def test_get_quaternion_for_restraint1(self):
# Origin is 0,0,0
# Ligand center
l_center = [-5., 5., -5.]
# Ligand residue
l_res = [-7., 7., -7.]
# Receptor residue
r_res = [3., 1., 0.]
# Calculate quaternion for rotation from l_res to point to r_res
rec_residue = Residue.dummy(r_res[0], r_res[1], r_res[2])
lig_residue = Residue.dummy(l_res[0], l_res[1], l_res[2])
q = get_quaternion_for_restraint(
rec_residue,
lig_residue,
l_center[0],
l_center[1],
l_center[2], # translation
[0., 0., 0.], # receptor translation
[5., -5., 5.] # ligand translation
)
e = Quaternion(w=0.14518697,
x=0.19403814,
y=-0.58211441,
z=-0.77615254)
assert e == q
def test_get_quaternion_for_restraint2d(self):
# Origin is 0,0,0
# Ligand center
l_center = [5., 5., 0.]
# Ligand residue
l_res = [7., 7., 0.]
# Receptor residue
r_res = [3., 1., 0.]
# Calculate quaternion for rotation from l_res to point to r_res
rec_residue = Residue.dummy(r_res[0], r_res[1], r_res[2])
lig_residue = Residue.dummy(l_res[0], l_res[1], l_res[2])
q = get_quaternion_for_restraint(
rec_residue,
lig_residue,
l_center[0],
l_center[1],
l_center[2], # translation
[0., 0., 0.], # receptor translation
[5., 5., 0.] # ligand translation
)
e = Quaternion(0.16018224, 0., 0., -0.98708746)
assert e == q
def test_get_quaternion_for_restraint2d_different_quadrant(self):
# Origin is 0,0,0
# Ligand center
l_center = [5., -5., 0.]
# Ligand residue
l_res = [7., -7., 0.]
# Receptor residue
r_res = [-3., 1., 0.]
# Calculate quaternion for rotation from l_res to point to r_res
rec_residue = Residue.dummy(r_res[0], r_res[1], r_res[2])
lig_residue = Residue.dummy(l_res[0], l_res[1], l_res[2])
q = get_quaternion_for_restraint(
rec_residue,
lig_residue,
l_center[0],
l_center[1],
l_center[2], # translation
[0., 0., 0.], # receptor translation
[5., -5., 0.] # ligand translation
)
e = Quaternion(0.07088902, 0., 0., -0.99748421)
assert e == q
def test_get_quaternion_for_restraint2(self):
# Origin is 0,0,0
# Ligand center
l_center = [-5., 5., -5.]
# Ligand residue
l_res = [-7., 6., -7.]
# Receptor residue
r_res = [3., 1., 0.]
# Calculate quaternion for rotation from l_res to point to r_res
rec_residue = Residue.dummy(r_res[0], r_res[1], r_res[2])
lig_residue = Residue.dummy(l_res[0], l_res[1], l_res[2])
q = get_quaternion_for_restraint(
rec_residue,
lig_residue,
l_center[0],
l_center[1],
l_center[2], # translation
[0., 0., 0.], # receptor translation
[5., -5., 5.] # ligand translation
)
e = Quaternion(0.10977233, -0.44451098, -0.88902195, 0.)
assert e == q
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_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_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 populate_poses(to_generate,
center,
radius,
number_generator,
rec_translation,
lig_translation,
rng_nm=None,
rec_nm=0,
lig_nm=0,
receptor_restraints=None,
ligand_restraints=None,
ligand_diameter=1.):
"""Creates new poses around a given center and a given radius"""
new_poses = []
# Flatten if necessary receptor_restraints
if receptor_restraints:
try:
receptor_restraints = receptor_restraints[
'active'] + receptor_restraints['passive']
except TypeError:
pass
# Calculate closest residue restraints
closest_residues = []
if receptor_restraints:
distances = []
for i, residue in enumerate(receptor_restraints):
ca = residue.get_calpha()
if not ca:
ca = residue.get_atom('P')
distances.append(
(i, cdistance(ca.x, ca.y, ca.z, center[0], center[1],
center[2])))
distances.sort(key=lambda tup: tup[1])
closest_residues = [x[0] for x in distances[:10]]
for _ in range(to_generate):
# First calculate a random translation within the swarm sphere
x, y, z = get_random_point_within_sphere(number_generator, radius)
tx = center[0] + x
ty = center[1] + y
tz = center[2] + z
# Restraints in both partners
if receptor_restraints and ligand_restraints:
# We select one of the closest residue restraints to point the quaternion
rec_residue = receptor_restraints[closest_residues[
number_generator.randint(0,
len(closest_residues) - 1)]]
# Random restraint on the ligand to use for pre-orientation
lig_residue = ligand_restraints[number_generator.randint(
0,
len(ligand_restraints) - 1)]
# Calculate the quaternion which rotates the ligand to point to the given receptor restraint
q = get_quaternion_for_restraint(rec_residue, lig_residue, tx, ty,
tz, rec_translation,
lig_translation)
# Only restraints in the ligand partner
elif ligand_restraints and not receptor_restraints:
# The strategy is similar to previous but for the receptor side we will use a simulated point
# over the receptor surface to point out the quaternion
coef = norm(center) / ligand_diameter
if coef > 1.0:
raise LightDockWarning(
'Found wrong coefficient on calculating poses with restraints'
)
# It is important to keep the coordinates as in the original complex without
# moving to the center of coordinates (applying translation)
rec_residue = Residue.dummy(center[0] * coef - rec_translation[0],
center[1] * coef - rec_translation[1],
center[2] * coef - rec_translation[2])
lig_residue = ligand_restraints[number_generator.randint(
0,
len(ligand_restraints) - 1)]
q = get_quaternion_for_restraint(rec_residue, lig_residue, tx, ty,
tz, rec_translation,
lig_translation)
# No restraints at all
else:
q = Quaternion.random(number_generator)
# Glowworm's optimization vector
op_vector = [tx, ty, tz, q.w, q.x, q.y, q.z]
# If ANM is enabled, we need to create random components for the extents
if rng_nm:
if rec_nm > 0:
op_vector.extend([rng_nm() for _ in range(rec_nm)])
if lig_nm > 0:
op_vector.extend([rng_nm() for _ in range(lig_nm)])
new_poses.append(op_vector)
return new_poses
def test_dummy_residue(self):
dummy = Residue.dummy(1.0, 2.0, 3.0)
assert 1 == len(dummy.atoms)
assert 'CA' == dummy.atoms[0].name
assert " CA 1.000 2.000 3.000" == str(dummy.atoms[0])
def test_dummy_residue(self):
dummy = Residue.dummy(1.0, 2.0, 3.0)
assert len(dummy.atoms) == 1
assert dummy.atoms[0].name == "CA"
assert str(dummy.atoms[0]) == " CA 1.000 2.000 3.000"