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Commit c1cae06a authored by Jason Swails's avatar Jason Swails
Browse files

Fixups and simplifications to PSF parser with inscodes

parent b21e3182
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Showing with 8 additions and 185 deletions
wrappers/python/simtk/openmm/app/charmmpsffile.py
View file @ c1cae06a
......@@ -195,16 +195,13 @@ class CharmmPsfFile(object):
atom_list = AtomList()
for i in xrange(natom):
words = psfsections['NATOM'][1][i].split()
atid = int(words[0])
if atid != i + 1:
raise CharmmPSFError('Nonsequential atoms detected!')
system = words[1]
rematch = _resre.match(words[2])
if not rematch:
raise RuntimeError('Could not parse residue number %s' %
words[2])
resid, inscode = rematch.groups()
resid = conv(resid, int, 'residue number')
resid = int(resid)
resname = words[3]
name = words[4]
attype = words[5]
......@@ -451,175 +448,6 @@ class CharmmPsfFile(object):
line = psf.readline().strip()
return title, pointers, data
def writePsf(self, dest, vmd=False):
"""
Writes a PSF file from the stored molecule
Parameters:
- dest (str or file-like) : The place to write the output PSF file.
If it has a "write" attribute, it will be used to print the
PSF file. Otherwise, it will be treated like a string and a
file will be opened, printed, then closed
- vmd (bool) : If True, it will write out a PSF in the format that
VMD prints it in (i.e., no NUMLP/NUMLPH or MOLNT sections)
Example:
>>> cs = CharmmPsfFile('testfiles/test.psf')
>>> cs.writePsf('testfiles/test2.psf')
"""
# See if this is an extended format
ext = 'EXT' in self.flags
own_handle = False
# Index the atoms and residues
self.residue_list.assign_indexes()
self.atom_list.assign_indexes()
if not hasattr(dest, 'write'):
own_handle = True
dest = open(dest, 'w')
# Assign the formats we need to write with
if ext:
atmfmt1 = ('%10d %-8s %-8i %-8s %-8s %4d %10.6f %13.4f' + 11*' ')
atmfmt2 = ('%10d %-8s %-8i %-8s %-8s %-4s %10.6f %13.4f' + 11*' ')
intfmt = '%10d' # For pointers
else:
atmfmt1 = ('%8d %-4s %-4i %-4s %-4s %4d %10.6f %13.4f' + 11*' ')
atmfmt2 = ('%8d %-4s %-4i %-4s %-4s %-4s %10.6f %13.4f' + 11*' ')
intfmt = '%8d' # For pointers
# Now print the header then the title
dest.write('PSF ' + ' '.join(self.flags) + '\n')
dest.write('\n')
dest.write(intfmt % len(self.title) + ' !NTITLE\n')
dest.write('\n'.join(self.title) + '\n\n')
# Now time for the atoms
dest.write(intfmt % len(self.atom_list) + ' !NATOM\n')
# atmfmt1 is for CHARMM format (i.e., atom types are integers)
# atmfmt is for XPLOR format (i.e., atom types are strings)
for i, atom in enumerate(self.atom_list):
if isinstance(atom.attype, str):
fmt = atmfmt2
else:
fmt = atmfmt1
atmstr = fmt % (i+1, atom.system, atom.residue.resnum,
atom.residue.resname, atom.name, atom.attype,
atom.charge, atom.mass)
dest.write(atmstr + ' '.join(atom.props) + '\n')
dest.write('\n')
# Bonds
dest.write(intfmt % len(self.bond_list) + ' !NBOND: bonds\n')
for i, bond in enumerate(self.bond_list):
dest.write((intfmt*2) % (bond.atom1.idx+1, bond.atom2.idx+1))
if i % 4 == 3: # Write 4 bonds per line
dest.write('\n')
# See if we need to terminate
if len(self.bond_list) % 4 != 0 or len(self.bond_list) == 0:
dest.write('\n')
dest.write('\n')
# Angles
dest.write(intfmt % len(self.angle_list) + ' !NTHETA: angles\n')
for i, angle in enumerate(self.angle_list):
dest.write((intfmt*3) % (angle.atom1.idx+1, angle.atom2.idx+1,
angle.atom3.idx+1)
)
if i % 3 == 2: # Write 3 angles per line
dest.write('\n')
# See if we need to terminate
if len(self.angle_list) % 3 != 0 or len(self.angle_list) == 0:
dest.write('\n')
dest.write('\n')
# Dihedrals
dest.write(intfmt % len(self.dihedral_list) + ' !NPHI: dihedrals\n')
for i, dih in enumerate(self.dihedral_list):
dest.write((intfmt*4) % (dih.atom1.idx+1, dih.atom2.idx+1,
dih.atom3.idx+1, dih.atom4.idx+1)
)
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(self.dihedral_list) % 2 != 0 or len(self.dihedral_list) == 0:
dest.write('\n')
dest.write('\n')
# Impropers
dest.write(intfmt % len(self.improper_list) + ' !NIMPHI: impropers\n')
for i, imp in enumerate(self.improper_list):
dest.write((intfmt*4) % (imp.atom1.idx+1, imp.atom2.idx+1,
imp.atom3.idx+1, imp.atom4.idx+1)
)
if i % 2 == 1: # Write 2 dihedrals per line
dest.write('\n')
# See if we need to terminate
if len(self.improper_list) % 2 != 0 or len(self.improper_list) == 0:
dest.write('\n')
dest.write('\n')
# Donor section
dest.write(intfmt % len(self.donor_list) + ' !NDON: donors\n')
for i, don in enumerate(self.donor_list):
dest.write((intfmt*2) % (don.atom1.idx+1, don.atom2.idx+1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(self.donor_list) % 4 != 0 or len(self.donor_list) == 0:
dest.write('\n')
dest.write('\n')
# Acceptor section
dest.write(intfmt % len(self.acceptor_list) + ' !NACC: acceptors\n')
for i, acc in enumerate(self.acceptor_list):
dest.write((intfmt*2) % (acc.atom1.idx+1, acc.atom2.idx+1))
if i % 4 == 3: # 4 donors per line
dest.write('\n')
if len(self.acceptor_list) % 4 != 0 or len(self.acceptor_list) == 0:
dest.write('\n')
dest.write('\n')
