def test_get_setup_from_file(self):
read = get_setup_from_file(self.golden_data_path / 'setup.json')
expected = {
"anm_lig": 10,
"anm_rec": 10,
"anm_seed": 324324,
"glowworms": 10,
"ligand_pdb": "2UUY_lig.pdb",
"membrane": False,
"noh": False,
"noxt": True,
"receptor_pdb": "2UUY_rec.pdb",
"restraints": None,
"starting_points_seed": 324324,
"surface_density": 50.0,
"swarm_radius": 10.0,
"swarms": 5,
"transmembrane": False,
"use_anm": True,
"verbose_parser": False,
"write_starting_positions": False
}
assert read == expected
def test_create_simulation_info_file(self):
setup = get_setup_from_file(self.golden_data_path /
'create_simulation_info_file' /
'setup.json')
class Args:
pass
args = Args()
for k, v in setup.items():
setattr(args, k, v)
file_name = create_simulation_info_file(args, path=self.test_path)
assert Path(file_name).name == 'lightdock.info'
file_name = create_simulation_info_file(args, path=self.test_path)
assert Path(file_name).name == 'lightdock.info.1'
def test_create_simulation_info_file(self):
setup = get_setup_from_file(
os.path.join(self.golden_data_path, 'create_simulation_info_file',
'setup.json'))
class Args:
pass
args = Args()
for k, v in setup.items():
setattr(args, k, v)
file_name = create_simulation_info_file(args, path=self.test_path)
assert os.path.basename(file_name) == 'lightdock.info'
file_name = create_simulation_info_file(args, path=self.test_path)
assert os.path.basename(file_name) == 'lightdock.info.1'
def test_get_setup_from_file(self):
read = get_setup_from_file(os.path.join(self.golden_data_path, 'setup.json'))
expected = {
"anm_lig": 10,
"anm_rec": 10,
"anm_seed": 324324,
"ftdock_file": None,
"glowworms": 10,
"ligand_pdb": "2UUY_lig.pdb",
"membrane": False,
"noh": False,
"noxt": True,
"receptor_pdb": "2UUY_rec.pdb",
"restraints": None,
"starting_points_seed": 324324,
"swarms": 5,
"use_anm": True,
"verbose_parser": False
}
assert read == expected
def run_simulation(parser):
"""Main program"""
try:
parser = CommandLineParser()
args = parser.args
# Read setup and add it to the actual args object
setup = get_setup_from_file(args.setup_file)
for k, v in setup.items():
setattr(args, k, v)
info_file = create_simulation_info_file(args)
log.info("simulation parameters saved to %s" % info_file)
# Read input structures (use parsed ones)
parsed_lightdock_receptor = os.path.join(
os.path.dirname(args.receptor_pdb),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(args.receptor_pdb))
receptor = read_input_structure(parsed_lightdock_receptor, args.noxt,
args.noh, args.verbose_parser)
parsed_lightdock_ligand = os.path.join(
os.path.dirname(args.ligand_pdb),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(args.ligand_pdb))
ligand = read_input_structure(parsed_lightdock_ligand, args.noxt,
args.noh, args.verbose_parser)
# CRITICAL to not break compatibility with previous results
receptor.move_to_origin()
ligand.move_to_origin()
if args.use_anm:
try:
receptor.n_modes = read_nmodes(
"%s%s" % (DEFAULT_REC_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for receptor molecule")
receptor.n_modes = None
try:
ligand.n_modes = read_nmodes(
"%s%s" % (DEFAULT_LIG_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for ligand molecule")
ligand.n_modes = None
starting_points_files = load_starting_positions(
args.swarms, args.glowworms, args.use_anm, args.anm_rec,
args.anm_lig)
scoring_functions, adapters = set_scoring_function(
parser, receptor, ligand)
tasks = prepare_gso_tasks(parser, adapters, scoring_functions,
starting_points_files)
# Preparing the parallel execution
kraken = Kraken(tasks, parser.args.cores, parser.args.profiling)
log.info("Monster spotted")
reports_queue = kraken.release()
log.info("Finished.")
except KeyboardInterrupt:
log.info("Caught interrupt...")
try:
kraken.sink()
except:
pass
log.info("bye.")
