4075885785

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push

github

Committed by Shyue Ping Ong

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Merge branch 'master' of github.com:materialsproject/pymatgen

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/pymatgen/analysis/tests/test_molecule_structure_comparator.py

# Copyright (c) Pymatgen Development Team.
# Distributed under the terms of the MIT License.


from __future__ import annotations

import os
import unittest
from unittest import TestCase

from pymatgen.analysis.molecule_structure_comparator import MoleculeStructureComparator
from pymatgen.core.structure import Molecule
from pymatgen.util.testing import PymatgenTest

__author__ = "xiaohuiqu"


test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change")


class TestMoleculeStructureComparator(TestCase):
    def test_are_equal(self):
        msc1 = MoleculeStructureComparator()
        mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))
        mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))
        mol3 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))
        assert not msc1.are_equal(mol1, mol2)
        assert msc1.are_equal(mol2, mol3)
        thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))
        thio2 = Molecule.from_file(os.path.join(test_dir, "thiophene2.xyz"))
        # noinspection PyProtectedMember
        msc2 = MoleculeStructureComparator(priority_bonds=msc1._get_bonds(thio1))
        assert msc2.are_equal(thio1, thio2)
        hal1 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_1.xyz"))
        hal2 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_2.xyz"))
        msc3 = MoleculeStructureComparator(priority_bonds=msc1._get_bonds(hal1))
        assert msc3.are_equal(hal1, hal2)

    def test_get_bonds(self):
        mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))
        msc = MoleculeStructureComparator()
        # noinspection PyProtectedMember
        bonds = msc._get_bonds(mol1)
        bonds_ref = [
            (0, 1),
            (0, 2),
            (0, 3),
            (0, 23),
            (3, 4),
            (3, 5),
            (5, 6),
            (5, 7),
            (7, 8),
            (7, 9),
            (7, 21),
            (9, 10),
            (9, 11),
            (9, 12),
            (12, 13),
            (12, 14),
            (12, 15),
            (15, 16),
            (15, 17),
            (15, 18),
            (18, 19),
            (18, 20),
            (18, 21),
            (21, 22),
            (21, 23),
            (23, 24),
            (23, 25),
        ]
        assert bonds == bonds_ref
        mol2 = Molecule.from_file(os.path.join(test_dir, "MgBH42.xyz"))
        bonds = msc._get_bonds(mol2)
        assert bonds == [(1, 3), (2, 3), (3, 4), (3, 5), (6, 8), (7, 8), (8, 9), (8, 10)]
        msc = MoleculeStructureComparator(ignore_ionic_bond=False)
        bonds = msc._get_bonds(mol2)
        assert bonds == [
            (0, 1),
            (0, 2),
            (0, 3),
            (0, 5),
            (0, 6),
            (0, 7),
            (0, 8),
            (0, 9),
            (1, 3),
            (2, 3),
            (3, 4),
            (3, 5),
            (6, 8),
            (7, 8),
            (8, 9),
            (8, 10),
        ]

        mol1 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_1.xyz"))
        msc = MoleculeStructureComparator()
        # noinspection PyProtectedMember
        bonds = msc._get_bonds(mol1)
        assert bonds == [
            (0, 12),
            (0, 13),
            (0, 14),
            (0, 15),
            (1, 12),
            (1, 16),
            (1, 17),
            (1, 18),
            (2, 4),
            (2, 11),
            (2, 19),
            (3, 5),
            (3, 10),
            (3, 20),
            (4, 6),
            (4, 10),
            (5, 11),
            (5, 12),
            (6, 7),
            (6, 8),
            (6, 9),
        ]

    def test_to_and_from_dict(self):
        msc1 = MoleculeStructureComparator()
        d1 = msc1.as_dict()
        d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
        assert d1 == d2
        thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))
        # noinspection PyProtectedMember
        msc2 = MoleculeStructureComparator(bond_length_cap=0.2, priority_bonds=msc1._get_bonds(thio1), priority_cap=0.5)
        d1 = msc2.as_dict()
        d2 = MoleculeStructureComparator.from_dict(d1).as_dict()
        assert d1 == d2

