Source code for MDAnalysis.topology.PSFParser

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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:


.. autoclass:: PSFParser

from __future__ import absolute_import, division
from six.moves import range
from six import raise_from

import logging
import functools
from math import ceil
import numpy as np

from ..lib.util import openany
from . import guessers
from .base import TopologyReaderBase, squash_by, change_squash
from ..core.topologyattrs import (
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: """ 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 = [ 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 : 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", int(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 = ("{0} is not valid PSF file" "".format(self.filename)) logger.error(err) raise_from(ValueError(err), 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