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Commit 04995236 authored by peastman's avatar peastman
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Merge pull request #577 from swails/fix_charmm_psf 

Fix charmm psf
parents d20e4edd 4b9221e3
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Showing with 107 additions and 71 deletions
wrappers/python/simtk/openmm/app/charmmparameterset.py
View file @ 04995236
......@@ -203,13 +203,12 @@ class CharmmParameterSet(object):
current_cmap_data = []
current_cmap_res = 0
nonbonded_types = dict() # Holder
needs_blank = False
parameterset = None
read_first_nonbonded = False
for line in f:
line = line.strip()
if not line:
# This is a blank line
needs_blank = False
continue
if parameterset is None and line.strip().startswith('*>>'):
parameterset = line.strip()[1:78]
......@@ -234,8 +233,8 @@ class CharmmParameterSet(object):
section = 'CMAP'
continue
if line.startswith('NONBONDED'):
read_first_nonbonded = False
section = 'NONBONDED'
needs_blank = True
continue
if line.startswith('NBFIX'):
section = 'NBFIX'
......@@ -414,7 +413,7 @@ class CharmmParameterSet(object):
current_cmap_res = res
current_cmap_data = []
continue
if section == 'NONBONDED' and not needs_blank:
if section == 'NONBONDED':
# Now get the nonbonded values
words = line.split()
try:
......@@ -423,7 +422,17 @@ class CharmmParameterSet(object):
epsilon = conv(words[2], float, 'vdW epsilon term')
rmin = conv(words[3], float, 'vdW Rmin/2 term')
except IndexError:
# If we haven't read our first nonbonded term yet, we may
# just be parsing the settings that should be used. So
# soldier on
if not read_first_nonbonded: continue
raise CharmmFileError('Could not parse nonbonded terms.')
except CharmmFileError, e:
if not read_first_nonbonded: continue
raise CharmmFileError(str(e))
else:
# OK, we've read our first nonbonded section for sure now
read_first_nonbonded = True
# See if we have 1-4 parameters
try:
# 4th column is ignored
......@@ -460,7 +469,7 @@ class CharmmParameterSet(object):
pass
except IndexError:
raise CharmmFileError('Could not parse NBFIX terms.')
self.nbfix_types[(min(at1, at2), max(at1, at2))] = (rmin, emin)
self.nbfix_types[(min(at1, at2), max(at1, at2))] = (emin, rmin)
# Now we're done. Load the nonbonded types into the relevant AtomType
# instances. In order for this to work, all keys in nonbonded_types
# must be in the self.atom_types_str dict. Raise a RuntimeError if this
......
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ 04995236
......@@ -45,14 +45,13 @@ from simtk.openmm.app.amberprmtopfile import HCT, OBC1, OBC2, GBn, GBn2
from simtk.openmm.app.internal.customgbforces import (GBSAHCTForce,
GBSAOBC1Force, GBSAOBC2Force, GBSAGBnForce, GBSAGBn2Force)
# CHARMM imports
from simtk.openmm.app.internal.charmm._charmmfile import CharmmFile
from simtk.openmm.app.internal.charmm.topologyobjects import (
ResidueList, AtomList, TrackedList, Bond, Angle, Dihedral,
Improper, AcceptorDonor, Group, Cmap, UreyBradley,
NoUreyBradley)
from simtk.openmm.app.internal.charmm.exceptions import (
CharmmPSFError, MoleculeError, CharmmPSFWarning,
MissingParameter)
MissingParameter, CharmmPsfEOF)
import warnings
TINY = 1e-8
......@@ -74,6 +73,29 @@ def _catchindexerror(func):
return newfunc
class _ZeroDict(dict):
"""
Contains a dict that returns dummy (zero) arguments when a key is not
present rather than raising a KeyError. The return value for non-existent
items is (0, []). It also special-case sections that have multiple pointers
to avoid index errors if those are not present in the PSF file
"""
def __getitem__(self, key):
try:
return dict.__getitem__(self, key)
except KeyError:
if key.startswith('NGRP'):
for k in self:
if k.startswith('NGRP'):
return dict.__getitem__(self, k)
return [0, 0], []
elif key.startswith('NUMLP'):
for k in self:
if k.startswith('NUMLP'):
return dict.__getitem__(self, k)
return [0, 0], []
return 0, []
# ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
class CharmmPsfFile(object):
......@@ -128,8 +150,8 @@ class CharmmPsfFile(object):
@_catchindexerror
def __init__(self, psf_name):
"""
Opens and parses a PSF file, then instantiates a CharmmPsfFile instance
from the data.
