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add unit tests for phosphorus atomtype
Unit test for phosphorus atomtype, test_phosphorus_types, is added. This tests all phosphorus atomtypes.
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‎rmgpy/molecule/atomtypeTest.py‎

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@@ -506,6 +506,110 @@ def setUp(self):
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self.mol79 = Molecule().from_adjacency_list('''1 H u0 p0 c0 {2,S}
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2 Br u0 p3 c0 {1,S}''')
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self.mol80 = Molecule().from_adjacency_list('''1 P u0 p3 c-2 {2,S}
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2 P u0 p0 c+1 {1,S} {3,T}
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3 P u0 p0 c+1 {2,T} {4,S}
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4 H u0 p0 c0 {3,S}''')
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self.mol81 = Molecule().from_adjacency_list('''1 P u0 p2 c0 {2,S}
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2 H u0 p0 c0 {1,S}''')
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self.mol82 = Molecule().from_adjacency_list('''1 P u0 p2 c-1 {2,S} {3,S}
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2 H u0 p0 c0 {1,S}
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3 P u0 p0 c+1 {1,S} {4,T}
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4 C u0 p0 c0 {3,T} {5,S}
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5 H u0 p0 c0 {4,S}''')
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self.mol83 = Molecule().from_adjacency_list('''1 H u0 p0 {3,S}
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2 H u0 p0 {3,S}
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3 P u0 p0 c+1 {1,S} {2,S} {4,D}
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4 P u0 p2 c-1 {3,D}''')
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self.mol84 = Molecule().from_adjacency_list('''1 P u0 p1 c0 {4,S} {7,S} {8,S}
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2 P u0 p1 c0 {3,D} {4,S}
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3 O u0 p2 c0 {2,D}
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4 C u0 p0 c0 {1,S} {2,S} {5,S} {6,S}
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5 H u0 p0 c0 {4,S}
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6 H u0 p0 c0 {4,S}
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7 H u0 p0 c0 {1,S}
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8 H u0 p0 c0 {1,S}''')
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self.mol85 = Molecule().from_adjacency_list('''1 P u0 p1 c0 {2,T}
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2 C u0 p0 c0 {1,T} {3,S}
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3 H u0 p0 c0 {2,S}''')
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self.mol86 = Molecule().from_adjacency_list('''1 P u0 p0 c+1 {2,B} {6,B} {7,S}
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2 C u0 p0 {1,B} {3,B} {8,S}
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3 C u0 p0 {2,B} {4,B} {9,S}
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4 C u0 p0 {3,B} {5,B} {10,S}
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5 C u0 p0 {4,B} {6,B} {11,S}
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6 P u0 p1 {1,B} {5,B}
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7 O u0 p3 c-1 {1,S}
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8 H u0 p0 {2,S}
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9 H u0 p0 {3,S}
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10 H u0 p0 {4,S}
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11 H u0 p0 {5,S}''')
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self.mol87 = Molecule().from_adjacency_list('''1 P u0 p0 c0 {2,S} {3,S} {4,S} {5,S} {6,S}
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2 Cl u0 p3 c0 {1,S}
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3 Cl u0 p3 c0 {1,S}
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4 Cl u0 p3 c0 {1,S}
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5 Cl u0 p3 c0 {1,S}
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6 Cl u0 p3 c0 {1,S}''')
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self.mol88 = Molecule().from_adjacency_list('''1 P u0 p0 c+1 {2,S} {3,S} {4,S} {5,S}
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2 O u0 p2 c0 {1,S} {6,S}
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3 O u0 p3 c-1 {1,S}
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4 H u0 p0 c0 {1,S}
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5 H u0 p0 c0 {1,S}
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6 H u0 p0 c0 {2,S}''')
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self.mol89 = Molecule().from_adjacency_list('''1 P u0 p0 c0 {2,S} {3,S} {4,S} {5,D}
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2 O u0 p2 c0 {1,S} {6,S}
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3 O u0 p2 c0 {1,S} {7,S}
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4 O u0 p2 c0 {1,S} {8,S}
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5 O u0 p2 c0 {1,D}
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6 H u0 p0 c0 {2,S}
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7 H u0 p0 c0 {3,S}
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8 H u0 p0 c0 {4,S}''')
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self.mol90 = Molecule().from_adjacency_list('''1 P u0 p0 c0 {2,D} {3,D} {4,S}
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2 O u0 p2 c0 {1,D}
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3 O u0 p2 c0 {1,D}
