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 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()
