def convert_molecule_to_molmod(molecule):
molModMolecule = Molecule(molecule.numbers,
molecule.coordinates,
molecule.label,
symbols=molecule.symbols)
molModMolecule.set_default_graph()
return molModMolecule
def test_one(xyz_fn, checks, reorder=False):
mol = Molecule.from_file(xyz_fn)
mol.set_default_graph()
zmat_gen = ZMatrixGenerator(mol.graph)
if reorder is False:
self.assertArraysEqual(zmat_gen.new_index, numpy.arange(mol.size))
self.assertArraysEqual(zmat_gen.old_index, numpy.arange(mol.size))
zmat0 = zmat_gen.cart_to_zmat(mol.coordinates)
for field, index, value in checks:
self.assertAlmostEqual(zmat0[field][index], value, 2, "%s:%i %f!=%f" % (field,index,zmat0[field][index],value))
numbers0, coordinates0 = zmat_to_cart(zmat0)
mol0 = Molecule(numbers0, coordinates0)
mol0.write_to_file("output/zmat_%s" % os.path.basename(xyz_fn))
mol0.set_default_graph()
zmat_gen0 = ZMatrixGenerator(mol0.graph)
self.assertArraysEqual(zmat_gen0.new_index, numpy.arange(mol.size))
self.assertArraysEqual(zmat_gen0.old_index, numpy.arange(mol.size))
zmat1 = zmat_gen0.cart_to_zmat(mol0.coordinates)
for field, index, value in checks:
self.assertAlmostEqual(zmat1[field][index], value, 2, "%s:%i %f!=%f" % (field,index,zmat1[field][index],value))
numbers1, coordinates1 = zmat_to_cart(zmat1)
self.assertArraysEqual(numbers0, numbers1)
self.assertArraysAlmostEqual(coordinates0, coordinates1, 1e-5)
