def create_positions(path, cid, pose):
positions = get_new_positions(pose)
positions_file = os.path.join(
path, "%s_%d.bild" % (DEFAULT_BILD_STARTING_PREFIX, cid))
create_bild_file(positions_file, positions)
pos_file_name = os.path.join(path,
'%s_%s.dat' % (DEFAULT_STARTING_PREFIX, cid))
create_file_from_poses(pos_file_name, positions)
def test_create_bild_file(self):
poses = [[0., 0., 0., 0.5, 0.5, 0.5, 0.5],
[2., 2., 2., 0., 0.7071, 0.7071, 0.],
[-2., -2., -2., 0., 0., 0.7071, 0.7071]]
generated_file = os.path.join(self.test_path, 'test.bild')
expected_file = os.path.join(self.golden_data_path, 'test.bild')
create_bild_file(generated_file, poses)
assert filecmp.cmp(generated_file, expected_file)
def calculate_initial_poses(receptor,
ligand,
num_clusters,
num_glowworms,
seed,
receptor_restraints,
ligand_restraints,
rec_translation,
lig_translation,
dest_folder,
ftdock_file='',
nm_mode=False,
nm_seed=0,
rec_nm=0,
lig_nm=0,
is_membrane=False):
"""Calculates the starting points for each of the glowworms using the center of swarms"""
# Random number generator for poses
rng = MTGenerator(seed)
# Random number generator for NM
if nm_mode:
rng_nm = NormalGenerator(nm_seed,
mu=DEFAULT_EXTENT_MU,
sigma=DEFAULT_EXTENT_SIGMA)
else:
rng_nm = None
# Calculate swarm centers
swarm_centers, receptor_diameter, ligand_diameter = calculate_surface_points(
receptor,
ligand,
num_clusters,
distance_step=1.0,
is_membrane=is_membrane)
# Filter swarms far from the restraints
if receptor_restraints:
regular_restraints = receptor_restraints[
'active'] + receptor_restraints['passive']
swarm_centers = apply_restraints(swarm_centers, regular_restraints,
receptor_restraints['blocked'],
ligand_diameter / 2., rec_translation)
# Filter out swarms which are not compatible with the explicit membrane
if is_membrane:
membrane_beads = [
residue for residue in receptor.residues if residue.name == 'MMB'
]
swarm_centers = apply_membrane(swarm_centers, membrane_beads,
rec_translation)
pdb_file_name = os.path.join(dest_folder, CLUSTERS_CENTERS_FILE)
create_pdb_from_points(pdb_file_name, swarm_centers)
ligand_center = ligand.center_of_coordinates()
radius = 10. # ligand_diameter / 2.
positions_files = []
# Populate the clusters using the FTDock poses
if ftdock_file:
if nm_mode:
raise NotImplementedError(
'Using FTDock poses with NM is not supported')
poses = FTDockCoordinatesParser.get_list_of_poses(
ftdock_file, ligand_center)
clusters = classify_ftdock_poses(poses, swarm_centers, radius)
for cluster_id, ftdock_poses in clusters.items():
# Translate FTDock poses into lightdock poses
poses = []
for pose in ftdock_poses:
poses.append([
pose.translation[0], pose.translation[1],
pose.translation[2], pose.q.w, pose.q.x, pose.q.y, pose.q.z
])
# Populate new poses if needed
if len(poses) < num_glowworms:
needed = num_glowworms - len(poses)
poses.extend(
populate_poses(needed, swarm_centers[cluster_id], radius,
rng, rec_translation, lig_translation))
# Save poses as pdb file
pdb_file_name = os.path.join(
dest_folder,
'%s_%s.pdb' % (DEFAULT_PDB_STARTING_PREFIX, cluster_id))
create_pdb_from_points(pdb_file_name,
[[pose[0], pose[1], pose[2]]
for pose in poses[:num_glowworms]])
# Save poses as initial_positions file
pos_file_name = os.path.join(
dest_folder,
'%s_%s.dat' % (DEFAULT_STARTING_PREFIX, cluster_id))
bild_file_name = os.path.join(
dest_folder,
'%s_%s.bild' % (DEFAULT_BILD_STARTING_PREFIX, cluster_id))
create_file_from_poses(pos_file_name, poses[:num_glowworms])
positions_files.append(pos_file_name)
create_bild_file(bild_file_name, poses)
else:
for swarm_id, swarm_center in enumerate(swarm_centers):
poses = populate_poses(num_glowworms, swarm_center, radius, rng,
