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 testMoleculeCode(self):
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) ),
]
)
self.assertEqual(mol.moleculeCode(), "AA-T73FCFQ-ZCQX6AY")
mol2 = XYZMolecule.XYZMolecule( [
(PeriodicTable.H, Measure.Measure( ( 0.0000000000,0.0000000000,1.0000000000 ), 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) ),
]
)
self.assertNotEqual(mol.moleculeCode(), mol2.moleculeCode())
self.assertEqual(mol.moleculeCode()[0:10], mol2.moleculeCode()[0:10])
def testMomentsOfInertia(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) ),
]
)
inertia = XYZMolecule.momentsOfInertia(mol)
self.assertEqual(len(inertia), 3)
self.assertAlmostEqual(inertia[0][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 12.836878, 5)
self.assertAlmostEqual(inertia[1][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 110.58507, 5)
self.assertAlmostEqual(inertia[2][0].asUnit(Units.dalton * Units.angstrom * Units.angstrom).value(), 123.421950, 5)
self.assertAlmostEqual(inertia[0][1].value()[0], 0.0)
self.assertAlmostEqual(inertia[0][1].value()[1], 0.994406, 5)
self.assertAlmostEqual(inertia[0][1].value()[2], 0.105628, 5)
self.assertAlmostEqual(inertia[1][1].value()[0], 0.0)
self.assertAlmostEqual(inertia[1][1].value()[1], -0.105628, 5)
self.assertAlmostEqual(inertia[1][1].value()[2], 0.994406, 5)
self.assertAlmostEqual(inertia[2][1].value()[0], 1.0)
self.assertAlmostEqual(inertia[2][1].value()[1], 0.0, 5)
self.assertAlmostEqual(inertia[2][1].value()[2], 0.0, 5)
def testTranslate(self): # fold>>
mol = XYZMolecule.XYZMolecule([
(PeriodicTable.Carbon, Measure.Measure((1.0, 1.0, 0.0),
Units.bohr)),
(PeriodicTable.Oxygen, Measure.Measure((-1.0, 1.0, 0.0),
Units.bohr)),
(PeriodicTable.Nitrogen,
Measure.Measure((-1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Fluorine,
Measure.Measure((1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Hydrogen,
Measure.Measure((0.0, 0.0, 1.0), Units.bohr)),
])
mol.translate(Measure.Measure((2.0, 3.0, 4.0), Units.bohr))
self.assertEqual(mol.atomPos()[0].value(), (3.0, 4.0, 4.0))
self.assertEqual(mol.atomPos()[0].unit(), Units.bohr)
self.assertEqual(mol.atomPos()[1].value(), (1.0, 4.0, 4.0))
self.assertEqual(mol.atomPos()[1].unit(), Units.bohr)
self.assertEqual(mol.atomPos()[2].value(), (1.0, 2.0, 4.0))
self.assertEqual(mol.atomPos()[2].unit(), Units.bohr)
self.assertEqual(mol.atomPos()[3].value(), (3.0, 2.0, 4.0))
self.assertEqual(mol.atomPos()[3].unit(), Units.bohr)
self.assertEqual(mol.atomPos()[4].value(), (2.0, 3.0, 5.0))
self.assertEqual(mol.atomPos()[4].unit(), Units.bohr)
mol = XYZMolecule.XYZMolecule([
(PeriodicTable.Carbon, Measure.Measure((1.0, 1.0, 0.0),
Units.bohr)),
(PeriodicTable.Oxygen, Measure.Measure((-1.0, 1.0, 0.0),
Units.bohr)),
(PeriodicTable.Nitrogen,
Measure.Measure((-1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Fluorine,
Measure.Measure((1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Hydrogen,
Measure.Measure((0.0, 0.0, 1.0), Units.bohr)),
])
mol.translate(Measure.Measure((2.0, 3.0, 4.0), Units.angstrom))
self.assertNotEqual(mol.atomPos()[0].value(), (3.0, 4.0, 4.0))
self.assertEqual(mol.atomPos()[0].unit(), Units.bohr)
self.assertNotEqual(mol.atomPos()[1].value(), (1.0, 4.0, 4.0))
self.assertEqual(mol.atomPos()[1].unit(), Units.bohr)
self.assertNotEqual(mol.atomPos()[2].value(), (1.0, -2.0, 4.0))
self.assertEqual(mol.atomPos()[2].unit(), Units.bohr)
self.assertNotEqual(mol.atomPos()[3].value(), (3.0, -2.0, 4.0))
self.assertEqual(mol.atomPos()[3].unit(), Units.bohr)
self.assertNotEqual(mol.atomPos()[3].value(), (2.0, 3.0, 5.0))
self.assertEqual(mol.atomPos()[3].unit(), Units.bohr)
def testRotate(self): # fold>>
mol = XYZMolecule.XYZMolecule( [
(PeriodicTable.Carbon, Measure.Measure( (1.0, 1.0, 0.0), Units.bohr)),
(PeriodicTable.Oxygen, Measure.Measure( (-1.0, 1.0, 0.0), Units.bohr)),
