def test_connected_substructs_converge(self):
from e3fp.fingerprint import fprinter
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
bonds_dict = {0: {1, 2}, 1: {0}, 2: {0}}
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45 * atom])
with mock.patch('e3fp.fingerprint.fprinter.bound_atoms_from_mol',
return_value=bonds_dict):
shells_gen = fprinter.ShellsGenerator(conf,
atoms,
radius_multiplier=0.5,
include_disconnected=False)
for i in range(4):
shells_dict = next(shells_gen)
substructs_dict = {
k: v.substruct
for k, v in shells_dict.items()
}
next_shells_dict = next(shells_gen)
next_substructs_dict = {
k: v.substruct
for k, v in next_shells_dict.items()
}
self.assertDictEqual(substructs_dict, next_substructs_dict)
def test_generates_correct_connected_shells_level2(self):
from e3fp.fingerprint import fprinter
from e3fp.fingerprint.structs import Shell
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
bonds_dict = {0: {1, 2}, 1: {0}, 2: {0}}
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45 * atom])
expected_shells_dict1 = {
0: Shell(0, {1}),
1: Shell(1, {0}),
2: Shell(2, {})
}
expected_shells_dict2 = {
0: Shell(0, {expected_shells_dict1[1], expected_shells_dict1[2]}),
1: Shell(1, {expected_shells_dict1[0]}),
2: Shell(2, {expected_shells_dict1[0]})
}
with mock.patch('e3fp.fingerprint.fprinter.bound_atoms_from_mol',
return_value=bonds_dict):
shells_gen = fprinter.ShellsGenerator(conf,
atoms,
radius_multiplier=0.5,
include_disconnected=False)
for i in range(3):
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict2)