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_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 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