Opens and parses a PSF file, then instantiates a CharmmPsfFile
instance from the data.
Parameters:
psf_name (str) : Name of the PSF file (it must exist)
......@@ -143,33 +165,32 @@ class CharmmPsfFile(object):
if not os.path.exists(psf_name):
raise IOError('Could not find PSF file %s' % psf_name)
# Open the PSF and read the first line. It must start with "PSF"
psf = CharmmFile(psf_name, 'r')
psf = open(psf_name, 'r')
line = psf.readline()
if not line.startswith('PSF'):
raise CharmmPSFError('Unrecognized PSF file. First line is %s' %
line.strip())
# Store the flags
psf_flags = line.split()[1:]
# Next line is blank
# Now get all of the sections and store them in a dict
psf.readline()
# The next line has one number -- the number of title lines
ntitle = conv(psf.readline().strip(), int, 'title count')
# Now get all of the sections
psfsections = _ZeroDict()
while True:
try:
sec, ptr, data = CharmmPsfFile._parse_psf_section(psf)
except CharmmPsfEOF:
break
psfsections[sec] = (ptr, data)
# store the title
title = list()
for i in range(ntitle):
title.append(psf.readline().rstrip())
# Skip all blank lines. Most of the time there is only 1, but I've seen
# a file that has 2
line = psf.readline().strip()
while not line:
line = psf.readline().strip()
title = psfsections['NTITLE'][1]
# Next is the number of atoms
natom = conv(line, int, 'natom')
natom = conv(psfsections['NATOM'][0], int, 'natom')
# Parse all of the atoms
residue_list = ResidueList()
atom_list = AtomList()
for i in xrange(natom):
words = psf.readline().split()
words = psfsections['NATOM'][1][i].split()
atid = int(words[0])
if atid != i + 1:
raise CharmmPSFError('Nonsequential atoms detected!')
......@@ -190,10 +211,10 @@ class CharmmPsfFile(object):
attype, charge, mass, props)
atom_list.append(atom)
atom_list.assign_indexes()
# Eat the next line
psf.readline()
atom_list.changed = False
# Now get the number of bonds
nbond, holder = CharmmPsfFile._parse_psf_section(psf, int)
nbond = conv(psfsections['NBOND'][0], int, 'number of bonds')
holder = psfsections['NBOND'][1]
bond_list = TrackedList()
if len(holder) != nbond * 2:
raise CharmmPSFError('Got %d indexes for %d bonds' %
......@@ -204,7 +225,8 @@ class CharmmPsfFile(object):
bond_list.append(Bond(atom_list[id1], atom_list[id2]))
bond_list.changed = False
# Now get the number of angles and the angle list
ntheta, holder = CharmmPsfFile._parse_psf_section(psf, int)
ntheta = conv(psfsections['NTHETA'][0], int, 'number of angles')
holder = psfsections['NTHETA'][1]
angle_list = TrackedList()
if len(holder) != ntheta * 3:
raise CharmmPSFError('Got %d indexes for %d angles' %
......@@ -218,7 +240,8 @@ class CharmmPsfFile(object):
)
angle_list.changed = False
# Now get the number of torsions and the torsion list
nphi, holder = CharmmPsfFile._parse_psf_section(psf, int)
nphi = conv(psfsections['NPHI'][0], int, 'number of torsions')
holder = psfsections['NPHI'][1]
dihedral_list = TrackedList()
if len(holder) != nphi * 4:
raise CharmmPSFError('Got %d indexes for %d torsions' %
......@@ -234,7 +257,8 @@ class CharmmPsfFile(object):
)
dihedral_list.changed = False
# Now get the number of improper torsions
nimphi, holder = CharmmPsfFile._parse_psf_section(psf, int)
nimphi = conv(psfsections['NIMPHI'][0], int, 'number of impropers')
holder = psfsections['NIMPHI'][1]
improper_list = TrackedList()
if len(holder) != nimphi * 4:
raise CharmmPSFError('Got %d indexes for %d impropers' %
......@@ -250,7 +274,8 @@ class CharmmPsfFile(object):
)
