def test_rename():
""" test vmat.rename
"""
ref_renamed_zma = (('C', (None, None, None), (None, None, None),
(None, None, None)), ('C', (0, None,
None), ('R1', None, None),
(2.894126135733367, None, None)),
('H', (0, 1, None), ('R2', 'A2', None),
(2.1002551784038714, 1.9218361502726833,
None)), ('H', (0, 1, 2), ('R3', 'A3', 'D3'),
(2.1008326855365818, 1.932519243247544,
4.182194537966691)),
('H', (0, 1, 2), ('R4NEW', 'A4', 'D4'),
(2.0985632786105715, 1.9267905467443245,
2.078543469899091)),
('C', (1, 0, 2), ('R5', 'A5', 'D5'),
(2.7809944542976193, 1.9090367411091194,
1.0264175778482927)),
('C', (1, 0, 5), ('R6', 'A6', 'D6'),
(2.905905476629344, 1.9462477957117656,
2.1246205025559037)),
('H', (1, 0, 5), ('R7', 'A7', 'D7'),
(2.1005624282579265, 1.8988979609840009,
4.223022677525844)),
('X', (5, 1, 0), ('R8', 'A8', 'D8'),
(1.8897261254578288, 1.5707963267948968,
4.216836292856281)), ('C', (5, 8, 1), ('R9', 'A9NEW',
'D9'),
(2.2778505841014964,
1.5732722619955628,
3.1519457859137696)),
('X', (9, 5, 8), ('R10', 'A10', 'D10'),
(1.8897261254578286, 1.56832039159423,
0.0)), ('H', (9, 10, 5), ('R11', 'A11', 'D11'),
(2.0003442808863467, 1.57550991099349,
3.14859478950736)),
('O', (6, 1, 0), ('R12', 'A12', 'D12'),
(2.65076899334649, 1.9387190313618887,
1.0262708014428483)), ('H', (6, 1, 12), ('R13', 'A13',
'D13NEW'),
(2.1058345184525726,
1.9323237957467607,
2.129177885999989)),
('H', (6, 1, 12), ('R14', 'A14', 'D14'),
(2.1010240316411886, 1.9207088798352128,
4.1894956154070275)), ('H', (12, 6, 1), ('R15', 'A15',
'D15'),
(1.8758293656194,
1.8624105681328567,
1.2477273554765336)))
renamed_zma = zmat.rename(C5H8O_ZMA, {
'R4': 'R4NEW',
'A9': 'A9NEW',
'D13': 'D13NEW'
})
assert zmat.almost_equal(ref_renamed_zma, renamed_zma)
def test__standardize():
""" test zmat.standard_form
test zmat.standard_name_matrix
"""
nonstandard_zma = (
('C', (None, None, None), (None, None, None), (None, None, None)),
('C', (0, None, None), ('R210', None, None),
(2.894126135733367, None,
None)), ('H', (0, 1, None), ('R220', 'A220', None),
(2.1002551784038714, 1.9218361502726833,
None)), ('H', (0, 1, 2), ('R230', 'A230', 'D230'),
(2.1008326855365818, 1.932519243247544,
4.182194537966691)),
('H', (0, 1, 2), ('R240', 'A240', 'D240'),
(2.0985632786105715, 1.9267905467443245, 2.078543469899091)),
('C', (1, 0, 2), ('R250', 'A250', 'D250'),
(2.7809944542976193, 1.9090367411091194, 1.0264175778482927)),
('C', (1, 0, 5), ('R260', 'A260', 'D260'),
(2.905905476629344, 1.9462477957117656,
2.1246205025559037)), ('H', (1, 0, 5), ('R270', 'A270', 'D270'),
(2.1005624282579265, 1.8988979609840009,
4.223022677525844)),
('X', (5, 1, 0), ('R280', 'A280', 'D280'),
