def test_calculate_initial_poses(self):
file_name = self.golden_data_path / '3p0g' / 'receptor_membrane.pdb'
_, _, chains = parse_complex_from_file(file_name)
receptor = Complex(chains, structure_file_name=file_name)
file_name = self.golden_data_path / '3p0g' / 'ligand.pdb'
_, _, chains = parse_complex_from_file(file_name)
ligand = Complex(chains, structure_file_name=file_name)
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
num_swarms = 100
num_glowworms = 10
surface_density = 50.
restraints = parse_restraints_file(self.golden_data_path / '3p0g' / 'restraints.list')
receptor_restraints = get_restraints(receptor, restraints['receptor'])
ligand_restraints = get_restraints(ligand, restraints['ligand'])
rec_restraints = receptor_restraints['active'] + receptor_restraints['passive']
lig_restraints = ligand_restraints['active'] + ligand_restraints['passive']
positions_files = calculate_initial_poses(receptor, ligand, num_swarms, num_glowworms,
STARTING_POINTS_SEED, rec_restraints, lig_restraints,
rec_translation, lig_translation, surface_density,
dest_folder=self.test_path, is_membrane=True)
assert filecmp.cmp(positions_files[0], self.golden_data_path / '3p0g' / 'init' / 'initial_positions_0.dat')
assert filecmp.cmp(positions_files[1], self.golden_data_path / '3p0g' / 'init' / 'initial_positions_1.dat')
def calculate_starting_positions(receptor,
ligand,
swarms,
glowworms,
starting_points_seed,
receptor_restraints,
ligand_restraints,
rec_translation,
lig_translation,
surface_density,
use_anm=False,
anm_seed=0,
anm_rec=DEFAULT_NMODES_REC,
anm_lig=DEFAULT_NMODES_LIG,
is_membrane=False,
is_transmembrane=False,
write_starting_positions=False,
swarm_radius=DEFAULT_SWARM_RADIUS):
"""Defines the starting positions of each glowworm in the simulation.
If the init folder already exists, uses the starting positions from this folder.
"""
log.info("Calculating starting positions...")
init_folder = DEFAULT_POSITIONS_FOLDER
if not os.path.isdir(init_folder):
os.mkdir(init_folder)
starting_points_files = calculate_initial_poses(
receptor, ligand, swarms, glowworms, starting_points_seed,
receptor_restraints, ligand_restraints, rec_translation,
lig_translation, surface_density, init_folder, use_anm, anm_seed,
anm_rec, anm_lig, is_membrane, is_transmembrane,
write_starting_positions, swarm_radius)
log.info(f"Generated {len(starting_points_files)} positions files")
else:
if receptor_restraints:
log.warning(
f"Folder {init_folder} already exists and restraints apply. Please check for consistency."
)
else:
log.warning(
f"Folder {init_folder} already exists, skipping calculation")
pattern = str(
Path(DEFAULT_POSITIONS_FOLDER) /
Path(f"{DEFAULT_STARTING_PREFIX}*.dat"))
starting_points_files = glob.glob(pattern)
for starting_point_file in starting_points_files:
if not check_starting_file(starting_point_file, glowworms, use_anm,
anm_rec, anm_lig):
raise LightDockError(
f"Error reading starting coordinates from file {starting_point_file}"
)
log.info("Done.")
return starting_points_files
def calculate_starting_positions(receptor,
ligand,
swarms,
glowworms,
starting_points_seed,
receptor_restraints,
ligand_restraints,
rec_translation,
lig_translation,
ftdock_file=None,
use_anm=False,
anm_seed=0,
anm_rec=DEFAULT_NMODES_REC,
anm_lig=DEFAULT_NMODES_LIG,
is_membrane=False):
"""Defines the starting positions of each glowworm in the simulation.
If the init_folder already exists, uses the starting positions from this folder.
