def test_tetra(self):
molecule = Molecule.from_file("input/tetra.xyz")
psf = PSFFile()
psf.add_molecule(molecule)
self.assert_(psf.bonds.shape[0] == 4)
self.assert_(psf.bends.shape[0] == 6)
psf.write_to_file("output/tetra.psf")
def test_tetra(self):
molecule = XYZFile("input/tetra.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(molecule)
self.assert_(psf.bonds.shape[0] == 4)
self.assert_(psf.bends.shape[0] == 6)
psf.write_to_file("output/tetra.psf")
def test_many_separate(self):
psf = PSFFile()
molecule = Molecule.from_file("input/ethene.xyz")
psf.add_molecule(molecule)
psf.add_molecule(molecule)
molecule = Molecule.from_file("input/tea.xyz")
psf.add_molecule(molecule)
psf.write_to_file("output/many_separate.psf")
def test_many_separate(self):
psf = PSFFile()
molecule = XYZFile("input/ethene.xyz").get_molecule()
psf.add_molecule(molecule)
psf.add_molecule(molecule)
molecule = XYZFile("input/tea.xyz").get_molecule()
psf.add_molecule(molecule)
psf.write_to_file("output/many_separate.psf")
def test_improper(self):
molecule = Molecule.from_file("input/formol.xyz")
psf = PSFFile()
psf.add_molecule(molecule)
self.assertEqual(psf.impropers.shape, (3,4))
test_block = set([(row[0], row[1]) for row in psf.impropers])
self.assert_((0,1) in test_block)
self.assert_((0,2) in test_block)
self.assert_((0,3) in test_block)
psf.write_to_file("output/tmp_impropers.psf")
psf2 = PSFFile("output/tmp_impropers.psf")
self.assertArraysEqual(psf.impropers, psf2.impropers)
def test_dump(self):
m = Molecule.from_file("input/thf.xyz")
psf = PSFFile()
psf.add_molecule(m)
psf.write_to_file("output/thf.psf")
def test_dump(self):
m = XYZFile("input/thf.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(m)
psf.write_to_file("output/thf.psf")
CC30A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,6))
CC31A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,1))
CC32A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,1,1))
CC33A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,1,1,1))
atom_filters = {
"CC30A": CC30A,
"CC31A": CC31A,
"CC32A": CC32A,
"CC33A": CC33A,
"HCA1": CritAnd(HasAtomNumber(1), HasNeighbors(CC31A)),
"HCA2": CritAnd(HasAtomNumber(1), HasNeighbors(CC32A)),
"HCA3": CritAnd(HasAtomNumber(1), HasNeighbors(CC33A)),
}
def get_atom_type(index, graph):
for atom_type, atom_filter in atom_filters.items():
if atom_filter(index, graph):
return atom_type
raise ValueError("Unrecognized atom (index %i)." % index)
args = sys.argv[1:]
molecule = XYZFile(args[0]).get_molecule()
graph = MolecularGraph.from_geometry(molecule)
atom_types = [get_atom_type(index, graph) for index in range(molecule.size)]
psf = PSFFile()
psf.add_molecular_graph(graph, atom_types=atom_types)
psf.write_to_file(args[0].replace(".xyz", ".psf"))
CC30A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,6))
CC31A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,6,1))
CC32A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,6,1,1))
CC33A = CritAnd(HasAtomNumber(6), HasNeighborNumbers(6,1,1,1))
atom_filters = {
"CC30A": CC30A,
"CC31A": CC31A,
"CC32A": CC32A,
"CC33A": CC33A,
"HCA1": CritAnd(HasAtomNumber(1), HasNeighbors(CC31A)),
"HCA2": CritAnd(HasAtomNumber(1), HasNeighbors(CC32A)),
"HCA3": CritAnd(HasAtomNumber(1), HasNeighbors(CC33A)),
}
def get_atom_type(index, graph):
for atom_type, atom_filter in atom_filters.iteritems():
if atom_filter(index, graph):
return atom_type
raise ValueError("Unrecognized atom (index %i)." % index)
args = sys.argv[1:]
molecule = XYZFile(args[0]).get_molecule()
graph = MolecularGraph.from_geometry(molecule)
atom_types = [get_atom_type(index, graph) for index in xrange(molecule.size)]
psf = PSFFile()
psf.add_molecular_graph(graph, atom_types=atom_types)
psf.write_to_file(args[0].replace(".xyz", ".psf"))
def test_dump(self):
m = XYZFile("input/thf.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(m)
psf.write_to_file("output/thf.psf")
