def _getAlignmentOperations(molecule): # fold>>
xyz_mol = molecule.createXYZMolecule()
center_of_mass = XYZMolecule.centerOfMass(xyz_mol)
xyz_mol.translate(-center_of_mass)
moments_of_inertia = XYZMolecule.momentsOfInertia(xyz_mol)
# we multiply the eigenvectors by -1 if needed.
# we want to keep the molecule oriented so that it does not change dramatically
# (ex. we don't want it to flip just because the diagonalization returned the
# inertial axis in the other direction)
v0 = numpy.array(moments_of_inertia[0][1].value())
if v0[0] < 0.0:
v0 = -v0
v1 = numpy.array(moments_of_inertia[1][1].value())
if v1[1] < 0.0:
v1 = -v1
v2 = numpy.array(moments_of_inertia[2][1].value())
if v2[2] < 0.0:
v2 = -v2
rotation = numpy.zeros((3, 3))
rotation[0, 0] = v0[0]
rotation[0, 1] = v0[1]
rotation[0, 2] = v0[2]
rotation[1, 0] = v1[0]
rotation[1, 1] = v1[1]
rotation[1, 2] = v1[2]
rotation[2, 0] = v2[0]
rotation[2, 1] = v2[1]
rotation[2, 2] = v2[2]
return (-center_of_mass, rotation)
def testCenterOfMass(self): # fold>>
mol = XYZMolecule.XYZMolecule( [
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,0.0000000000,0.0000000000 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,1.7920231678,-3.1038751750 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,4.0095495535,2.3149145141 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,6.3710924130,-3.1870231249 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,8.5886187987,2.2317665642 ), Units.bohr) ),
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,10.3806419665,-0.8721086108), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,1.7920231678,-1.0346250583 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,4.0095495535,0.2456643974 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,6.3710924130,-1.1177730082 ), Units.bohr) ),
(PeriodicTable.C, Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr) ),
]
)
center_of_mass = XYZMolecule.centerOfMass(mol)
self.assertAlmostEqual(center_of_mass.value()[0], 0.000000, 6)
self.assertAlmostEqual(center_of_mass.value()[1], 5.190321, 6)
self.assertAlmostEqual(center_of_mass.value()[2], -0.436054, 6)
def main(argv): # fold>>
options = _getOptions(argv)
infile = XYZFile.XYZFile(options.input_filename)
outfile = XYZFile.XYZFile()
for mol_idx in xrange(infile.numOfMolecules()):
atom_list = []
for atom_idx in xrange(infile.numOfAtoms(mol_idx)):
atom_list.append(infile.atom(mol_idx, atom_idx))
molecule = XYZMolecule.XYZMolecule(atom_list)
molecule.translate(-XYZMolecule.centerOfMass(molecule))
new_mol_index = outfile.createMolecule()
for atom in zip(molecule.elements(), molecule.atomPos()):
outfile.addAtom(new_mol_index,atom)
outfile.saveTo(options.output_filename)