improper_list.changed = False
# Now handle the donors (what is this used for??)
ndon, holder = CharmmPsfFile._parse_psf_section(psf, int)
ndon = conv(psfsections['NDON'][0], int, 'number of donors')
holder = psfsections['NDON'][1]
donor_list = TrackedList()
if len(holder) != ndon * 2:
raise CharmmPSFError('Got %d indexes for %d donors' %
......@@ -261,7 +286,8 @@ class CharmmPsfFile(object):
donor_list.append(AcceptorDonor(atom_list[id1], atom_list[id2]))
donor_list.changed = False
# Now handle the acceptors (what is this used for??)
nacc, holder = CharmmPsfFile._parse_psf_section(psf, int)
nacc = conv(psfsections['NACC'][0], int, 'number of acceptors')
holder = psfsections['NACC'][1]
acceptor_list = TrackedList()
if len(holder) != nacc * 2:
raise CharmmPSFError('Got %d indexes for %d acceptors' %
......@@ -271,16 +297,13 @@ class CharmmPsfFile(object):
id2 = holder[2*i+1] - 1
acceptor_list.append(AcceptorDonor(atom_list[id1], atom_list[id2]))
acceptor_list.changed = False
# Now get the NNB section. Not sure what this section is for or what it
# does...
nnb, holder = CharmmPsfFile._parse_psf_section(psf, int)
# Now get the group sections
pointers, holder = CharmmPsfFile._parse_psf_section(psf, int)
group_list = TrackedList()
try:
ngrp, nst2 = pointers
ngrp, nst2 = psfsections['NGRP NST2'][0]
except ValueError:
raise CharmmPSFError('Could not unpack GROUP pointers')
holder = psfsections['NGRP NST2'][1]
group_list.nst2 = nst2
# Now handle the groups
if len(holder) != ngrp * 3:
......@@ -292,19 +315,8 @@ class CharmmPsfFile(object):
i3 = holder[3*i+2]
group_list.append(Group(i1, i2, i3))
group_list.changed = False
# The next section might be the number of molecules or it might be the
# cross-term (cmap) section. The first thing we'll do is determine
# molecularity based on the atom connectivity. If every PSF file was
# guaranteed to be "correct", we could just compare the MOLNT
# section with the one we compute here. However, CHARMM GUI appears
# to assign MOLNT as a dummy section (with all 1's), so this
# approach will not work. Instead, look at the value of the pointer
# and the number of entries in the group. If the # of entries is
# NATOM, assume we have MOLNT section. Warn if the MOLNT section is
# 'wrong'...
pointer, holder = CharmmPsfFile._parse_psf_section(psf, int)
# Assign all of the atoms to molecules recursively
holder = psfsections['MOLNT'][1]
set_molecules(atom_list)
molecule_list = [atom.marked for atom in atom_list]
if len(holder) == len(atom_list):
......@@ -312,21 +324,14 @@ class CharmmPsfFile(object):
warnings.warn('Detected PSF molecule section that is WRONG. '
'Resetting molecularity.', CharmmPSFWarning)
# We have a CHARMM PSF file; now do NUMLP/NUMLPH sections
words = psf.readline().split()
numlp = conv(words[0], int, 'numlp')
numlph = conv(words[1], int, 'numlph')
numlp, numlph = psfsections['NUMLP NUMLPH'][0]
if numlp != 0 or numlph != 0:
raise NotImplemented('Cannot currently handle PSFs with lone '
'pairs defined in the NUMLP/NUMLPH '
'section.')