rec_translation, lig_translation, rng_nm,
rec_nm, lig_nm, receptor_restraints,
ligand_restraints, ligand_diameter)
# Save poses as pdb file
pdb_file_name = os.path.join(
dest_folder,
'%s_%s.pdb' % (DEFAULT_PDB_STARTING_PREFIX, swarm_id))
create_pdb_from_points(pdb_file_name,
[[pose[0], pose[1], pose[2]]
for pose in poses[:num_glowworms]])
# Save poses as initial_positions file
pos_file_name = os.path.join(
dest_folder, '%s_%s.dat' % (DEFAULT_STARTING_PREFIX, swarm_id))
bild_file_name = os.path.join(
dest_folder,
'%s_%s.bild' % (DEFAULT_BILD_STARTING_PREFIX, swarm_id))
create_file_from_poses(pos_file_name, poses[:num_glowworms])
positions_files.append(pos_file_name)
create_bild_file(bild_file_name, poses)
return positions_files
def calculate_initial_poses(receptor,
ligand,
num_swarms,
num_glowworms,
seed,
receptor_restraints,
ligand_restraints,
rec_translation,
lig_translation,
surface_density,
dest_folder,
nm_mode=False,
nm_seed=0,
rec_nm=0,
lig_nm=0,
is_membrane=False,
is_transmembrane=False,
writing_starting_positions=False,
swarm_radius=10.):
"""Calculates the starting points for each of the glowworms using the center of swarms"""
# Random number generator for poses
rng = MTGenerator(seed)
# Random number generator for NM
if nm_mode:
rng_nm = NormalGenerator(nm_seed,
mu=DEFAULT_EXTENT_MU,
sigma=DEFAULT_EXTENT_SIGMA)
else:
rng_nm = None
# Calculate swarm centers
has_membrane = is_membrane or is_transmembrane
swarm_centers, receptor_diameter, ligand_diameter = calculate_surface_points(
receptor,
ligand,
num_swarms,
rec_translation,
surface_density,
seed=seed,
has_membrane=has_membrane)
# Filter swarms far from the restraints
if receptor_restraints:
regular_restraints = receptor_restraints[
'active'] + receptor_restraints['passive']
swarm_centers = apply_restraints(swarm_centers, regular_restraints,
receptor_restraints['blocked'],
ligand_diameter / 2., rec_translation)
# Filter out swarms which are not compatible with the explicit membrane
if has_membrane:
membrane_beads = [
residue for residue in receptor.residues if residue.name == 'MMB'
]
swarm_centers = apply_membrane(swarm_centers, membrane_beads,
rec_translation, is_transmembrane)
pdb_file_name = os.path.join(dest_folder, SWARM_CENTERS_FILE)
create_pdb_from_points(pdb_file_name, swarm_centers)
ligand_center = ligand.center_of_coordinates()
positions_files = []
for swarm_id, swarm_center in enumerate(swarm_centers):
poses = populate_poses(num_glowworms, swarm_center, swarm_radius, rng,
rec_translation, lig_translation, rng_nm,
rec_nm, lig_nm, receptor_restraints,
ligand_restraints, ligand_diameter)
if writing_starting_positions:
# Save poses as pdb file
pdb_file_name = os.path.join(
dest_folder,
'%s_%s.pdb' % (DEFAULT_PDB_STARTING_PREFIX, swarm_id))
create_pdb_from_points(pdb_file_name,
[[pose[0], pose[1], pose[2]]
for pose in poses[:num_glowworms]])
# Generate bild files for glowworm orientations
bild_file_name = os.path.join(
dest_folder,
'%s_%s.bild' % (DEFAULT_BILD_STARTING_PREFIX, swarm_id))
create_bild_file(bild_file_name, poses)
# Save poses as initial_positions file
pos_file_name = os.path.join(
dest_folder, '%s_%s.dat' % (DEFAULT_STARTING_PREFIX, swarm_id))
create_file_from_poses(pos_file_name, poses[:num_glowworms])
positions_files.append(pos_file_name)
return positions_files
def create_positions(path, cid, pose):
positions = get_new_positions(pose)
positions_file = os.path.join(path, "%s_%d.bild" % (DEFAULT_BILD_STARTING_PREFIX, cid))
create_bild_file(positions_file, positions)
pos_file_name = os.path.join(path, '%s_%s.dat' % (DEFAULT_STARTING_PREFIX, cid))
create_file_from_poses(pos_file_name, positions)
