Esempio n. 1
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 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())
Esempio n. 2
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 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))
Esempio n. 4
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 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
Esempio n. 6
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 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