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_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 _full_mutate(self, x):
c = self.c0.copy()
trans_vec = x[:3]
rot_vec = x[3:6]
rotors_vec = x[6:]
c = rotate(c, *rot_vec) + trans_vec * self.box_size
for i in range(len(rotors_vec)):
a = self.engine.rotors[i]['atoms']
mask = self.engine.rotors[i]['mask']
c = change_dihedral(c, a[0], a[1], a[2], a[3], rotors_vec[i], mask)
self.c1 = c.copy()
self.x1 = x.copy()
return c
def _inc_mutate(self, x, c):
c = c.copy()
trans_vec = x[:3]
rot_vec = x[3:6]
rotors_vec = x[6:]
if (rot_vec != 0).any():
c = rotate(c, *rot_vec)
if (trans_vec != 0).any():
c += trans_vec * self.box_size
for i in np.where(rotors_vec != 0)[0]:
a = self.engine.rotors[i]['atoms']
mask = self.engine.rotors[i]['mask']
c = change_dihedral(c, a[0], a[1], a[2], a[3], rotors_vec[i], mask)
return c
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)
# 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))
assert_array_almost_equal([rmsd(mols[0], mol) for mol in mols[1:]], [
4.753552, 2.501487, 2.7941732, 1.1281863, 0.74440968, 1.6256877,
4.762476, 2.7167852, 2.5504358, 1.9303833, 2.6200771, 3.1741529,
3.225431, 4.7784939, 4.8035369, 7.8962774, 2.2385094, 4.8625236,
3.2036853
])
assert_array_almost_equal(
[rmsd(mols[0], mol, method='hungarian') for mol in mols[1:]], [
0.90126, 1.073049, 1.053131, 1.028578, 0.735297, 1.409403,
0.539091, 1.329666, 1.088053, 1.779618, 2.606429, 3.157684,
3.213502, 0.812635, 1.290902, 2.521703, 2.083612, 1.832457,
3.187363
])
def test_spatial():
"""Test spatial computations"""
# 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)
mol = oddt.toolkit.readstring('smi', 'c1ccccc1')
mol.make3D()
# Check benzene ring angle
assert_array_almost_equal(angle(mol.coords[0],
mol.coords[1],
mol.coords[2]), 120, decimal=1)
# 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
assert_array_almost_equal(dihedral(mol.coords[0],
mol.coords[1],
mol.coords[2],
mol.coords[3]), 0, decimal=1)
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)
# 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))
assert_array_almost_equal([rmsd(mols[0], mol) for mol in mols[1:]],
[4.753552, 2.501487, 2.7941732, 1.1281863, 0.74440968,
1.6256877, 4.762476, 2.7167852, 2.5504358, 1.9303833,
2.6200771, 3.1741529, 3.225431, 4.7784939, 4.8035369,
7.8962774, 2.2385094, 4.8625236, 3.2036853])
assert_array_almost_equal([rmsd(mols[0], mol, method='hungarian') for mol in mols[1:]],
[2.5984519, 1.7295024, 1.1268076, 1.0285776, 0.73529714,
1.4094033, 2.5195069, 1.7449125, 1.5116163, 1.7796179,
2.6064286, 3.1576841, 3.2135022, 3.1675091, 2.7001681,
5.1263351, 2.0836117, 3.542397, 3.1873631])