psf.readline() # blank
# Now we get to the cross-term section
ncrterm, holder = CharmmPsfFile._parse_psf_section(psf, int)
else:
ncrterm = pointer
# At this point, ncrterm and holder are both set to the CMAP list for
# VMD and non-VMD PSFs.
# Now get the cmaps
# Now do the CMAPs
ncrterm = conv(psfsections['NCRTERM'][0], int, 'Number of cross-terms')
holder = psfsections['NCRTERM'][1]
cmap_list = TrackedList()
if len(holder) != ncrterm * 8:
raise CharmmPSFError('Got %d CMAP indexes for %d cmap terms' %
......@@ -347,7 +352,6 @@ class CharmmPsfFile(object):
)
cmap_list.changed = False
# Now set the instance attributes
self.residue_list = residue_list
self.atom_list = atom_list
self.bond_list = bond_list
......@@ -381,18 +385,18 @@ class CharmmPsfFile(object):
raise CharmmPSFError('Could not convert %s' % message)
@staticmethod
def _parse_psf_section(psf, dtype):
def _parse_psf_section(psf):
"""
This method parses a section of the PSF file
Parameters:
- psf (CharmmFile) : Open file that is pointing to the first line
of the section that is to be parsed
- dtype (type) : The data type to convert all of the data into
Returns:
(pointers, data)
(title, pointers, data)
- title (str) : The label of the PSF section we are parsing
- pointers (int/tuple of ints) : If one pointer is set, pointers is
simply the integer that is value of that pointer. Otherwise
it is a tuple with every pointer value defined in the first
......@@ -401,22 +405,42 @@ class CharmmPsfFile(object):
to `dtype'
"""
conv = CharmmPsfFile._convert
words = psf.readline().split()
line = psf.readline()
while not line.strip():
if not line:
raise CharmmPsfEOF('Unexpected EOF in PSF file')
else:
line = psf.readline()
if '!' in line:
words = line[:line.index('!')].split()
title = line[line.index('!')+1:].strip().upper()
# Strip out description
if ':' in title:
title = title[:title.index(':')]
else:
raise CharmmPSFError('Could not determine section title')
if len(words) == 1:
pointers = conv(words[0], int, 'pointer')
else:
pointers = tuple([conv(w, int, 'pointer') for w in words])
line = psf.readline().strip()
if not line:
if not line and title.startswith('NNB'):
# This will correctly handle the NNB section (which has a spurious
# blank line) as well as any sections that have 0 members.
line = psf.readline().strip()
data = []
while line:
words = line.split()
data.extend([conv(w, dtype, 'PSF data') for w in words])
line = psf.readline().strip()
return pointers, data
if title == 'NATOM' or title == 'NTITLE':
# Store these two sections as strings (ATOM section we will parse
# later). The rest of the sections are integer pointers
while line:
data.append(line)
line = psf.readline().strip()
else:
while line:
words = line.split()
data.extend([conv(w, int, 'PSF data') for w in words])
line = psf.readline().strip()
return title, pointers, data
def writePsf(self, dest, vmd=False):
"""
......
wrappers/python/simtk/openmm/app/internal/charmm/exceptions.py
View file @ 04995236
......@@ -42,6 +42,9 @@ class CharmmWarning(Warning):
class CharmmPSFError(CharmmError):
""" If there is a problem parsing CHARMM PSF files """
class CharmmPsfEOF(CharmmError):
""" Raised when the end-of-file is reached on a CHARMM PSF file """
class SplitResidueWarning(CharmmWarning):
""" For if a residue with the same number but different names is split """
......
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