(1.8897261254578288, 1.5707963267948968,
4.216836292856281)), ('C', (5, 8, 1), ('R290', 'A290', 'D290'),
(2.2778505841014964, 1.5732722619955628,
3.1519457859137696)),
('X', (9, 5, 8), ('R2100', 'A2100', 'D2100'),
(1.8897261254578286, 1.56832039159423,
0.0)), ('H', (9, 10, 5), ('R2110', 'A2110', 'D2110'),
(2.0003442808863467, 1.57550991099349,
3.14859478950736)),
('O', (6, 1, 0), ('R2120', 'A2120', 'D2120'),
(2.65076899334649, 1.9387190313618887,
1.0262708014428483)), ('H', (6, 1, 12), ('R2130', 'A2130', 'D2130'),
(2.1058345184525726, 1.9323237957467607,
2.129177885999989)),
('H', (6, 1, 12), ('R2140', 'A2140', 'D2140'),
(2.1010240316411886, 1.9207088798352128,
4.1894956154070275)), ('H', (12, 6, 1), ('R2150', 'A2150', 'D2150'),
(1.8758293656194, 1.8624105681328567,
1.2477273554765336)))
assert zmat.almost_equal(C5H8O_ZMA, zmat.standard_form(nonstandard_zma))
def test__string():
""" test zmat.string
"""
zma = zmat.from_string(zmat.string(CH4O2_ZMA))
assert zmat.almost_equal(zma, CH4O2_ZMA)
def test__equality():
""" test zmat.almost_equal
"""
assert not zmat.almost_equal(HOOH_ZMA_C2, HOOH_ZMA_CS)
assert zmat.almost_equal(HOOH_ZMA_C2, HOOH_ZMA_CS, just_dist=True)
def test__set():
""" test zmat.set_key_matrix
test zmat.set_name_matrix
"""
# Increment keys by 1 (not physical, but just for testing)
ref_reset_zma1 = (
('C', (None, None, None), (None, None, None), (None, None, None)),
('C', (1, None, None), ('R1', None, None),
(2.894126135733367, None,
None)), ('H', (1, 2, None), ('R2', 'A2', None),
(2.1002551784038714, 1.9218361502726833,
None)), ('H', (1, 2, 3), ('R3', 'A3', 'D3'),
(2.1008326855365818, 1.932519243247544,
4.182194537966691)),
('H', (1, 2, 3), ('R4', 'A4', 'D4'),
(2.0985632786105715, 1.9267905467443245, 2.078543469899091)),
('C', (2, 1, 3), ('R5', 'A5', 'D5'),
(2.7809944542976193, 1.9090367411091194,
1.0264175778482927)), ('C', (2, 1, 6), ('R6', 'A6', 'D6'),
(2.905905476629344, 1.9462477957117656,
2.1246205025559037)),
('H', (2, 1, 6), ('R7', 'A7', 'D7'),
(2.1005624282579265, 1.8988979609840009,
4.223022677525844)), ('X', (6, 2, 1), ('R8', 'A8', 'D8'),
(1.8897261254578288, 1.5707963267948968,
4.216836292856281)),
('C', (6, 9, 2), ('R9', 'A9', 'D9'),
(2.2778505841014964, 1.5732722619955628,
3.1519457859137696)), ('X', (10, 6, 9), ('R10', 'A10', 'D10'),
(1.8897261254578286, 1.56832039159423, 0.0)),
('H', (10, 11, 6), ('R11', 'A11', 'D11'),
(2.0003442808863467, 1.57550991099349, 3.14859478950736)),
('O', (7, 2, 1), ('R12', 'A12', 'D12'),
(2.65076899334649, 1.9387190313618887,
1.0262708014428483)), ('H', (7, 2, 13), ('R13', 'A13', 'D13'),
