import os
import numpy as np
from numpy.testing import assert_array_equal, assert_array_almost_equal
import oddt
from oddt.interactions import (close_contacts,
hbonds,
distance,
halogenbonds,
halogenbond_acceptor_halogen,
pi_stacking,
salt_bridges,
pi_cation,
hydrophobic_contacts)
test_data_dir = os.path.dirname(os.path.abspath(__file__))
mols = list(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
list(map(lambda x: x.addh(only_polar=True), mols))
rec = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data/dude/xiap/receptor_rdkit.pdb')))
rec.protein = True
rec.addh(only_polar=True)
def test_close_contacts():
"""Close contacts test"""
cc = [len(close_contacts(rec.atom_dict[rec.atom_dict['atomicnum'] != 1],
mol.atom_dict[mol.atom_dict['atomicnum'] != 1],
cutoff=3)[0]) for mol in mols]
assert_array_equal(cc,
[5, 7, 6, 5, 3, 6, 5, 6, 6, 6, 5, 4, 7, 6, 6, 6, 7, 5,
6, 5, 5, 7, 4, 5, 6, 7, 6, 5, 7, 5, 6, 4, 5, 4, 3, 7,
6, 6, 3, 5, 4, 3, 1, 7, 3, 2, 4, 1, 2, 7, 4, 4, 6, 4,
6, 7, 7, 6, 6, 6, 5, 6, 5, 4, 4, 7, 3, 6, 6, 4, 7, 7,
4, 5, 4, 7, 3, 6, 6, 6, 5, 6, 4, 5, 4, 4, 6, 5, 5, 7,
6, 2, 6, 5, 1, 8, 6, 5, 7, 4])
def test_hbonds():
"""H-Bonds test"""
hbonds_count = np.array([hbonds(rec, mol)[2].sum() for mol in mols])
if oddt.toolkit.backend == 'ob':
exp_count = [2, 5, 4, 4, 3, 4, 2, 3, 4, 3, 3, 3, 3, 3, 5, 4, 3, 5,
4, 5, 5, 3, 4, 6, 3, 4, 4, 4, 3, 3, 4, 3, 4, 3, 3, 3,
3, 3, 3, 4, 3, 4, 4, 3, 4, 3, 5, 4, 3, 3, 3, 6, 4, 2,
2, 3, 4, 4, 4, 4, 5, 2, 3, 4, 4, 3, 3, 3, 2, 5, 3, 4,
3, 3, 5, 2, 3, 2, 2, 3, 5, 3, 3, 2, 3, 4, 2, 4, 3, 3,
3, 5, 3, 4, 6, 4, 5, 3, 3, 2]
else:
exp_count = [2, 5, 4, 4, 3, 4, 2, 3, 4, 3, 3, 3, 3, 3, 5, 4, 3, 5,
4, 5, 5, 3, 4, 6, 3, 4, 4, 4, 3, 3, 4, 3, 4, 3, 3, 3,
3, 3, 3, 4, 3, 4, 4, 3, 4, 3, 5, 4, 3, 3, 3, 6, 4, 2,
2, 3, 4, 4, 4, 4, 5, 2, 3, 4, 4, 4, 3, 3, 2, 5, 3, 4,
3, 3, 5, 2, 3, 2, 2, 3, 5, 3, 3, 2, 3, 4, 2, 4, 3, 3,
3, 5, 3, 4, 6, 4, 5, 3, 3, 2]
assert_array_equal(hbonds_count, exp_count)
def test_pi_stacking_parallel_pdb():
pocket = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data/pdb/4bfq_pocket.pdb')))
pocket.protein = True
ligand = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/pdb/4bfq_ligand.sdf')))
pi1, pi2, strict_parallel, strict_perpendicular = pi_stacking(pocket, ligand, tolerance=30)
assert strict_parallel.sum() == 2
assert strict_perpendicular.sum() == 0
assert pi1['resname'].tolist() == ['TYR', 'TYR']
pi1, pi2, strict_parallel, strict_perpendicular = pi_stacking(ligand, pocket, tolerance=30)
assert strict_parallel.sum() == 2
assert strict_perpendicular.sum() == 0
assert pi2['resname'].tolist() == ['TYR', 'TYR']
def test_pi_stacking_perpendicular_pdb():
pocket = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data/pdb/4ljh_pocket.pdb')))
pocket.protein = True
ligand = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/pdb/4ljh_ligand.sdf')))
pi1, pi2, strict_parallel, strict_perpendicular = pi_stacking(pocket, ligand, tolerance=30)
assert strict_parallel.sum() == 0
assert strict_perpendicular.sum() == 1
assert pi1['resname'].tolist() == ['HIS']
pi1, pi2, strict_parallel, strict_perpendicular = pi_stacking(ligand, pocket, tolerance=30)
