def test_reader2(self):
sdf_reader = SDFReader("input/CID_22898828.sdf")
mol = sdf_reader.next()
self.assertEqual(mol.title, "22898828")
self.assertEqual(mol.size, 14)
self.assertEqual(len(mol.graph.edges), 13)
self.assert_(frozenset([4,6]) in mol.graph.edges)
self.assertEqual(len(mol.graph.independent_vertices), 1)
self.assertAlmostEqual(mol.coordinates[0,0]/angstrom, 6.8671)
self.assertAlmostEqual(mol.coordinates[9,1]/angstrom, 0.2500)
self.assertAlmostEqual(mol.coordinates[13,0]/angstrom, 12.6002)
self.assert_((mol.formal_charges[:12]==-1).all())
self.assert_((mol.formal_charges[12:]==0).all())
def test_reader2(self):
sdf_reader = SDFReader("input/CID_22898828.sdf")
mol = sdf_reader.next()
self.assertEqual(mol.title, "22898828")
self.assertEqual(mol.size, 14)
self.assertEqual(len(mol.graph.pairs), 13)
self.assert_(frozenset([4, 6]) in mol.graph.pairs)
self.assertEqual(len(mol.graph.independent_nodes), 1)
self.assertAlmostEqual(mol.coordinates[0, 0] / angstrom, 6.8671)
self.assertAlmostEqual(mol.coordinates[9, 1] / angstrom, 0.2500)
self.assertAlmostEqual(mol.coordinates[13, 0] / angstrom, 12.6002)
self.assert_((mol.formal_charges[:12] == -1).all())
self.assert_((mol.formal_charges[12:] == 0).all())
def test_fingerprint_collisions(self):
# 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 = SDFReader(os.path.join("input", fn0)).next().graph
g1 = SDFReader(os.path.join("input", fn1)).next().graph
self.assertNotEqual(str(g0.fingerprint.data),
str(g1.fingerprint.data))
def test_reader(self):
sdf_reader = SDFReader("input/example.sdf")
mol = sdf_reader.next()
self.assertEqual(mol.title, "24978498")
self.assertEqual(mol.size, 16)
self.assertEqual(len(mol.graph.edges), 15)
self.assert_(frozenset([1,14]) in mol.graph.edges)
self.assertAlmostEqual(mol.coordinates[0,0]/angstrom, 2.8660)
self.assertAlmostEqual(mol.coordinates[4,1]/angstrom, -1.9400)
self.assertAlmostEqual(mol.coordinates[15,1]/angstrom, -2.5600)
mol = sdf_reader.next()
self.assertEqual(mol.title, "24978481")
self.assertEqual(mol.size, 21)
self.assertEqual(len(mol.graph.edges), 19)
self.assert_(frozenset([3,9]) in mol.graph.edges)
self.assertEqual(len(mol.graph.independent_vertices), 2)
self.assertAlmostEqual(mol.coordinates[0,0]/angstrom, 2.2690)
self.assertAlmostEqual(mol.coordinates[9,1]/angstrom, 2.5790)
self.assertAlmostEqual(mol.coordinates[20,0]/angstrom, 1.7130)
try:
sdf_reader.next()
self.fail("Expecting a StopIteration.")
except StopIteration:
pass
def iter_molecules(self, allow_multi=False):
xyz_fns = [
"water.xyz",
"cyclopentane.xyz",
"ethene.xyz",
"funny.xyz",
"tea.xyz",
"tpa.xyz",
"thf_single.xyz",
"precursor.xyz",
"butane.xyz",
"octane.xyz",
]
for xyz_fn in xyz_fns:
molecule = self.load_molecule(xyz_fn)
if allow_multi or len(molecule.graph.independent_nodes) == 1:
molecule.title = xyz_fn[:-4]
yield molecule
sdf_fns = [
"example.sdf",
"CID_22898828.sdf",
"SID_55127927.sdf",
"SID_56274343.sdf",
"SID_40363570.sdf",
"SID_40363571.sdf",
"SID_31646548.sdf",
"SID_31646545.sdf",
"SID_41893278.sdf",
"SID_41893280.sdf",
"SID_54258192.sdf",
"SID_55488598.sdf",
]
for sdf_fn in sdf_fns:
for i, molecule in enumerate(
SDFReader(os.path.join("input", sdf_fn))):
if allow_multi or len(molecule.graph.independent_nodes) == 1:
molecule.title = "%s_%i" % (sdf_fn[:-4], i)
yield molecule
def test_reader(self):
sdf_reader = SDFReader("input/example.sdf")
mol = sdf_reader.next()
self.assertEqual(mol.title, "24978498")
self.assertEqual(mol.size, 16)
self.assertEqual(len(mol.graph.pairs), 15)
self.assert_(frozenset([1, 14]) in mol.graph.pairs)
self.assertAlmostEqual(mol.coordinates[0, 0] / angstrom, 2.8660)
self.assertAlmostEqual(mol.coordinates[4, 1] / angstrom, -1.9400)
self.assertAlmostEqual(mol.coordinates[15, 1] / angstrom, -2.5600)
mol = sdf_reader.next()
self.assertEqual(mol.title, "24978481")
self.assertEqual(mol.size, 21)
self.assertEqual(len(mol.graph.pairs), 19)
self.assert_(frozenset([3, 9]) in mol.graph.pairs)
self.assertEqual(len(mol.graph.independent_nodes), 2)
self.assertAlmostEqual(mol.coordinates[0, 0] / angstrom, 2.2690)
self.assertAlmostEqual(mol.coordinates[9, 1] / angstrom, 2.5790)
self.assertAlmostEqual(mol.coordinates[20, 0] / angstrom, 1.7130)
try:
sdf_reader.next()
self.fail("Expecting a StopIteration.")
except StopIteration:
pass