def _check_topology(self):
'''
Check wether all topology information (bonds, bends, dihedrals,
out-of-plane patterns and neighborlist) is present and complete if
necessary.
'''
assert self.numbers is not None
if self.bonds is None:
molecule = Molecule(self.numbers, coordinates=self.ref.coords)
graph = MolecularGraph.from_geometry(molecule)
psf = PSFFile()
psf.add_molecule(molecule)
self.bonds = np.array(psf.bonds)
self.bends = np.array(psf.bends)
self.diheds = np.array(psf.dihedrals)
self.opdists = find_opdist_patterns(graph)
self.nlist = graph.neighbors
else:
graph = MolecularGraph(self.bonds, self.numbers)
psf = PSFFile()
psf.add_molecular_graph(graph)
if self.bends is None:
self.bends = np.array(psf.bends)
if self.diheds is None:
self.diheds = np.array(psf.dihedrals)
if self.opdists is None:
self.opdists = find_opdist_patterns(graph)
if self.nlist is None:
self.nlist = graph.neighbors
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")
def test_dump(self):
m = XYZFile("input/thf.xyz").get_molecule()
psf = PSFFile()
psf.add_molecule(m)
psf.write_to_file("output/thf.psf")