    # def test_structural_change_in_geom_opt(self):
    #     qcout_path = os.path.join(test_dir, "mol_1_3_bond.qcout")
    #     qcout = QcOutput(qcout_path)
    #     mol1 = qcout.data[0]["molecules"][0]
    #     mol2 = qcout.data[0]["molecules"][-1]
    #     priority_bonds = [[0, 1], [0, 2], [1, 3], [1, 4], [1, 7], [2, 5], [2, 6], [2, 8], [4, 6], [4, 10], [6, 9]]
    #     msc = MoleculeStructureComparator(priority_bonds=priority_bonds)
    #     self.assertTrue(msc.are_equal(mol1, mol2))

    def test_get_13_bonds(self):
        priority_bonds = [
            [0, 1],
            [0, 2],
            [1, 3],
            [1, 4],
            [1, 7],
            [2, 5],
            [2, 6],
            [2, 8],
            [4, 6],
            [4, 10],
            [6, 9],
        ]
        bonds_13 = MoleculeStructureComparator.get_13_bonds(priority_bonds)
        ans = (
            (0, 3),
            (0, 4),
            (0, 5),
            (0, 6),
            (0, 7),
            (0, 8),
            (1, 2),
            (1, 6),
            (1, 10),
            (2, 4),
            (2, 9),
            (3, 4),
            (3, 7),
            (4, 7),
            (4, 9),
            (5, 6),
            (5, 8),
            (6, 8),
            (6, 10),
        )
        assert bonds_13 == tuple(ans)


if __name__ == "__main__":
    unittest.main()

