def parse(self):
"""
DOCME
"""
super(RTFFile, self).parse()
self._parse_mass()
self._parse_decl()
self._parse_defa()
self._parse_auto()
iterator = ( line for line in self.body if not line.startswith('!') )
iterator = paragraphs(logicalLines(iterator), self._sections)
self.resi = {}
self.pres = {}
self._wtf = []
for taco in iterator:
if taco[0][:4] == 'resi':
tmp = taco[0].split()[1]
self.resi[tmp] = TopRes(taco)
elif taco[0][:4] == 'pres':
tmp = taco[0].split()[1]
self.pres[tmp] = TopRes(taco)
else:
self._wtf.append(taco)
self.chemResiDict = dict(( (k, v.chemDict) for k, v in self.resi.iteritems() ))
self.chemPresDict = dict(( (k, v.chemDict) for k, v in self.pres.iteritems() ))
self.chargeResiDict = dict(( (k, v.chargeDict) for k, v in self.resi.iteritems() ))
self.chargePresDict = dict(( (k, v.chargeDict) for k, v in self.pres.iteritems() ))
def __init__(self, arg):
super(TopRes, self).__init__()
tmp1 = []
tmp2 = []
for line in cleanStrings(arg, CC='!'):
if line.startswith(('group', 'atom')):
tmp1.append(line) # atom data
else:
tmp2.append(line) # everything else
# turn tmp1 into a list
self.groups = []
for group in paragraphs(tmp1, ['grou']):
self.groups.append([ tuple(line.split()[1:]) for line in group[1:] ])
self.atoms = flatten(self.groups, ltypes=list)
# turn tmp2 into a dict
meta = {}
for line in tmp2:
key = line.split()[0]
value = line.split(key)[1].lstrip()
if key not in meta.keys():
meta[key] = [value]
else:
meta[key].append(value)
self.meta = meta
# dicts
self.chemDict = dict(( line[:2] for line in self.atoms ))
self.chargeDict = dict(( [line[0], float(line[2])] for line in self.atoms ))
def parse(self):
super(PRMFile, self).parse()
iterator = ( line for line in self.body if not line.startswith('!') )
iterator = paragraphs(logicalLines(iterator), self._sections)
for taco in iterator:
try:
if taco[0][:4] in self._sections:
self.cmd[taco[0][:4]] = taco[0]
self.prm[taco[0][:4]] = taco[1:]
else:
self.comments.append(taco)
except IndexError:
pass
# discard empties
tmp = []
for key, value in self.prm.iteritems():
if not value:
tmp.append(key)
for key in tmp:
try:
del self.cmd[key]
except KeyError:
pass
try:
del self.prm[key]
except KeyError:
pass
# rename sections
def rename(old, new):
if old in self.cmd.keys():
self.cmd[new] = self.cmd[old]
del self.cmd[old]
self.prm[new] = self.prm[old]
del self.prm[old]
rename('thet', 'angl')
rename('phi', 'dihe')
rename('imph', 'impr')
rename('nonb', 'nbon')
# parse sections
self._parse('atom', MassPRM)
self._parse('bond', BondPRM)
self._parse('angl', AnglePRM)
self._parse('dihe', DihedralPRM)
self._parse('impr', ImproperPRM)
self._parse('nbon', NonBondPRM)
self._parse('nbfi', NBFixPRM)
# self._parse('hbon', HBondPRM) TODO -- implement HBondPRM objects in lib.toppar
self._parse_cmap()
def _build_models(self):
"""
Parse the crd section, and load the coordinates into :class:`Mol`
objects, one :class:`Mol` object per model section in the .pdb file.
"""
models = paragraphs(self.crd, splitter=["model"])
for model in models:
if model[0].startswith("model"):
modelNum = int(model[0].split()[1])
else:
modelNum = 0
iterator = (
Atom(text=line, informat=self.inFormat, index=i, autofix=self._autoFix)
for i, line in enumerate(model)
if line.startswith(("atom", "hetatm"))
)
self._mols["model%02d" % modelNum] = Mol(
iterable=iterator, name="model%d" % modelNum, code=self.code, autofix=True
)
def getProp(iterable, *props, **kwargs):
"""
Returns a dictionary whose keys are the requested properties, and
whose values are list(prop(t)). Two key/value pairs are created
per property: propX and propX_time.
Usage: getProp(iterable,props*)
Example:
>>> getProp(open('charmm.out'),'averener','dynavdw')
Each prop is of the form prefixsuffix, for example 'avertote'
Valid prefixes are:
['dyna','aver','fluc','lave','lflc']
Valid suffixes are:
['ener','hbon','volu','dihe','virk','vire','hfct','tote',
'totk','presse','pressi','ehfc','asp','hfck','step','user',
'urey','grms','impr','elec','vdw','temp','angl','time','viri',
'bond']
Valid kwargs:
`stopIter` = int
"""
props = [prop.lower() for prop in props]
assert len(props) >= 1
# Make sure properties are valid
propList = []
for prop in props:
propList.append(parse_prop(prop))
# kwargs
if "stopIter" in kwargs.keys():
stopIter = int(kwargs["stopIter"])
else:
stopIter = None
# Initialize Lists
outDict = {}
for prop in propList:
outDict["%s_time" % prop[0]] = []
outDict[prop[0]] = []
stepIterator = paragraphs(iterable, ["DYNA>", " DYNA>"])
stepIterator.next() # Discard Header
stepIterator.next() # Discard Step 0
# Do Work
for i, step in enumerate(stepIterator):
if stopIter:
if i >= stopIter:
return outDict
subSteps = paragraphs(step, [" ----------"])
for subStep in subSteps:
# Strip extraneous lines
tmp = [line for line in subStep if not line.startswith(" ")]
# Ignore empty blocks
if tmp:
# Ignore label block
if tmp[0].startswith("AVER DYN"):
continue
tmpSuffix = tmp[0][0:4].lower()
for prop in propList:
if prop[1] == tmpSuffix:
lineNum, start, stop = propSuffixes[prop[2]]
outDict["%s_time" % prop[0]].append(i + 1)
outDict[prop[0]].append(float(tmp[lineNum][start:stop]))
return outDict