(PeriodicTable.Nitrogen, Measure.Measure( (-1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Fluorine, Measure.Measure( (1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Hydrogen, Measure.Measure( (0.0, 0.0, 1.0), Units.bohr)),
]
)
mol.rotate( Measure.Measure( (0.0,0.0,1.0) ,Units.bohr), Measure.Measure(45.0, Units.degrees) )
self.assertAlmostEqual(mol.atomPos()[0].value()[0], 0.0)
self.assertAlmostEqual(mol.atomPos()[0].value()[1], math.sqrt(2.0))
self.assertAlmostEqual(mol.atomPos()[0].value()[2], 0.0)
self.assertEqual(mol.atomPos()[0].unit(), Units.bohr )
self.assertAlmostEqual(mol.atomPos()[1].value()[0], -math.sqrt(2.0))
self.assertAlmostEqual(mol.atomPos()[1].value()[1], 0.0)
self.assertAlmostEqual(mol.atomPos()[1].value()[2], 0.0)
self.assertEqual(mol.atomPos()[1].unit(), Units.bohr )
self.assertAlmostEqual(mol.atomPos()[2].value()[0], 0.0)
self.assertAlmostEqual(mol.atomPos()[2].value()[1], -math.sqrt(2.0))
self.assertAlmostEqual(mol.atomPos()[2].value()[2], 0.0)
self.assertEqual(mol.atomPos()[2].unit(), Units.bohr )
self.assertAlmostEqual(mol.atomPos()[3].value()[0], math.sqrt(2.0))
self.assertAlmostEqual(mol.atomPos()[3].value()[1], 0.0)
self.assertAlmostEqual(mol.atomPos()[3].value()[2], 0.0)
self.assertEqual(mol.atomPos()[3].unit(), Units.bohr )
def testXYZMolecule(self): # fold>>
mol = XYZMolecule.XYZMolecule( [
(PeriodicTable.Carbon, Measure.Measure((1.0, 1.0, 0.0), Units.bohr)),
(PeriodicTable.Oxygen, Measure.Measure((-1.0, 1.0, 0.0), Units.bohr)),
(PeriodicTable.Nitrogen, Measure.Measure((-1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Fluorine, Measure.Measure((1.0, -1.0, 0.0), Units.bohr)),
(PeriodicTable.Hydrogen, Measure.Measure((0.0, 0.0, 1.0), Units.bohr)),
]
)
self.assertEqual(len(mol.elements()), 5)
self.assertEqual(mol.elements()[0], PeriodicTable.Carbon)
self.assertEqual(mol.elements()[1], PeriodicTable.Oxygen)
self.assertEqual(mol.elements()[2], PeriodicTable.Nitrogen)
self.assertEqual(mol.elements()[3], PeriodicTable.Fluorine)
self.assertEqual(mol.elements()[4], PeriodicTable.Hydrogen)
self.assertEqual(len(mol.atomPos()), 5)
self.assertEqual(mol.atomPos()[0].__class__, Measure.Measure)
self.assertEqual(mol.atomPos()[1].__class__, Measure.Measure)
self.assertEqual(mol.atomPos()[2].__class__, Measure.Measure)
self.assertEqual(mol.atomPos()[3].__class__, Measure.Measure)
self.assertEqual(mol.atomPos()[4].__class__, Measure.Measure)
self.assertEqual(mol.atomPos()[0].value(), (1.0,1.0,0.0) )
self.assertEqual(mol.atomPos()[0].unit(), Units.bohr )
self.assertEqual(mol.atomPos()[1].value(), (-1.0,1.0,0.0) )
self.assertEqual(mol.atomPos()[1].unit(), Units.bohr )
self.assertEqual(mol.atomPos()[2].value(), (-1.0,-1.0,0.0) )
self.assertEqual(mol.atomPos()[2].unit(), Units.bohr )
self.assertEqual(mol.atomPos()[3].value(), (1.0,-1.0,0.0) )
self.assertEqual(mol.atomPos()[3].unit(), Units.bohr )
self.assertEqual(mol.atomPos()[4].value(), (0.0,0.0,1.0) )
self.assertEqual(mol.atomPos()[4].unit(), Units.bohr )
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 testFromGraph(self):
g = Graph.Graph()
elements = Infoset.Infoset(g, InfosetType.getElementType())
coords = Infoset.Infoset(g, InfosetType.getCoordsType())
e = g.createEntity()
elements.setValue(e, PeriodicTable.C)
coords.setValue(e,Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr))
e = g.createEntity()
elements.setValue(e, PeriodicTable.C)
coords.setValue(e,Measure.Measure( ( 0.0000000000,8.5886187987,0.1625164475 ), Units.bohr))
mol = XYZMolecule.fromGraph(g)
self.assertEqual(mol.__class__, XYZMolecule.XYZMolecule)
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)
def createXYZMolecule(self): # fold>>
atom_list = []
for element, coords in zip(self.elements_list, self.coordinates_list):
atom_list.append((element, coords))
return XYZMolecule.XYZMolecule(atom_list)