assert strict_parallel.sum() == 0
assert strict_perpendicular.sum() == 1
assert pi2['resname'].tolist() == ['HIS']
def test_pi_cation_pdb():
pocket = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data/pdb/1lpi_pocket.pdb')))
pocket.protein = True
ligand = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/pdb/1lpi_ligand.sdf')))
atom_pi, atom_cation, strict = pi_cation(pocket, ligand, tolerance=30)
assert strict.sum() == 2
assert atom_pi[strict]['resname'].tolist() == ['TRP', 'TRP']
assert atom_cation[strict]['atomtype'].tolist() == ['Na', 'Na']
atom_pi, atom_cation, strict = pi_cation(pocket, ligand, tolerance=10)
assert strict.sum() == 1
assert atom_pi[strict]['resname'].tolist() == ['TRP']
assert atom_cation[strict]['atomtype'].tolist() == ['Na']
def test_acceptor_halogen_pdb():
pocket = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data/pdb/4lb3_pocket.pdb')))
pocket.protein = True
ligand = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/pdb/4lb3_ligand.sdf')))
acceptors, halogens, strict = halogenbond_acceptor_halogen(pocket, ligand, tolerance=20)
assert strict.sum() == 0
acceptors, halogens, strict = halogenbond_acceptor_halogen(pocket, ligand, tolerance=30)
assert strict.sum() == 1
assert acceptors[strict]['resname'].tolist() == ['THR']
assert halogens[strict]['atomtype'].tolist() == ['I']
acceptors, halogens, strict = halogenbond_acceptor_halogen(pocket, ligand, tolerance=40)
assert strict.sum() == 2
assert acceptors[strict]['resname'].tolist() == ['VAL', 'THR']
assert halogens[strict]['atomtype'].tolist() == ['Cl', 'I']
def test_halogenbonds():
"""Halogen-Bonds test"""
halogenbonds_count = np.array([len(halogenbonds(rec, mol)[2]) for mol in mols])
assert_array_equal(halogenbonds_count,
[0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0])
def test_pi_stacking():
"""Pi-stacking test"""
lig = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data',
'pdbbind', '10gs',
'10gs_ligand.sdf')))
rec = next(oddt.toolkit.readfile('pdb', os.path.join(test_data_dir, 'data',
'pdbbind', '10gs',
'10gs_pocket.pdb')))
rec.protein = True
ring, _, strict_parallel, strict_perpendicular = pi_stacking(rec, lig, cutoff=7.5, tolerance=60)
lig_centroids = [[5.4701666, 6.1994996, 30.8313350],
[8.1811666, 2.5846664, 28.4028320]]
lig_vectors = [[-0.474239, 0.898374, 1.326541],
[0.62094, 1.120537, 1.086084]]
rec_centroids = [[5.6579995, 2.2964999, 23.4626674],
[7.8634004, 7.7310004, 34.8283996],
[9.8471670, 8.5676660, 34.9915008],
[9.9951667, 3.7756664, 32.8191680],
[10.055333, -1.4720000, 17.2121658],
[14.519165, 1.8759999, 29.8346652],
[16.490833, 16.873500, 27.9169998],
[18.718666, 12.703166, 33.3141670],
[25.716165, 4.9741668, 31.8198337]]
rec_vectors = [[-1.610038, 0.445293, 0.219816],
[-1.465347, -0.270806, -0.786749],
[-1.451653, -0.268732, 0.791577],
[-1.108574, 1.233418, -0.239182],
[-0.448415, -0.427071, -1.564852],
[0.230433, 0.007991, 1.662302],
[0.475315, -0.971355, -0.778596],
[0.484955, 1.471549, 0.672478],
[0.600022, -1.235512, -0.987680]]
centroids_dist = [[8.3406204, 5.5546951],
[4.9040379, 8.2385464],
[6.4863953, 9.0544131],
[5.5047319, 4.9206809],
[16.2897951, 12.0498984],
[10.0782127, 6.5362510],