(2.1058345184525726, 1.9323237957467607,
2.129177885999989)),
('H', (7, 2, 13), ('R14', 'A14', 'D14'),
(2.1010240316411886, 1.9207088798352128,
4.1894956154070275)), ('H', (13, 7, 2), ('R15', 'A15', 'D15'),
(1.8758293656194, 1.8624105681328567,
1.2477273554765336)))
new_key_mat = ((None, None, None), (1, None, None), (1, 2, None),
(1, 2, 3), (1, 2, 3), (2, 1, 3), (2, 1, 6), (2, 1, 6),
(6, 2, 1), (6, 9, 2), (10, 6, 9), (10, 11, 6), (7, 2, 1),
(7, 2, 13), (7, 2, 13), (13, 7, 2))
reset_zma1 = zmat.set_key_matrix(C5H8O_ZMA, new_key_mat)
assert zmat.almost_equal(ref_reset_zma1, reset_zma1)
# Increment all the numbers on the name by 1
ref_reset_zma2 = (
('C', (None, None, None), (None, None, None), (None, None, None)),
('C', (0, None, None), ('R2', None, None),
(2.894126135733367, None,
None)), ('H', (0, 1, None), ('R3', 'A3', None),
(2.1002551784038714, 1.9218361502726833,
None)), ('H', (0, 1, 2), ('R4', 'A4', 'D4'),
(2.1008326855365818, 1.932519243247544,
4.182194537966691)),
('H', (0, 1, 2), ('R5', 'A5', 'D5'),
(2.0985632786105715, 1.9267905467443245, 2.078543469899091)),
('C', (1, 0, 2), ('R6', 'A6', 'D6'),
(2.7809944542976193, 1.9090367411091194,
1.0264175778482927)), ('C', (1, 0, 5), ('R7', 'A7', 'D7'),
(2.905905476629344, 1.9462477957117656,
2.1246205025559037)),
('H', (1, 0, 5), ('R8', 'A8', 'D8'),
(2.1005624282579265, 1.8988979609840009,
4.223022677525844)), ('X', (5, 1, 0), ('R9', 'A9', 'D9'),
(1.8897261254578288, 1.5707963267948968,
4.216836292856281)),
('C', (5, 8, 1), ('R10', 'A10', 'D10'),
(2.2778505841014964, 1.5732722619955628,
3.1519457859137696)), ('X', (9, 5, 8), ('R11', 'A11', 'D11'),
(1.8897261254578286, 1.56832039159423, 0.0)),
('H', (9, 10, 5), ('R12', 'A12', 'D12'),
(2.0003442808863467, 1.57550991099349, 3.14859478950736)),
('O', (6, 1, 0), ('R13', 'A13', 'D13'),
(2.65076899334649, 1.9387190313618887,
1.0262708014428483)), ('H', (6, 1, 12), ('R14', 'A14', 'D14'),
(2.1058345184525726, 1.9323237957467607,
2.129177885999989)),
('H', (6, 1, 12), ('R15', 'A15', 'D15'),
(2.1010240316411886, 1.9207088798352128,
4.1894956154070275)), ('H', (12, 6, 1), ('R16', 'A16', 'D16'),
(1.8758293656194, 1.8624105681328567,
1.2477273554765336)))
new_name_mat = ((None, None, None), ('R2', None, None), ('R3', 'A3', None),
('R4', 'A4', 'D4'), ('R5', 'A5', 'D5'), ('R6', 'A6', 'D6'),
('R7', 'A7', 'D7'), ('R8', 'A8', 'D8'), ('R9', 'A9', 'D9'),
('R10', 'A10', 'D10'), ('R11', 'A11', 'D11'),
('R12', 'A12', 'D12'), ('R13', 'A13', 'D13'),
('R14', 'A14', 'D14'), ('R15', 'A15',
'D15'), ('R16', 'A16', 'D16'))
reset_zma2 = zmat.set_name_matrix(C5H8O_ZMA, new_name_mat)
assert zmat.almost_equal(ref_reset_zma2, reset_zma2)