1	# Copyright (c) Pymatgen Development Team.
2	# Distributed under the terms of the MIT License.
3
4
5	from __future__ import annotations	1✔
6
7	import os	1✔
8	import unittest	1✔
9	from unittest import TestCase	1✔
10
11	from pymatgen.analysis.molecule_structure_comparator import MoleculeStructureComparator	1✔
12	from pymatgen.core.structure import Molecule	1✔
13	from pymatgen.util.testing import PymatgenTest	1✔
14
15	__author__ = "xiaohuiqu"	1✔
16
17
18	test_dir = os.path.join(PymatgenTest.TEST_FILES_DIR, "molecules", "structural_change")	1✔
19
20
21	class TestMoleculeStructureComparator(TestCase):	1✔
22	def test_are_equal(self):	1✔
23	msc1 = MoleculeStructureComparator()	1✔
24	mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))	1✔
25	mol2 = Molecule.from_file(os.path.join(test_dir, "t2.xyz"))	1✔
26	mol3 = Molecule.from_file(os.path.join(test_dir, "t3.xyz"))	1✔
27	assert not msc1.are_equal(mol1, mol2)	1✔
28	assert msc1.are_equal(mol2, mol3)	1✔
29	thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))	1✔
30	thio2 = Molecule.from_file(os.path.join(test_dir, "thiophene2.xyz"))	1✔
31	# noinspection PyProtectedMember
32	msc2 = MoleculeStructureComparator(priority_bonds=msc1._get_bonds(thio1))	1✔
33	assert msc2.are_equal(thio1, thio2)	1✔
34	hal1 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_1.xyz"))	1✔
35	hal2 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_2.xyz"))	1✔
36	msc3 = MoleculeStructureComparator(priority_bonds=msc1._get_bonds(hal1))	1✔
37	assert msc3.are_equal(hal1, hal2)	1✔
38
39	def test_get_bonds(self):	1✔
40	mol1 = Molecule.from_file(os.path.join(test_dir, "t1.xyz"))	1✔
41	msc = MoleculeStructureComparator()	1✔
42	# noinspection PyProtectedMember
43	bonds = msc._get_bonds(mol1)	1✔
44	bonds_ref = [	1✔
45	(0, 1),
46	(0, 2),
47	(0, 3),
48	(0, 23),
49	(3, 4),
50	(3, 5),
51	(5, 6),
52	(5, 7),
53	(7, 8),
54	(7, 9),
55	(7, 21),
56	(9, 10),
57	(9, 11),
58	(9, 12),
59	(12, 13),
60	(12, 14),
61	(12, 15),
62	(15, 16),
63	(15, 17),
64	(15, 18),
65	(18, 19),
66	(18, 20),
67	(18, 21),
68	(21, 22),
69	(21, 23),
70	(23, 24),
71	(23, 25),
72	]
73	assert bonds == bonds_ref	1✔
74	mol2 = Molecule.from_file(os.path.join(test_dir, "MgBH42.xyz"))	1✔
75	bonds = msc._get_bonds(mol2)	1✔
76	assert bonds == [(1, 3), (2, 3), (3, 4), (3, 5), (6, 8), (7, 8), (8, 9), (8, 10)]	1✔
77	msc = MoleculeStructureComparator(ignore_ionic_bond=False)	1✔
78	bonds = msc._get_bonds(mol2)	1✔
79	assert bonds == [	1✔
80	(0, 1),
81	(0, 2),
82	(0, 3),
83	(0, 5),
84	(0, 6),
85	(0, 7),
86	(0, 8),
87	(0, 9),
88	(1, 3),
89	(2, 3),
90	(3, 4),
91	(3, 5),
92	(6, 8),
93	(7, 8),
94	(8, 9),
95	(8, 10),
96	]
97
98	mol1 = Molecule.from_file(os.path.join(test_dir, "molecule_with_halogen_bonds_1.xyz"))	1✔
99	msc = MoleculeStructureComparator()	1✔
100	# noinspection PyProtectedMember
101	bonds = msc._get_bonds(mol1)	1✔
102	assert bonds == [	1✔
103	(0, 12),
104	(0, 13),
105	(0, 14),
106	(0, 15),
107	(1, 12),
108	(1, 16),
109	(1, 17),
110	(1, 18),
111	(2, 4),
112	(2, 11),
113	(2, 19),
114	(3, 5),
115	(3, 10),
116	(3, 20),
117	(4, 6),
118	(4, 10),
119	(5, 11),
120	(5, 12),
121	(6, 7),
122	(6, 8),
123	(6, 9),
124	]
125
126	def test_to_and_from_dict(self):	1✔
127	msc1 = MoleculeStructureComparator()	1✔
128	d1 = msc1.as_dict()	1✔
129	d2 = MoleculeStructureComparator.from_dict(d1).as_dict()	1✔
130	assert d1 == d2	1✔
131	thio1 = Molecule.from_file(os.path.join(test_dir, "thiophene1.xyz"))	1✔
132	# noinspection PyProtectedMember
133	msc2 = MoleculeStructureComparator(bond_length_cap=0.2, priority_bonds=msc1._get_bonds(thio1), priority_cap=0.5)	1✔
134	d1 = msc2.as_dict()	1✔
135	d2 = MoleculeStructureComparator.from_dict(d1).as_dict()	1✔
136	assert d1 == d2	1✔
137
138	# def test_structural_change_in_geom_opt(self):
139	# qcout_path = os.path.join(test_dir, "mol_1_3_bond.qcout")
140	# qcout = QcOutput(qcout_path)
141	# mol1 = qcout.data[0]["molecules"][0]
142	# mol2 = qcout.data[0]["molecules"][-1]
143	# priority_bonds = [[0, 1], [0, 2], [1, 3], [1, 4], [1, 7], [2, 5], [2, 6], [2, 8], [4, 6], [4, 10], [6, 9]]
144	# msc = MoleculeStructureComparator(priority_bonds=priority_bonds)
145	# self.assertTrue(msc.are_equal(mol1, mol2))
146
147	def test_get_13_bonds(self):	1✔
148	priority_bonds = [	1✔
149	[0, 1],
150	[0, 2],
151	[1, 3],
152	[1, 4],
153	[1, 7],
154	[2, 5],
155	[2, 6],
156	[2, 8],
157	[4, 6],
158	[4, 10],
159	[6, 9],
160	]
161	bonds_13 = MoleculeStructureComparator.get_13_bonds(priority_bonds)	1✔
162	ans = (	1✔
163	(0, 3),
164	(0, 4),
165	(0, 5),
166	(0, 6),
167	(0, 7),
168	(0, 8),
169	(1, 2),
170	(1, 6),
171	(1, 10),
172	(2, 4),
173	(2, 9),
174	(3, 4),
175	(3, 7),
176	(4, 7),
177	(4, 9),
178	(5, 6),
179	(5, 8),
180	(6, 8),
181	(6, 10),
182	)
183	assert bonds_13 == tuple(ans)	1✔
184
185
186	if __name__ == "__main__":	1✔
187	unittest.main()	×

materialsproject / pymatgen / 4075885785

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