def test_populate_poses_restraints_only_ligand(self):
to_generate = 3
center = [15., 15., 15.]
radius = 10.
seed = 1984
number_generator = MTGenerator(seed)
# No needed if no restraints are provided
rec_translation = [0., 0., 0.]
lig_translation = [-15.0, -15.0, -15.0]
# Restraints
ligand_restraints = [Residue.dummy(16.0, 16.0, 16.0)]
ligand_diameter = 30.
poses = populate_poses(to_generate, center, radius, number_generator, rec_translation, lig_translation,
ligand_restraints=ligand_restraints, ligand_diameter=ligand_diameter)
expected = [[12.270567117106161, 14.884113636383933, 11.792201743436038, 0.7092076459798842, 0.5346980891115, -0.08272585379354264, -0.4519722353179574],
[22.833743558777538, 15.523806353077699, 17.906625032282104, 0.24053986913227657, -0.25327548418133206, -0.5237151871050496, 0.7769906712863817],
[8.903837618881248, 8.747779486586737, 19.195006601282643, 0.7560980480558669, -0.46621474071247004, 0.45925053854810693, 0.00696420216436307]]
# We generate 3 poses
assert len(poses) == 3
# We generate poses with ANM
assert len(poses[0]) == 7
# We generate the expected poses
assert np.allclose(expected, poses)
def test_populate_poses_both_restraints(self):
to_generate = 3
center = [15., 15., 15.]
radius = 10.
seed = 1984
number_generator = MTGenerator(seed)
# No needed if no restraints are provided
rec_translation = [0., 0., 0.]
lig_translation = [-15.0, -15.0, -15.0]
# Restraints
receptor_restraints = [Residue.dummy(1.0, 1.0, 1.0)]
ligand_restraints = [Residue.dummy(16.0, 16.0, 16.0)]
ligand_diameter = 10.
poses = populate_poses(to_generate, center, radius, number_generator, rec_translation, lig_translation,
receptor_restraints=receptor_restraints, ligand_restraints=ligand_restraints,
ligand_diameter=ligand_diameter)
expected = [[12.270567117106161, 14.884113636383933, 11.792201743436038, 0.05643308208136652, 0.7572287178886188, -0.11715469622945059, -0.6400740216591683],
[21.986658842426436, 12.715708176897868, 9.881149636072841, 0.17754420770338322, 0.179865123253213, -0.7681474466249519, 0.5882823233717389],
[22.833743558777538, 15.523806353077699, 17.906625032282104, 0.0847943426151146, -0.2599970108635702, -0.5376137514110186, 0.7976107622745888]]
# We generate 3 poses
assert len(poses) == 3
# We generate poses with ANM
assert len(poses[0]) == 7
# We generate the expected poses
assert np.allclose(expected, poses)
def test_populate_poses_restraints_only_receptor(self):
to_generate = 3
center = [15., 15., 15.]
radius = 10.
seed = 1984
number_generator = MTGenerator(seed)
# No needed if no restraints are provided
rec_translation = [0., 0., 0.]
lig_translation = [-15.0, -15.0, -15.0]
# Restraints
receptor_restraints = [Residue.dummy(1.0, 1.0, 1.0)]
ligand_diameter = 10.
poses = populate_poses(to_generate, center, radius, number_generator, rec_translation, lig_translation,
receptor_restraints=receptor_restraints, ligand_diameter=ligand_diameter)
expected = [[12.270567117106161, 14.884113636383933, 11.792201743436038, -0.6725323168859286, 0.5755106199757826, -0.37756439233549577, 0.27190612107759393],
[12.715708176897868, 9.881149636072841, 18.262252550718056, -0.6132005094145724, 0.757439137867041, -0.0367297456106423, -0.22118321244687617],
[17.906625032282104, 11.374830853855302, 8.903837618881248, -0.8727759595729266, -0.22555077047578467, -0.2572320124803007, 0.3481675833340481]]
# We generate 3 poses
assert len(poses) == 3
# We generate poses with ANM
assert len(poses[0]) == 7
# We generate the expected poses
assert np.allclose(expected, poses)
def test_populate_poses(self):
to_generate = 3
center = [0., 0., 0.]
radius = 10.
seed = 1984
number_generator = MTGenerator(seed)
# No needed if no restraints are provided
rec_translation = [0., 0., 0.]
lig_translation = [-15.0, -15.0, -15.0]
poses = populate_poses(to_generate, center, radius, number_generator, rec_translation, lig_translation)
expected = [[-2.7294328828938386, -0.11588636361606675, -3.2077982565639607, -0.6725323168859286, 0.5755106199757826, -0.37756439233549577, 0.27190612107759393],
[-2.2842918231021314, -5.118850363927159, 3.2622525507180566, -0.6132005094145724, 0.757439137867041, -0.0367297456106423, -0.22118321244687617],
[2.906625032282104, -3.6251691461446978, -6.096162381118752, -0.8727759595729266, -0.22555077047578467, -0.2572320124803007, 0.3481675833340481]]
# We generate 3 poses
assert len(poses) == 3
# We generate poses without ANM
assert len(poses[0]) == 7
# We generate the expected poses
assert np.allclose(expected, poses)