def test_misc() -> None:
dihedral_1 = Dihedral_Fragment("C,C,H|C|C|C,H,H")
print(dihedral_1)
dihedral_2 = Dihedral_Fragment("C,H,H|C|C|C,C,H")
print(dihedral_2)
print(dihedral_1 == dihedral_2)
dihedral_3 = Dihedral_Fragment(atom_list=(['H', 'H'], 'C', 'C',
['Cl', 'Cl']))
print(dihedral_3)
print(dihedral_3 == dihedral_2)
def test_CYP() -> None:
for dihedral_angles in TEST_ANGLES:
print(
str(
Dihedral_Fragment(atom_list=(['C', 'H',
'O'], 'C', 'C', ['C', 'H', 'O']),
dihedral_angles=dihedral_angles)), )
for dihedral_angles in TEST_ANGLES:
print(
Dihedral_Fragment(
atom_list=(['C', 'H', 'H'], 'C', 'C', ['C', 'H', 'O']),
dihedral_angles=dihedral_angles,
), )
def re_pattern_matching_for(
pattern: Dihedral_Matching_Pattern,
debug: bool = False,
metadata: Any = None) -> Callable[[Dihedral_Fragment_Str], bool]:
if not (has_substitution_pattern(pattern) or has_regex_pattern(pattern)):
return lambda test_string: test_string == str(
Dihedral_Fragment(pattern))
else:
patterns = [
FORMAT_UNESCAPED(re_pattern)
for re_pattern in re_patterns(pattern,
full_regex=True,
flavour='re',
debug=debug,
metadata=metadata)
]
def match_pattern_to(test_string):
if debug:
print(metadata)
print(pattern)
print(patterns)
print(test_string)
print(
any([
search(match_pattern, test_string)
for match_pattern in patterns
]))
print()
return any([
search(match_pattern, test_string)
for match_pattern in patterns
])
return match_pattern_to
def test_canonical_rep() -> None:
test_cases = (
('H,C4,H|SI|C|C2,H,C4', 'C4,H,H|SI|C|C4,C2,H'), # M(SI) > M(C)
('H,C4,H|C|C|C4,H', 'C4,H,H|C|C|C4,H'), #M(C) == M(C), 3 > 2
('H,C4,H|C|C|C3,H,H',
'C4,H,H|C|C|C3,H,H'), #M(C) == M(C), 3 ==3, 4 > 3
('O2|C|C|N2,H', 'N2,H|C|C|O2'), # M(O) > M(N)
('F,C4|C|C|O1,N3', 'F,C4|C|C|O1,N3'), # M(F) > M(O)
)
for (dihedral_string, solution) in test_cases:
print('TEST: {0}'.format(dihedral_string))
answer = str(Dihedral_Fragment(dihedral_string))
assert answer == solution, '"{0}" (answer) != "{1}" (expected)'.format(
answer, solution)
cyclic_answer = str(Dihedral_Fragment(answer))
assert cyclic_answer == answer, '"{0}" (answer) != "{1}" (expected)'.format(
cyclic_answer, answer)
def main():
for (atom_2, atom_3) in combinations_with_replacement(CENTRAL_ATOMS, 2):
if is_forbidden_bond((atom_2, atom_3)):
continue
for (len_neighbours_1,
len_neighbours_4) in product(number_neighbours(atom_2),
number_neighbours(atom_3)):
neighbours_1 = combinations_with_replacement(
ATOMS, len_neighbours_1)
neighbours_4 = combinations_with_replacement(
ATOMS, len_neighbours_4)
for a, b in product(neighbours_1, neighbours_4):
d = str(
Dihedral_Fragment(atom_list=(list(a), atom_2, atom_3,
list(b))))
tags = tags_for_dihedral(d)
if len(tags) > 0:
print(d, tags)
def sql_pattern_matching_for(pattern: Dihedral_Matching_Pattern,
matching_field_name: str = 'dihedral_string'):
if not (has_substitution_pattern(pattern) or has_regex_pattern(pattern)):
return '{matching_field_name}="{pattern}"'.format(
matching_field_name=matching_field_name,
pattern=Dihedral_Fragment(pattern),
)
else:
use_full_regex = has_regex_pattern(pattern)
all_patterns = re_patterns(pattern,
full_regex=use_full_regex,
flavour='sql')
#patterns = [FORMAT_UNESCAPED(re_pattern) for re_pattern in re_patterns(pattern, full_regex=True, flavour='sql')]
