def _get_OPT_XYZ(self):
coordinateLines = re.compile("Standard orientation.*?X.*?Z(.*?)Rotational constants", re.DOTALL).findall(self.fileText)
allCoordinates = []
for entry in coordinateLines:
allCoordinates.append([])
xyzArray = entry.splitlines()[2:-2]
for line in xyzArray:
[number, atomicNumber, x, y, z] = map(eval, line.strip().split())
from Molecules import getAtomFromInfo
atomName = getAtomFromInfo("ATOMIC NUMBER", atomicNumber)
allCoordinates[-1].append([atomName, x, y, z])
return allCoordinates
def _get_INITIAL_XYZ(self):
coordinateLines = re.compile("Standard orientation.*?X.*?Z(.*?)Rotational constants", re.DOTALL).search(self.fileText).groups()[0].strip().splitlines()[1:-1]
geom = []
atoms = []
for line in coordinateLines:
values = map(eval, line.strip().split())
atomicNumber = values[1]
xyz = values[-3:]
from Molecules import getAtomFromInfo
atomName = getAtomFromInfo("ATOMIC NUMBER", atomicNumber)
geom.append(xyz)
atoms.append(atomName)
return atoms, geom