"""
log.info("Calculating starting positions...")
init_folder = DEFAULT_POSITIONS_FOLDER
if not os.path.isdir(init_folder):
os.mkdir(init_folder)
starting_points_files = calculate_initial_poses(
receptor, ligand, swarms, glowworms, starting_points_seed,
receptor_restraints, ligand_restraints, rec_translation,
lig_translation, init_folder, ftdock_file, use_anm, anm_seed,
anm_rec, anm_lig, is_membrane)
log.info("Generated %d positions files" % len(starting_points_files))
else:
if receptor_restraints:
log.warning(
"Folder %s already exists and restraints apply. Check for consistency, possible error!"
% init_folder)
else:
log.warning("Folder %s already exists, skipping calculation" %
init_folder)
pattern = os.path.join(DEFAULT_POSITIONS_FOLDER,
"%s*.dat" % DEFAULT_STARTING_PREFIX)
starting_points_files = glob.glob(pattern)
if len(starting_points_files) != swarms:
raise LightDockError(
"The number of initial positions files does not correspond with the number of swarms"
)
for starting_point_file in starting_points_files:
if not check_starting_file(starting_point_file, glowworms, use_anm,
anm_rec, anm_lig):
raise LightDockError(
"Error reading starting coordinates from file %s" %
starting_point_file)
log.info("Done.")
return starting_points_files
def test_calculate_initial_poses(self):
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g',
'receptor_membrane.pdb'))
receptor = Complex(chains)
atoms, residues, chains = parse_complex_from_file(
os.path.join(self.golden_data_path, '3p0g', 'ligand.pdb'))
ligand = Complex(chains)
rec_translation = receptor.move_to_origin()
lig_translation = ligand.move_to_origin()
num_swarms = 10
num_glowworms = 10
seed = 324324
restraints = parse_restraints_file(
os.path.join(self.golden_data_path, '3p0g', 'restraints.list'))
receptor_restraints = get_restraints(receptor, restraints['receptor'])
ligand_restraints = get_restraints(ligand, restraints['ligand'])
rec_restraints = receptor_restraints['active'] + receptor_restraints[
'passive']
lig_restraints = ligand_restraints['active'] + ligand_restraints[
'passive']
positions_files = calculate_initial_poses(receptor,
ligand,
num_swarms,
num_glowworms,
seed,
rec_restraints,
lig_restraints,
rec_translation,
lig_translation,
dest_folder=self.test_path,
is_membrane=True)
assert filecmp.cmp(
positions_files[0],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_0.dat'))
assert filecmp.cmp(
positions_files[1],
os.path.join(self.golden_data_path, '3p0g', 'init',
'initial_positions_1.dat'))
def calculate_starting_positions(receptor, ligand, swarms, glowworms, starting_points_seed,
receptor_restraints, ligand_restraints, rec_translation, lig_translation, ftdock_file=None,
use_anm=False, anm_seed=0, anm_rec=DEFAULT_NMODES_REC, anm_lig=DEFAULT_NMODES_LIG,
is_membrane=False):
"""Defines the starting positions of each glowworm in the simulation.
If the init_folder already exists, uses the starting positions from this folder.
"""
log.info("Calculating starting positions...")
init_folder = DEFAULT_POSITIONS_FOLDER
if not os.path.isdir(init_folder):
os.mkdir(init_folder)
starting_points_files = calculate_initial_poses(receptor, ligand,
swarms, glowworms,
starting_points_seed,
receptor_restraints, ligand_restraints,
rec_translation, lig_translation,
init_folder,
ftdock_file, use_anm,
anm_seed, anm_rec, anm_lig,
is_membrane)
log.info("Generated %d positions files" % len(starting_points_files))
else:
if receptor_restraints:
log.warning("Folder %s already exists and restraints apply. Check for consistency, possible error!" % init_folder)
else:
log.warning("Folder %s already exists, skipping calculation" % init_folder)
pattern = os.path.join(DEFAULT_POSITIONS_FOLDER, "%s*.dat" % DEFAULT_STARTING_PREFIX)
starting_points_files = glob.glob(pattern)
if len(starting_points_files) != swarms:
raise LightDockError("The number of initial positions files does not correspond with the number of swarms")
for starting_point_file in starting_points_files:
if not check_starting_file(starting_point_file, glowworms, use_anm, anm_rec, anm_lig):
raise LightDockError("Error reading starting coordinates from file %s" % starting_point_file)
log.info("Done.")
return starting_points_files