def get_molecules(self):
tpa = Molecule.from_file("input/tpa.xyz")
tea = Molecule.from_file("input/tea.xyz")
water = Molecule.from_file("input/water.xyz")
cyclopentane = Molecule.from_file("input/cyclopentane.xyz")
return [tpa, tea, water, cyclopentane]
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_zirconium(self):
mol = Molecule.from_file('input/oh3siozroh3.xyz')
mol.set_default_graph()
assert len(mol.graph.edges)==14
mol = Molecule.from_file('input/osih2osihosih2osih2ozrh2oh.xyz')
mol.set_default_graph()
assert len(mol.graph.edges)==21
mol = Molecule.from_file('input/h3zrosihohosioh3.xyz')
mol.set_default_graph()
assert len(mol.graph.edges)==16
mol = Molecule.from_file('input/zr4o8-3.xyz')
mol.set_default_graph()
assert len(mol.graph.edges)==12
def test_fingerprint_collisions(self):
raise SkipTest
# These are collisions with older versions, found by scanning the
# pubchem database.
cases = [
('SID_55127927.sdf', 'SID_56274343.sdf'),
('SID_55488598.sdf', 'SID_54258192.sdf'),
('SID_41893280.sdf', 'SID_41893278.sdf'),
('SID_40363570.sdf', 'SID_40363571.sdf'),
('SID_31646548.sdf', 'SID_31646545.sdf')
]
for fn0, fn1 in cases:
g0 = Molecule.from_file(os.path.join("input", fn0)).graph
g1 = Molecule.from_file(os.path.join("input", fn1)).graph
self.assertNotEqual(str(g0.fingerprint.data), str(g1.fingerprint.data))
def test_consistency(self):
molecules = [
Molecule.from_file("input/cyclopentane.xyz"),
Molecule.from_file("input/funny.xyz"),
]
for m in molecules:
m.set_default_graph()
dump_cml("output/tmp.cml", molecules)
check = load_cml("output/tmp.cml")
for m1, m2 in zip(molecules, check):
self.assertEqual(m1.title, m2.title)
self.assert_((m1.numbers==m2.numbers).all())
self.assert_((m1.coordinates==m2.coordinates).all())
self.assertEqual(m1.graph.num_vertices, m2.graph.num_vertices)
self.assertEqual(set(m1.graph.edges), set(m2.graph.edges))
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_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)
def setup(filename="ethane.pdb"):
mol = Molecule.from_file(filename)
# setup stuff
mol.set_default_graph()
mol.set_default_symbols()
return mol
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_example_periodic(self):
mol = Molecule.from_file("input/caplayer.cml")
unit_cell = UnitCell(
numpy.array([
[14.218, 7.109, 0.0],
[ 0.0 , 12.313, 0.0],
[ 0.0 , 0.0 , 10.0],
])*angstrom,
numpy.array([True, True, False]),
)
dm = mol.distance_matrix
dm = dm + dm.max()*numpy.identity(len(dm))
mol = tune_geometry(mol.graph, mol, unit_cell)
mol.write_to_file("output/caplayer.xyz")
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 load_molecule(self, fn):
molecule = Molecule.from_file(os.path.join("input", fn))
if molecule.graph is None:
molecule.set_default_graph()
return molecule
def test_rotsym_ethane(self):
molecule = Molecule.from_file("input/ethane.xyz")
molecule.set_default_graph()
rotsym = compute_rotsym(molecule, molecule.graph, threshold=0.01)
self.assertEqual(rotsym, 6)
def test_rotsym_cyclopentane(self):
molecule = Molecule.from_file("input/cyclopentane.xyz")
molecule.set_default_graph()
rotsym = compute_rotsym(molecule, molecule.graph)
self.assertEqual(rotsym, 1)
def iter_test_molecules(self):
for filename in ["tpa.xyz", "water.xyz", "thf_single.xyz"]:
molecule = Molecule.from_file(os.path.join("input", filename))
molecule.filename = filename
molecule.set_default_graph()
yield molecule
