import os
import pytest
from numpy.testing import (assert_almost_equal,
assert_array_equal,
assert_array_almost_equal)
import numpy as np
import oddt
from oddt.spatial import (angle,
dihedral,
rmsd,
distance,
rotate)
from .utils import shuffle_mol
test_data_dir = os.path.dirname(os.path.abspath(__file__))
ASPIRIN_SDF = """
RDKit 3D
13 13 0 0 0 0 0 0 0 0999 V2000
3.3558 -0.4356 -1.0951 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0868 -0.6330 -0.3319 C 0 0 0 0 0 0 0 0 0 0 0 0
2.0284 -0.9314 0.8534 O 0 0 0 0 0 0 0 0 0 0 0 0
1.0157 -0.4307 -1.1906 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.2079 -0.5332 -0.5260 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.9020 -1.7350 -0.6775 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1373 -1.8996 -0.0586 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6805 -0.8641 0.6975 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.9933 0.3419 0.8273 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7523 0.5244 0.2125 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.0600 1.8264 0.3368 C 0 0 0 0 0 0 0 0 0 0 0 0
0.9397 2.1527 -0.2811 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.6931 2.6171 1.2333 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
2 4 1 0
4 5 1 0
5 6 2 0
6 7 1 0
7 8 2 0
8 9 1 0
9 10 2 0
10 11 1 0
11 12 2 0
11 13 1 0
10 5 1 0
M END
"""
def test_angles():
"""Test spatial computations - angles"""
# Angles
assert_array_almost_equal(angle(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0))), 90)
assert_array_almost_equal(angle(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((1, 1, 0))), 45)
# Check benzene ring angle
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
assert_array_almost_equal(angle(mol.coords[0],
mol.coords[1],
mol.coords[2]), 120, decimal=1)
def test_dihedral():
"""Test dihedrals"""
# Dihedrals
assert_array_almost_equal(dihedral(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0)),
np.array((1, 1, 0))), 0)
assert_array_almost_equal(dihedral(np.array((1, 0, 0)),
np.array((0, 0, 0)),
np.array((0, 1, 0)),
np.array((1, 1, 1))), -45)
# Check benzene ring dihedral
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
assert abs(dihedral(*mol.coords[:4])) < 2.
def test_distance():
mol1 = oddt.toolkit.readstring('sdf', ASPIRIN_SDF)
d = distance(mol1.coords, mol1.coords)
n_atoms = len(mol1.coords)
assert d.shape, (n_atoms == n_atoms)
assert_array_equal(d[np.eye(len(mol1.coords), dtype=bool)], np.zeros(n_atoms))
d = distance(mol1.coords, mol1.coords.mean(axis=0).reshape(1, 3))
assert d.shape, (n_atoms == 1)
ref_dist = [[3.556736951371501], [2.2058040428631056], [2.3896002745745415],
[1.6231668718498249], [0.7772981740050453], [2.0694947503940004],
[2.8600587871157184], [2.9014207091233857], [2.1850791695403564],
[0.9413368403116871], [1.8581710293650173], [2.365629642108773],
[2.975007440512798]]
assert_array_almost_equal(d, ref_dist)
def test_spatial():
"""Test spatial misc computations"""
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol2 = mol.clone
# Test rotation
assert_almost_equal(mol2.coords, rotate(mol2.coords, np.pi, np.pi, np.pi))
# Rotate perpendicular to ring
mol2.coords = rotate(mol2.coords, 0, 0, np.pi)
# RMSD
assert_almost_equal(rmsd(mol, mol2, method=None), 2.77, decimal=1)
# Hungarian must be close to zero (RDKit is 0.3)
assert_almost_equal(rmsd(mol, mol2, method='hungarian'), 0, decimal=0)
# Minimized by symetry must close to zero
assert_almost_equal(rmsd(mol, mol2, method='min_symmetry'), 0, decimal=0)
def test_rmsd():
# pick one molecule from docked poses
mols = list(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
mols = list(filter(lambda x: x.title == '312335', mols))
res = {
'method=None':
[4.7536, 2.5015, 2.7942, 1.1282, 0.7444, 1.6257, 4.7625,
2.7168, 2.5504, 1.9304, 2.6201, 3.1742, 3.2254, 4.7785,
4.8035, 7.8963, 2.2385, 4.8625, 3.2037],
'method=hungarian':
[0.9013, 1.0730, 1.0531, 1.0286, 0.7353, 1.4094, 0.5391,
1.3297, 1.0881, 1.7796, 2.6064, 3.1577, 3.2135, 0.8126,
1.2909, 2.5217, 2.0836, 1.8325, 3.1874],
'method=min_symmetry':
[0.9013, 1.0732, 1.0797, 1.0492, 0.7444, 1.6257, 0.5391,
1.5884, 1.0935, 1.9304, 2.6201, 3.1742, 3.2254, 1.1513,
1.5206, 2.5361, 2.2385, 1.971, 3.2037],
}
kwargs_grid = [{'method': None},
{'method': 'hungarian'},
{'method': 'min_symmetry'}]
for kwargs in kwargs_grid:
res_key = '_'.join('%s=%s' % (k, v)
for k, v in sorted(kwargs.items()))
assert_array_almost_equal([rmsd(mols[0], mol, **kwargs)
for mol in mols[1:]],
res[res_key], decimal=4)
# test shuffled rmsd
for _ in range(5):
for kwargs in kwargs_grid:
# dont use method=None in shuffled tests
if kwargs['method'] is None:
continue
res_key = '_'.join('%s=%s' % (k, v)
for k, v in sorted(kwargs.items()))
assert_array_almost_equal([rmsd(mols[0],
shuffle_mol(mol),
**kwargs)
for mol in mols[1:]],
res[res_key], decimal=4)
def test_rmsd_errors():
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
mol.addh()
mol2 = next(oddt.toolkit.readfile('sdf', os.path.join(test_data_dir, 'data/dude/xiap/actives_docked.sdf')))
for method in [None, 'hungarian', 'min_symmetry']:
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(mol, mol2, method=method)
for _ in range(5):
with pytest.raises(ValueError, match='Unequal number of atoms'):
rmsd(shuffle_mol(mol), shuffle_mol(mol2), method=method)
Datasets
Models