return sql_OR([
'{matching_field_name} {sql_operator} "{match_pattern}"'.format(
matching_field_name=matching_field_name,
sql_operator=('LIKE' if not use_full_regex else 'REGEXP'),
match_pattern=match_pattern,
) for match_pattern in all_patterns
])
('thiol', 'J+|C|S|H'),
('thioether', 'J+|C|S|C'),
('disulfide', 'C|S|S|C'),
('sulfinyl', '%|C|S|C,O'),
('sulfonyl', '%|C|S|C,O,O'),
('sulfino', 'C,O|S|O|H'),
('sulfo', 'C,O,O|S|O|H'),
('thiocyanate', 'C|S|C|N'),
('isothiocyanate', 'C|N|C|S'),
('carbonothioyl', '%|J|C|S,J'),
# Groups containing phosphorus
('phosphino', '%|C|P|C{2}'),
('phosphono', '%|C|P|O{3}'),
('phosphate', 'C|O|P|O{3}'),
# Groups containing boron
('borono', '%|C|B|O{2}'),
)
CHEMICAL_GROUPS = list(
map(
lambda moiety_pattern:
(moiety_pattern[0],
str(Dihedral_Fragment(dihedral_string=moiety_pattern[1]))),
CHEMICAL_GROUPS,
))
if __name__ == '__main__':
print(CHEMICAL_GROUPS)
def test_cyclic_fragments() -> None:
cyclic_fragment = Dihedral_Fragment(atom_list=(['H', 'H', 'C'], 'C', 'C',
['H', 'C', 'H'],
[[2, 0, 1]]))
print(str(cyclic_fragment))
assert str(cyclic_fragment) == 'C,H,H|C|C|C,H,H|000', cyclic_fragment
polycyclic_fragment, answer = Dihedral_Fragment(
atom_list=(['H', 'C', 'C'], 'C', 'C', ['C', 'C', 'H'],
[[2, 2, 1], [1, 3, 0]])), 'C,C,H|C|C|C,C,H|020,131'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
print(Dihedral_Fragment(str(polycyclic_fragment)))
polycyclic_fragment, answer = Dihedral_Fragment(
atom_list=(['H', 'N', 'O'], 'C', 'C', ['C', 'C', 'H'],
[[2, 2, 1], [1, 2, 0]])), 'O,N,H|C|C|C,C,H|020,121'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
print(Dihedral_Fragment(str(polycyclic_fragment)))
polycyclic_fragment, answer = Dihedral_Fragment(atom_list=(
['C', 'N', 'O'], 'C', 'C', ['O', 'O', 'O'],
[[0, 6, 2], [1, 5, 1], [2, 4, 0]])), 'O,O,O|C|C|O,N,C|040,151,262'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
polycyclic_fragment, answer = Dihedral_Fragment(atom_list=(
['C', 'N', 'O'], 'C', 'C', ['O', 'O', 'O'],
[[0, 6, 2], [1, 5, 2], [2, 4, 2]])), 'O,O,O|C|C|O,N,C|040,051,062'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
polycyclic_fragment, answer = str(
Dihedral_Fragment(
'C,C,C|C|C|C,C,C|002,101,200')), 'C,C,C|C|C|C,C,C|000,101,202'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
polycyclic_fragment, answer = str(
Dihedral_Fragment(
'C,C,N|C|C|C,C,C|002,101,200')), 'N,C,C|C|C|C,C,C|000,101,202'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
polycyclic_fragment, answer = str(
Dihedral_Fragment('C,C,C,C,C|P|P|C,C,C,C,C|004,103,212,311,420')
), 'C,C,C,C,C|P|P|C,C,C,C,C|000,101,212,313,424'
print(str(polycyclic_fragment))
assert str(polycyclic_fragment) == answer, '{0} != {1} (expected)'.format(
str(polycyclic_fragment),
answer,
)
try:
Dihedral_Fragment('C,C,C|C|C|C,C,C|0100')
raise Exception('This should have failed.')
except AssertionError:
print('Rings length > 9 failed as expected.')
def test_chiral_str() -> None:
dihedral_1 = Dihedral_Fragment("C,C,H|C|C|C,H,H")
print(dihedral_1.__str__())
print(dihedral_1.__str__(flag_chiral_sides=True))
def test_atom_list_init() -> None:
fragment = Dihedral_Fragment(atom_list=(['C'], 'C', 'C', ['C']))