# NNB section ??
dest.write(intfmt % 0 + ' !NNB\n\n')
for i in range(len(self.atom_list)):
dest.write(intfmt % 0)
if i % 8 == 7: # Write 8 0's per line
dest.write('\n')
if len(self.atom_list) % 8 != 0: dest.write('\n')
dest.write('\n')
# Group section
dest.write((intfmt*2) % (len(self.group_list), self.group_list.nst2))
dest.write(' !NGRP NST2\n')
for i, gp in enumerate(self.group_list):
dest.write((intfmt*3) % (gp.bs, gp.type, gp.move))
if i % 3 == 2: dest.write('\n')
if len(self.group_list) % 3 != 0 or len(self.group_list) == 0:
dest.write('\n')
dest.write('\n')
# The next two sections are never found in VMD prmtops...
if not vmd:
# Molecule section; first set molecularity
set_molecules(self.atom_list)
mollist = [a.marked for a in self.atom_list]
dest.write(intfmt % max(mollist) + ' !MOLNT\n')
for i, atom in enumerate(self.atom_list):
dest.write(intfmt % atom.marked)
if i % 8 == 7: dest.write('\n')
if len(self.atom_list) % 8 != 0: dest.write('\n')
dest.write('\n')
# NUMLP/NUMLPH section
dest.write((intfmt*2) % (0, 0) + ' !NUMLP NUMLPH\n')
dest.write('\n')
# CMAP section
dest.write(intfmt % len(self.cmap_list) + ' !NCRTERM: cross-terms\n')
for i, cmap in enumerate(self.cmap_list):
dest.write((intfmt*4) % (cmap.atom1.idx+1, cmap.atom2.idx+1,
cmap.atom3.idx+1, cmap.atom4.idx+1)
)
if cmap.consecutive:
dest.write((intfmt*4) % (cmap.atom2.idx+1, cmap.atom3.idx+1,
cmap.atom4.idx+1, cmap.atom5.idx+1)
)
else:
dest.write((intfmt*4) % (cmap.atom5.idx+1, cmap.atom6.idx+1,
cmap.atom7.idx+1, cmap.atom8.idx+1)
)
dest.write('\n')
# Done!
# If we opened our own handle, close it
if own_handle:
dest.close()
def loadParameters(self, parmset):
"""
Loads parameters from a parameter set that was loaded via CHARMM RTF,
......
wrappers/python/simtk/openmm/app/internal/charmm/topologyobjects.py
View file @ c1cae06a
......@@ -467,22 +467,17 @@ class ResidueList(list):
Returns:
The Atom instance created and added to the list of residues
"""
if self._last_residue is None:
lr = self._last_residue
if lr is None:
res = self._last_residue = Residue(resname, resnum, inscode)
list.append(self, res)
elif (self._last_residue != (resname, resnum, inscode) or
system != self._last_residue.system):
if (self._last_residue.idx == resnum and
self._last_residue.system == system and
self._last_residue.inscode == inscode):
lresname = self._last_residue.resname
warnings.warn('Residue %d split into separate residues %s '
'and %s' % (resnum, lresname, resname),
SplitResidueWarning)
res = self._last_residue = Residue(resname, resnum)
elif (lr.resname != resname or lr.idx != resname or
lr.inscode != inscode or system != lr.system):
res = self._last_residue = Residue(resname, resnum, inscode)
res.system = system
list.append(self, res)
else:
res = self._last_residue
res = lr
atom = Atom(system, name, attype, float(charge), float(mass), props)
res.add_atom(atom)
return atom
......
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