[15.6167449, 16.5365460],
[14.9661240, 15.4124670],
[20.3071175, 18.0239224]]
assert_array_almost_equal(distance(rec_centroids, lig_centroids), centroids_dist)
assert len(lig.ring_dict) == 2
assert_array_almost_equal(sorted(lig.ring_dict['centroid'].tolist()), lig_centroids, decimal=5)
assert_array_almost_equal(sorted(lig.ring_dict['vector'].tolist()), lig_vectors, decimal=5)
assert len(rec.ring_dict) == 9
assert_array_almost_equal(sorted(rec.ring_dict['centroid'].tolist()), rec_centroids, decimal=5)
assert_array_almost_equal(sorted(rec.ring_dict['vector'].tolist()), rec_vectors, decimal=5)
assert len(ring) == 6
assert strict_parallel.sum() == 4
assert strict_perpendicular.sum() == 3
resids = sorted(ring['resid'])
# assert_array_equal(resids, [1, 2, 2, 17, 17, 58])
# re-check indexing of residues
assert_array_equal(rec.res_dict[resids]['resnum'], [7, 8, 8, 38, 38, 108])
assert_array_equal(sorted(ring['resnum']), [7, 8, 8, 38, 38, 108])
assert_array_equal(sorted(ring['resname']), ['PHE', 'PHE', 'TRP', 'TRP', 'TYR', 'TYR'])
def test_salt_bridges():
"""Salt bridges test"""
salt_bridges_count = np.array([len(salt_bridges(rec, mol)[0]) for mol in mols])
assert_array_equal(salt_bridges_count,
[2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2, 2,
2, 2, 2, 2, 1, 2, 2, 2, 2, 2])
def test_pi_cation():
"""Pi-cation test"""
pi_cation_count = np.array([len(pi_cation(rec, mol)[2]) for mol in mols])
if oddt.toolkit.backend == 'ob':
exp_count = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 2, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 2, 0, 0, 0, 0, 0]
else:
exp_count = [0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 1, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 0]
assert_array_equal(pi_cation_count, exp_count)
pi_cation_count = np.array([len(pi_cation(mol, rec)[2]) for mol in mols])
assert_array_equal(pi_cation_count,
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 1, 0, 1, 0, 2, 1, 0,
2, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1,
0, 1, 0, 0, 1, 2, 2, 1, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 2, 1, 0, 1, 0, 0, 1, 0, 1, 1,
0, 1, 0, 0, 0, 0, 2, 0, 0, 1])
# Strict
pi_cation_count = np.array([pi_cation(mol, rec)[2].sum() for mol in mols])
assert_array_equal(pi_cation_count,
[1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1, 1,
2, 1, 1, 1, 1, 0, 0, 1, 0, 0, 1, 0, 0, 1, 0, 2, 1, 0,
1, 0, 0, 1, 1, 1, 1, 0, 1, 1, 0, 1, 1, 0, 1, 0, 1, 1,
0, 1, 0, 0, 0, 2, 1, 0, 0, 1, 1, 1, 1, 0, 0, 1, 0, 0,
0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 1, 1,
0, 1, 0, 0, 0, 0, 0, 0, 0, 1]
)
def test_hyd_contacts():
"""Hydrophobic Contacts test"""
hyd_contacts_count = [len(hydrophobic_contacts(rec, mol)[0]) for mol in mols]
assert_array_equal(hyd_contacts_count,
[14, 10, 7, 14, 10, 13, 17, 14, 17, 12, 12, 10, 10, 11,
9, 8, 8, 4, 9, 16, 15, 6, 9, 8, 5, 5, 8, 11, 7, 10, 7,
13, 4, 13, 9, 9, 9, 4, 6, 16, 10, 13, 10, 9, 8, 9, 13,
15, 13, 9, 11, 9, 7, 10, 5, 3, 5, 7, 7, 10, 11, 7, 10,
20, 9, 6, 6, 3, 7, 7, 4, 7, 6, 2, 5, 6, 14, 9, 4, 6,
11, 10, 9, 6, 10, 8, 6, 5, 6, 11, 8, 16, 9, 9, 11, 6,
8, 5, 8, 15])
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