def test_connected_match_atoms_rad0_correct(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
shells_gen = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
match_atoms = shells_gen.get_match_atoms(0.)
expect_match_atoms = {k: set() for k in atoms}
self.assertDictEqual(match_atoms, expect_match_atoms)
def test_shells_generator_next_works_correctly(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = [x.GetIdx() for x in mol.GetAtoms()]
shells_gen1 = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
shells_gen2 = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
self.assertDictEqual(next(shells_gen1), next(shells_gen2))
def test_connected_match_atoms_rad1_correct2(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, atom*.75])
shells_gen = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
match_atoms = shells_gen.get_match_atoms(1.)
expect_match_atoms = {0: {1}, 1: {0, 2}, 2: {1}}
self.assertDictEqual(match_atoms, expect_match_atoms)
def test_generates_correct_disconnected_shells_level2(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
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))
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45 * atom])
expected_shells_dict1 = {
0: Shell(0, {1}),
1: Shell(1, {0, 2}),
2: Shell(2, {1})
}
expected_shells_dict2 = {
0: Shell(0, {expected_shells_dict1[1], expected_shells_dict1[2]}),
1: Shell(1, {expected_shells_dict1[0], expected_shells_dict1[2]}),
2: Shell(2, {expected_shells_dict1[0], expected_shells_dict1[1]})
}
shells_gen = ShellsGenerator(conf,
atoms,
radius_multiplier=0.5,
include_disconnected=True)
for i in range(3):
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict2)
def test_shells_generator_creation_success(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = [x.GetIdx() for x in mol.GetAtoms()]
ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
def test_generates_correct_disconnected_shells_level0(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
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))
expected_shells_dict = {0: Shell(0), 1: Shell(1), 2: Shell(2)}
shells_gen = ShellsGenerator(conf, atoms)
shells_dict = next(shells_gen)
self.assertDictEqual(shells_dict, expected_shells_dict)
def test_disconnected_substructs_converge(self):
from e3fp.fingerprint.fprinter import ShellsGenerator
from e3fp.conformer.util import mol_from_sdf
mol = mol_from_sdf(PLANAR_SDF_FILE)
conf = mol.GetConformers()[0]
atoms = list(range(3))
for atom in atoms:
conf.SetAtomPosition(atom, [0, 0, .45*atom])
shells_gen = ShellsGenerator(conf, atoms, radius_multiplier=0.5,
include_disconnected=True)
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)