def test_align_ligands_autodock4():
from rdkit.rdBase import DisableLog
DisableLog('rdApp.*')
ligands_dict = {
'FXR_10': 'test_data/align_ligands_autodock4/FXR_10.dlg',
'FXR_12': 'test_data/align_ligands_autodock4/FXR_12.dlg'
}
align_data = align_ligands(
pybel.readfile(
'pdb',
'test_data/align_ligands_autodock4/1dvwb_altered.pdb').__next__(),
ligands_dict,
poses_reference_structure=
'test_data/align_ligands_autodock4/FXR_receptor.pdbqt',
pose_loader='autodock4',
cluster_docking_data={'FXR_12': 2},
verbosity=-1)
with open('test_data/align_ligands_autodock4/results_autodock4.pkl',
'rb') as fh:
reference_position = pickle.load(fh)
for each_name, each_mol in align_data.items():
assert (extract_coordinates(each_mol) -
reference_position[each_name]).sum() < dist_tolerance
def test_align_ligands_superimpose1():
from rdkit.rdBase import DisableLog
DisableLog('rdApp.*')
from mol_util import adjust_query_properties
from rdkit.Chem.rdMolAlign import GetBestRMS
ligands_dict = {
'FXR_10': 'test_data/align_ligands_superimpose/FXR_10.mol2',
'FXR_12': 'test_data/align_ligands_superimpose/FXR_12.mol2'
}
result_file = 'test_data/align_ligands_superimpose/FXR_10_result.pdb'
align_data = align_ligands(
pybel.readfile(
'pdb', 'test_data/align_ligands_pdb/1dvwb_altered.pdb').__next__(),
ligands_dict,
reference_pose_superimpose=
'test_data/align_ligands_superimpose/FXR_10_ref.mol2',
poses_reference_structure='test_data/align_ligands_pdb/1dvwb.pdb',
pose_loader='superimpose',
verbosity=-1)
resultmol = adjust_query_properties(rdkit.Chem.MolFromPDBFile(result_file))
assert (GetBestRMS(resultmol, align_data['FXR_10'])) < 0.1
fxr12rms = GetBestRMS(resultmol,
align_data['FXR_12'],
map=[[(30, 0), (11, 1), (23, 2), (20, 3), (26, 35),
(32, 34), (28, 6), (12, 7), (1, 8), (2, 9),
(16, 10), (3, 11), (8, 12), (18, 13), (7, 14),
(19, 15), (9, 16), (0, 17), (14, 18), (13, 19),
(4, 27), (17, 28), (27, 29),
(33, 30), (29, 31), (15, 32), (5, 33), (31, 5),
(25, 4)]])
assert fxr12rms < 1
def test_align_ligands_pdb1():
ligands_dict = {
'FXR_10': 'test_data/align_ligands_pdb/FXR_10.pdb',
'FXR_12': 'test_data/align_ligands_pdb/FXR_12.pdb'
}
align_data = align_ligands(
pybel.readfile('pdb',
'test_data/align_ligands_pdb/1dvwb.pdb').__next__(),
ligands_dict,
poses_reference_structure='test_data/align_ligands_pdb/1dvwb.pdb',
pose_loader='pdb',
ligand_residue_name='LIG',
verbosity=-1)
with open('test_data/align_ligands_pdb/results_pdb1.pkl', 'rb') as fh:
reference_position = pickle.load(fh)
for each_name, each_mol in align_data.items():
assert (extract_coordinates(each_mol) -
reference_position[each_name]).sum() < dist_tolerance
