10,1X,A8,1X,A8,1X,A8,1X,A8,1X,A4,1X,2G14.6,I8) XPLOR
NAMD PSF
space separated, see release notes for VMD 1.9.1, psfplugin at
http://www.ks.uiuc.edu/Research/vmd/current/devel.html :
psfplugin: Added more logic to the PSF plugin to determine cases where the
CHARMM "EXTended" PSF format cannot accomodate long atom types, and we add
a "NAMD" keyword to the PSF file flags line at the top of the file. Upon
reading, if we detect the "NAMD" flag there, we know that it is possible
to parse the file correctly using a simple space-delimited scanf() format
string, and we use that strategy rather than holding to the inflexible
column-based fields that are a necessity for compatibility with CHARMM,
CNS, X-PLOR, and other formats. NAMD and the psfgen plugin already assume
this sort of space-delimited formatting, but that's because they aren't
expected to parse the PSF variants associated with the other programs. For
the VMD PSF plugin, having the "NAMD" tag in the flags line makes it
absolutely clear that we're dealing with a NAMD-specific file so we can
take the same approach.
"""
# how to partition the line into the individual atom components
atom_parsers = {
'STANDARD': lambda l:
(l[:8], l[9:13].strip() or "SYSTEM", l[14:18],
l[19:23].strip(), l[24:28].strip(),
l[29:33].strip(), l[34:48], l[48:62]),
# l[62:70], l[70:84], l[84:98] ignore IMOVE, ECH and EHA,
'EXTENDED': lambda l:
(l[:10], l[11:19].strip() or "SYSTEM", l[20:28],
l[29:37].strip(), l[38:46].strip(),
l[47:51].strip(), l[52:66], l[66:70]),
# l[70:78], l[78:84], l[84:98] ignore IMOVE, ECH and EHA,
'NAMD': lambda l: l.split()[:8],
}
atom_parser = atom_parsers[self._format]
# once partitioned, assigned each component the correct type
set_type = lambda x: (int(x[0]) - 1, x[1] or "SYSTEM",
atoi(x[2]), x[3],
x[4], x[5], float(x[6]), float(x[7]))
# Oli: I don't think that this is the correct OUTPUT format:
# psf_atom_format = " %5d %4s %4d %4s %-4s %-4s %10.6f %7.4f%s\n"
# It should be rather something like:
# psf_ATOM_format = '%(iatom)8d %(segid)4s %(resid)-4d %(resname)4s '+\
# '%(name)-4s %(type)4s %(charge)-14.6f%(mass)-14.4f%(imove)8d\n'
# source/psfres.src (CHEQ and now can be used for CHEQ EXTended), see comments above
# II,LSEGID,LRESID,LRES,TYPE(I),IAC(I),CG(I),AMASS(I),IMOVE(I),ECH(I),EHA(I)
# (I8,1X,A4, 1X,A4, 1X,A4, 1X,A4, 1X,I4, 1X,2G14.6, I8, 2G14.6)
# 0:8 9:13 14:18 19:23 24:28 29:33 34:48 48:62 62:70 70:84 84:98
# Allocate arrays
atomids = np.zeros(numlines, dtype=np.int32)
segids = np.zeros(numlines, dtype=object)
resids = np.zeros(numlines, dtype=np.int32)
resnames = np.zeros(numlines, dtype=object)
atomnames = np.zeros(numlines, dtype=object)
atomtypes = np.zeros(numlines, dtype=object)
charges = np.zeros(numlines, dtype=np.float32)
masses = np.zeros(numlines, dtype=np.float64)
for i in range(numlines):
try:
line = lines()
except StopIteration:
err = f"{self.filename} is not valid PSF file"
logger.error(err)
raise ValueError(err) from None
try:
vals = set_type(atom_parser(line))
except ValueError:
# last ditch attempt: this *might* be a NAMD/VMD
# space-separated "PSF" file from VMD version < 1.9.1
atom_parser = atom_parsers['NAMD']
vals = set_type(atom_parser(line))
logger.warning("Guessing that this is actually a"
" NAMD-type PSF file..."
" continuing with fingers crossed!")
logger.debug("First NAMD-type line: {0}: {1}"
"".format(i, line.rstrip()))
atomids[i] = vals[0]
segids[i] = vals[1]
resids[i] = vals[2]
resnames[i] = vals[3]
atomnames[i] = vals[4]
atomtypes[i] = vals[5]
charges[i] = vals[6]
masses[i] = vals[7]
# Atom
atomids = Atomids(atomids)
atomnames = Atomnames(atomnames)
atomtypes = Atomtypes(atomtypes)
charges = Charges(charges)
masses = Masses(masses)
# Residue
# resids, resnames
residx, (new_resids, new_resnames, perres_segids) = change_squash(
(resids, resnames, segids),
(resids, resnames, segids))
# transform from atom:Rid to atom:Rix
residueids = Resids(new_resids)
residuenums = Resnums(new_resids.copy())
residuenames = Resnames(new_resnames)
# Segment
segidx, perseg_segids = squash_by(perres_segids)[:2]
segids = Segids(perseg_segids)
top = Topology(len(atomids), len(new_resids), len(segids),
attrs=[atomids, atomnames, atomtypes,
charges, masses,
residueids, residuenums, residuenames,
segids],
atom_resindex=residx,
residue_segindex=segidx)
return top
def _parsesection(self, lines, atoms_per, numlines):
section = []
for i in range(numlines):
# Subtract 1 from each number to ensure zero-indexing for the atoms
fields = np.int64(lines().split()) - 1
for j in range(0, len(fields), atoms_per):
section.append(tuple(fields[j:j+atoms_per]))
return section