def test_xyz_to_pybel_mol(self):
"""Test xyz conversion into Open Babel"""
pbmol1 = converter.xyz_to_pybel_mol(self.xyz1)
pbmol2 = converter.xyz_to_pybel_mol(self.xyz2)
pbmol3 = converter.xyz_to_pybel_mol(self.xyz3)
pbmol4 = converter.xyz_to_pybel_mol(self.xyz4)
# These tests check that the atoms we expect appear in the correct order:
self.assertEqual(pbmol1.atoms[0].idx, 1) # C
self.assertAlmostEqual(pbmol1.atoms[0].atomicmass, 12.0107, 2)
self.assertEqual(pbmol1.atoms[0].coords, (0.0, 0.0, 0.0))
self.assertAlmostEqual(pbmol1.atoms[1].atomicmass, 1.00794, 2) # H
self.assertEqual(pbmol1.atoms[1].coords,
(0.6300326, 0.6300326, 0.6300326))
self.assertAlmostEqual(pbmol2.atoms[0].atomicmass, 15.9994, 2) # O
self.assertEqual(pbmol2.atoms[0].coords, (1.1746411, -0.15309781, 0.0))
self.assertAlmostEqual(pbmol2.atoms[1].atomicmass, 14.0067, 2) # N
self.assertEqual(pbmol2.atoms[1].coords, (0.06304988, 0.35149648, 0.0))
self.assertAlmostEqual(pbmol2.atoms[2].atomicmass, 12.0107, 2) # C
self.assertEqual(pbmol2.atoms[2].coords,
(-1.12708952, -0.11333971, 0.0))
self.assertAlmostEqual(pbmol2.atoms[3].atomicmass, 1.00794, 2) # H
self.assertEqual(pbmol2.atoms[3].coords,
(-1.93800144, 0.60171738, 0.0))
self.assertAlmostEqual(pbmol3.atoms[0].atomicmass, 32.065, 2) # S
self.assertEqual(pbmol3.atoms[0].coords,
(1.02558264, -0.04344404, -0.07343859))
self.assertAlmostEqual(pbmol3.atoms[1].atomicmass, 15.9994, 2) # O
self.assertEqual(pbmol3.atoms[1].coords,
(-0.25448248, 1.10710477, 0.18359696))
self.assertAlmostEqual(pbmol3.atoms[2].atomicmass, 14.0067, 2) # N
self.assertEqual(pbmol3.atoms[2].coords,
(-1.30762173, 0.15796567, -0.1048929))
self.assertAlmostEqual(pbmol3.atoms[3].atomicmass, 12.0107, 2) # C
self.assertEqual(pbmol3.atoms[3].coords,
(-0.49011438, -1.0370438, 0.15365747))
self.assertAlmostEqual(pbmol3.atoms[-1].atomicmass, 1.00794, 2) # H
self.assertEqual(pbmol3.atoms[-1].coords,
(-1.43009127, 0.23517346, -1.11797908))
self.assertAlmostEqual(pbmol4.atoms[0].atomicmass, 32.065, 2) # S
self.assertEqual(pbmol4.atoms[0].coords,
(-0.06618943, -0.12360663, -0.07631983))
self.assertAlmostEqual(pbmol4.atoms[3].atomicmass, 14.0067, 2) # N
self.assertEqual(pbmol4.atoms[3].coords,
(0.01546439, -1.54297548, 0.44580391))
def test_pybel_to_inchi(self):
"""Tests the conversion of Open Babel molecules to InChI"""
pbmol1 = converter.xyz_to_pybel_mol(self.xyz1)
pbmol2 = converter.xyz_to_pybel_mol(self.xyz2)
pbmol3 = converter.xyz_to_pybel_mol(self.xyz3)
pbmol4 = converter.xyz_to_pybel_mol(self.xyz4)
inchi1 = converter.pybel_to_inchi(pbmol1)
inchi2 = converter.pybel_to_inchi(pbmol2)
inchi3 = converter.pybel_to_inchi(pbmol3)
inchi4 = converter.pybel_to_inchi(pbmol4)
self.assertEqual(inchi1, 'InChI=1/CH4/h1H4')
self.assertEqual(inchi2, 'InChI=1/CH2NO/c1-2-3/h1H2')
self.assertEqual(inchi3, 'InChI=1/CH3NOS/c1-2-3-4-1/h2H,1H2')
self.assertEqual(inchi4, 'InChI=1/CH5NO2S/c1-5(2,3)4/h2-3H,1H3')