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 _partitions(self):
"""
Partition the file into _header/_crd/_footer sections.
"""
iterator = (line for line in cleanStrings(open(self.filename)))
# Populate header
self._header = []
tmp = None
for line in iterator:
if line.startswith(("atom", "hetatm", "model")):
tmp = line
break
else:
self._header.append(line)
# Populate coordinates
if tmp is None:
self._crd = []
else:
self._crd = [tmp]
tmp = None
for line in iterator:
if not line.startswith(("atom", "anisou", "hetatm", "model", "ter", "endmdl")):
tmp = line
break
else:
self._crd.append(line)
# Populate footer
if tmp is None:
self._footer = []
else:
self._footer = [tmp]
for line in iterator:
self._footer.append(line)
def _partition(self):
inHeader = False
inCrd = False
inBonds = False
iterator = ( line for line in cleanStrings(open(self.filename) ))
self._header = []
self._crd = []
self._bondstext = []
for line in iterator:
if not line:
continue
if line.startswith('@<tripos>'):
sectionName = line[9:].strip()
if sectionName == 'molecule':
inHeader = True
inCrd = False
inBonds = False
if self._header:
raise('Multiple header sections')
elif sectionName == 'atom':
inHeader = False
inCrd = True
inBonds = False
elif sectionName == 'bond':
if not self._crd:
raise('')
inHeader = False
inCrd = False
inBonds = True
else:
# Throw away other sections
inHeader = False
inCrd = False
inBonds = False
else:
if inHeader:
self._header.append(line)
elif inCrd:
self._crd.append(line)
elif inBonds:
self._bondstext.append(line)