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4 C u0 p0 c0 {1,S} {5,S} {6,S} {7,S}
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5 H u0 p0 c0 {4,S}
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6 H u0 p0 c0 {4,S}
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7 H u0 p0 c0 {4,S}''')
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self.mol91 = Molecule().from_adjacency_list('''1 P u0 p0 c+1 {2,D} {3,D}
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2 N u0 p2 c-1 {1,D}
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3 C u0 p0 c0 {1,D} {4,S} {5,S}
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4 H u0 p0 c0 {3,S}
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5 H u0 p0 c0 {3,S}''')
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self.mol92 = Molecule().from_adjacency_list('''1 P u0 p0 c0 {2,T} {3,S} {4,S}
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2 N u0 p1 c0 {1,T}
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3 Cl u0 p3 c0 {1,S}
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4 Cl u0 p3 c0 {1,S}''')
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self.mol93 = Molecule().from_adjacency_list('''1 P u0 p0 c0 {2,D} {3,T}
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2 O u0 p2 c0 {1,D}
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3 C u0 p0 c0 {1,T} {4,S}
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4 H u0 p0 c0 {3,S}''')
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self.mol94 = Molecule().from_adjacency_list('''1 P u0 p0 {2,B} {6,B} {7,D}
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2 C u0 p0 {1,B} {3,B} {8,S}
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3 C u0 p0 {2,B} {4,B} {9,S}
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4 C u0 p0 {3,B} {5,B} {10,S}
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5 C u0 p0 {4,B} {6,B} {11,S}
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6 C u0 p0 {1,B} {5,B} {12,S}
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7 S u0 p2 {1,D}
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8 H u0 p0 {2,S}
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9 H u0 p0 {3,S}
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10 H u0 p0 {4,S}
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11 H u0 p0 {5,S}
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12 H u0 p0 {6,S}''')
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def atom_type(self, mol, atom_id):
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atom = mol.atoms[atom_id]
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atom_type = get_atomtype(atom, mol.get_bonds(atom))
@@ -590,6 +694,30 @@ def test_silicon_types(self):
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self.assertEqual(self.atom_type(self.mol4, 4), 'Sidd')
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self.assertEqual(self.atom_type(self.mol4, 7), 'Sit') # todo: add in Siq unit test?
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def test_phosphorus_types(self):
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"""
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Test that get_atomtype() returns appropriate phosphorus atom types.
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"""
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self.assertEqual(self.atom_type(self.mol80, 0), 'P0sc')
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self.assertEqual(self.atom_type(self.mol81, 0), 'P1s')
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self.assertEqual(self.atom_type(self.mol82, 0), 'P1sc')
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self.assertEqual(self.atom_type(self.mol83, 3), 'P1dc')
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self.assertEqual(self.atom_type(self.mol84, 0), 'P3s')
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self.assertEqual(self.atom_type(self.mol84, 1), 'P3d')
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self.assertEqual(self.atom_type(self.mol85, 0), 'P3t')
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self.assertEqual(self.atom_type(self.mol86, 5), 'P3b')
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self.assertEqual(self.atom_type(self.mol87, 0), 'P5s')
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self.assertEqual(self.atom_type(self.mol88, 0), 'P5sc')
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self.assertEqual(self.atom_type(self.mol89, 0), 'P5d')
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self.assertEqual(self.atom_type(self.mol90, 0), 'P5dd')
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self.assertEqual(self.atom_type(self.mol83, 2), 'P5dc')
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self.assertEqual(self.atom_type(self.mol91, 0), 'P5ddc')
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self.assertEqual(self.atom_type(self.mol92, 0), 'P5t')
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self.assertEqual(self.atom_type(self.mol93, 0), 'P5td')
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self.assertEqual(self.atom_type(self.mol80, 1), 'P5tc')
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self.assertEqual(self.atom_type(self.mol86, 0), 'P5b')
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self.assertEqual(self.atom_type(self.mol94, 0), 'P5bd')
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def test_sulfur_types(self):
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"""
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Test that get_atomtype() returns appropriate sulfur atom types.

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