def test_get_random(self):
q1 = Quaternion.random()
assert_almost_equals(1.0, q1.norm())
rng = MTGenerator(1379)
q2 = Quaternion.random(rng)
expected = Quaternion(0.53224081, -0.00589472, 0.84280352, 0.07979471)
assert expected == q2
def test_get_random(self):
q1 = Quaternion.random()
assert_almost_equals(1.0, q1.norm())
rng = MTGenerator(1379)
q2 = Quaternion.random(rng)
expected = Quaternion(0.53224081, -0.00589472, 0.84280352, 0.07979471)
assert expected == q2
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
