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test_capping_dihedral_fragments.py
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test_capping_dihedral_fragments.py
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from sys import stderr
from traceback import format_exc
import unittest
from fragment_capping.helpers.types_helpers import Atom
from fragment_capping.helpers.molecule import Molecule
CAN_FAIL, CAN_NOT_FAIL = True, False
USE_OCTET_RULE, DO_NOT_USE_OCTET_RULE = True, False
ALL_EXAMPLES = {
Molecule(
[
Atom(index=1, element='C', valence=4, capped=True, coordinates=None),
Atom(index=2, element='C', valence=3, capped=True, coordinates=None),
Atom(index=3, element='H', valence=None, capped=False, coordinates=None),
Atom(index=4, element='H', valence=None, capped=False, coordinates=None),
Atom(index=5, element='H', valence=None, capped=False, coordinates=None),
Atom(index=6, element='N', valence=None, capped=False, coordinates=None),
Atom(index=7, element='C', valence=None, capped=False, coordinates=None),
],
[
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 6),
(2, 7),
],
name='H,H,H_C_C_N,C',
): (0, 0, 'C3H7N', USE_OCTET_RULE, CAN_NOT_FAIL),
Molecule(
[
Atom(index=1, element='C', valence=4, capped=True, coordinates=None),
Atom(index=2, element='C', valence=4, capped=True, coordinates=None),
Atom(index=3, element='H', valence=None, capped=False, coordinates=None),
Atom(index=4, element='H', valence=None, capped=False, coordinates=None),
Atom(index=5, element='H', valence=None, capped=False, coordinates=None),
Atom(index=6, element='H', valence=None, capped=False, coordinates=None),
Atom(index=7, element='H', valence=None, capped=False, coordinates=None),
Atom(index=8, element='H', valence=None, capped=False, coordinates=None),
],
[
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 6),
(2, 7),
(2, 8),
],
name='H,H,H_C_C_H,H,H',
): (0, 0, 'C2H6', USE_OCTET_RULE, CAN_NOT_FAIL),
Molecule(
[
Atom(index=1, element='C', valence=4, capped=True, coordinates=None),
Atom(index=2, element='C', valence=4, capped=True, coordinates=None),
Atom(index=3, element='C', valence=None, capped=False, coordinates=None),
Atom(index=4, element='C', valence=None, capped=False, coordinates=None),
Atom(index=5, element='C', valence=None, capped=False, coordinates=None),
Atom(index=6, element='C', valence=None, capped=False, coordinates=None),
Atom(index=7, element='C', valence=None, capped=False, coordinates=None),
Atom(index=8, element='C', valence=None, capped=False, coordinates=None),
],
[
(1, 2),
(1, 3),
(1, 4),
(1, 5),
(2, 6),
(2, 7),
(2, 8),
],
name='C,C,C_C_C_C,C,C',
): (0, 0, 'C8H18', USE_OCTET_RULE, CAN_NOT_FAIL),
Molecule(
[
Atom(index=1, element='C', valence=3, capped=True, coordinates=None),
Atom(index=2, element='C', valence=3, capped=True, coordinates=None),
Atom(index=3, element='C', valence=None, capped=False, coordinates=None),
Atom(index=4, element='C', valence=None, capped=False, coordinates=None),
Atom(index=5, element='C', valence=None, capped=False, coordinates=None),
Atom(index=6, element='C', valence=None, capped=False, coordinates=None),
],
[
(1, 2),
(1, 3),
(1, 4),
(2, 5),
(2, 6),
],
name='C,C_C_C_C,C',
): (0, 0, 'C6H12', USE_OCTET_RULE, CAN_FAIL),
Molecule(
[
Atom(index=1, element='O', valence=2, capped=False, coordinates=None),
Atom(index=2, element='N', valence=2, capped=False, coordinates=None),
Atom(index=3, element='C', valence=None, capped=True, coordinates=None),
Atom(index=4, element='C', valence=None, capped=True, coordinates=None),
Atom(index=5, element='N', valence=None, capped=False, coordinates=None),
Atom(index=6, element='C', valence=3, capped=False, coordinates=None),
],
[
(1, 3),
(2, 3),
(3, 4),
(4, 5),
(4, 6),
],
name='O,N_C_C_N,C',
): (0, 0, 'C3H6N2O', USE_OCTET_RULE, CAN_NOT_FAIL),
Molecule(
[
Atom(index=1, element='O', valence=None, capped=False, coordinates=None),
Atom(index=2, element='N', valence=None, capped=False, coordinates=None),
Atom(index=3, element='C', valence=3, capped=True, coordinates=None),
Atom(index=4, element='C', valence=3, capped=True, coordinates=None),
Atom(index=5, element='H', valence=None, capped=False, coordinates=None),
Atom(index=6, element='H', valence=None, capped=False, coordinates=None),
],
[
(1, 3),
(2, 3),
(3, 4),
(4, 5),
(4, 6),
],
name='O,N_C_C_H,H',
): (0, 0, 'C2H5NO', USE_OCTET_RULE, CAN_NOT_FAIL),
Molecule(
[
Atom(index=1, element='O', valence=None, capped=False, coordinates=None),
Atom(index=2, element='N', valence=None, capped=False, coordinates=None),
Atom(index=3, element='C', valence=3, capped=True, coordinates=None),
Atom(index=4, element='C', valence=3, capped=True, coordinates=None),
Atom(index=5, element='C', valence=None, capped=False, coordinates=None),
Atom(index=6, element='H', valence=None, capped=False, coordinates=None),
],
[
(1, 3),
(2, 3),
(3, 4),
(4, 5),
(4, 6),
],
name='O,N_C_C_C,H',
): (0, 0, 'C3H7NO', USE_OCTET_RULE, CAN_NOT_FAIL),
}
class Test_Dihedral_Fragment_Capping(unittest.TestCase):
pass
for (molecule, (expected_netcharge, expected_abs_netcharge, expected_formula, use_octet_rule, can_fail)) in sorted(ALL_EXAMPLES.items()):
def dynamic_test(self, molecule=molecule, expected_netcharge=expected_netcharge, expected_abs_netcharge=expected_abs_netcharge, expected_formula=expected_formula, use_octet_rule=use_octet_rule, can_fail=can_fail):
molecule.write_graph('uncapped')
print(molecule.name + '...', end='')
molecule.get_best_capped_molecule_with_ILP(enforce_octet_rule=use_octet_rule)
molecule.write_graph('capped')
print('OK')
try:
assert molecule.netcharge() == expected_netcharge, (molecule.netcharge(), molecule.formal_charges)
assert molecule.net_abs_charges() == expected_abs_netcharge, (molecule.net_abs_charges(), molecule.formal_charges)
assert molecule.formula() == expected_formula, molecule.formula()
except AssertionError as e:
print(molecule.name)
if can_fail:
print(str(e))
print(format_exc())
else:
raise
setattr(
Test_Dihedral_Fragment_Capping,
'test_' + molecule.name,
dynamic_test,
)
if __name__ == '__main__':
unittest.main()