except OSError as e:
log.error("OS error found")
try:
kraken.sink()
except:
pass
raise e
def run_simulation(parser):
"""Main program, includes MPI directives"""
try:
comm = MPI.COMM_WORLD
parser = CommandLineParser()
args = parser.args
# Read setup and add it to the actual args object
setup = get_setup_from_file(args.setup_file)
for k, v in setup.items():
setattr(args, k, v)
minion_id = comm.rank
if minion_id == 0:
info_file = create_simulation_info_file(args)
log.info("simulation parameters saved to %s" % info_file)
comm.Barrier()
# Read input structures (use parsed ones)
parsed_lightdock_receptor = os.path.join(
os.path.dirname(args.receptor_pdb),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(args.receptor_pdb))
receptor = read_input_structure(parsed_lightdock_receptor, args.noxt,
args.noh, args.verbose_parser)
parsed_lightdock_ligand = os.path.join(
os.path.dirname(args.ligand_pdb),
DEFAULT_LIGHTDOCK_PREFIX % os.path.basename(args.ligand_pdb))
ligand = read_input_structure(parsed_lightdock_ligand, args.noxt,
args.noh, args.verbose_parser)
# CRITICAL to not break compatibility with previous results
receptor.move_to_origin()
ligand.move_to_origin()
if args.use_anm:
try:
receptor.n_modes = read_nmodes(
"%s%s" % (DEFAULT_REC_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for receptor molecule")
receptor.n_modes = None
try:
ligand.n_modes = read_nmodes(
"%s%s" % (DEFAULT_LIG_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for ligand molecule")
ligand.n_modes = None
starting_points_files = load_starting_positions(
args.swarms, args.glowworms, args.use_anm, args.anm_rec,
args.anm_lig)
comm.Barrier()
num_workers = comm.size
for worker_id in range(num_workers):
if worker_id == minion_id:
starting_points_files = glob.glob(
'init/initial_positions*.dat')
scoring_functions, adapters = set_scoring_function(
parser, receptor, ligand, minion_id)
# Check if scoring functions are compatible with ANM if activated
if args.use_anm and minion_id == 0:
for s in scoring_functions:
if not s.anm_support:
raise NotSupportedInScoringError(
f"ANM is activated while {type(s).__name__} has no support for it"
)
# Prepare tasks depending on swarms to simulate
if parser.args.swarm_list:
swarm_ids = parser.args.swarm_list
if min(swarm_ids) < 0 or max(
swarm_ids) >= parser.args.swarms:
raise SwarmNumError("Wrong list of swarms")
else:
swarm_ids = list(range(parser.args.swarms))
for id_swarm in swarm_ids:
if worker_id == (id_swarm % num_workers):
print('GSO cluster %d - Minion %d' %
(id_swarm, minion_id))
gso = set_gso(
parser.args.glowworms, adapters, scoring_functions,
starting_points_files[id_swarm],
parser.args.gso_seed, parser.args.translation_step,
parser.args.rotation_step,
parser.args.configuration_file,
parser.args.use_anm, parser.args.nmodes_step,
parser.args.anm_rec, parser.args.anm_lig,
parser.args.local_minimization)
saving_path = "%s%d" % (DEFAULT_SWARM_FOLDER, id_swarm)
task = GSOClusterTask(id_swarm, gso, parser.args.steps,
saving_path)
task.run()
comm.Barrier()
except NotSupportedInScoringError as score_error:
log.error("Error found in selected scoring function:")
log.error(score_error)
except KeyboardInterrupt:
log.info("Caught interrupt...")
log.info("bye.")
help="number of glowworms",
type=valid_integer_number)
# Optional, setup file
parser.add_argument("--setup",
"-setup",
"-s",
help="Simulation setup file",
dest="setup_file",
metavar="setup_file",
type=valid_file,
default=None)
args = parser.parse_args()
# Load setup configuration if provided
setup = get_setup_from_file(args.setup_file) if args.setup_file else None
num_anm_rec = DEFAULT_NMODES_REC
num_anm_lig = DEFAULT_NMODES_LIG
if setup and setup['use_anm']:
num_anm_rec = setup['anm_rec']
num_anm_lig = setup['anm_lig']
# Receptor
structures = []
for structure in get_lightdock_structures(args.receptor_structures):
log.info("Reading %s receptor PDB file..." % structure)
atoms, residues, chains = parse_complex_from_file(structure)
structures.append({
'atoms': atoms,
'residues': residues,
def run_simulation(parser):
"""Main program, includes MPI directives"""
try:
comm = MPI.COMM_WORLD
parser = CommandLineParser()
args = parser.args
# Read setup and add it to the actual args object
setup = get_setup_from_file(args.setup_file)
for k, v in setup.iteritems():
setattr(args, k, v)
minion_id = comm.rank
if minion_id == 0:
info_file = create_simulation_info_file(args)
log.info("simulation parameters saved to %s" % info_file)
comm.Barrier()
# Read input structures
receptor = read_input_structure(args.receptor_pdb, args.noxt)
ligand = read_input_structure(args.ligand_pdb, args.noxt)
# CRITICAL to not break compatibility with previous results
receptor.move_to_origin()
ligand.move_to_origin()
if args.use_anm:
try:
receptor.n_modes = read_nmodes(
"%s%s" % (DEFAULT_REC_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for receptor molecule")
receptor.n_modes = None
try:
ligand.n_modes = read_nmodes(
"%s%s" % (DEFAULT_LIG_NM_FILE, NUMPY_FILE_SAVE_EXTENSION))
except:
log.warning("No ANM found for ligand molecule")
ligand.n_modes = None
starting_points_files = load_starting_positions(
args.swarms, args.glowworms, args.use_anm, args.anm_rec,
args.anm_lig)
comm.Barrier()
num_workers = comm.size
for worker_id in xrange(num_workers):
if worker_id == minion_id:
starting_points_files = glob.glob(
'init/initial_positions*.dat')
scoring_functions, adapters = set_scoring_function(
parser, receptor, ligand, minion_id)
for id_swarm in xrange(parser.args.swarms):
if worker_id == (id_swarm % num_workers):
print 'GSO cluster %d - Minion %d' % (id_swarm,
minion_id)
gso = set_gso(
parser.args.glowworms, adapters, scoring_functions,
starting_points_files[id_swarm],
parser.args.gso_seed, parser.args.translation_step,
parser.args.rotation_step,
parser.args.configuration_file,
parser.args.use_anm, parser.args.nmodes_step,
parser.args.anm_rec, parser.args.anm_lig,
parser.args.local_minimization)
saving_path = "%s%d" % (DEFAULT_SWARM_FOLDER, id_swarm)
task = GSOClusterTask(id_swarm, gso, parser.args.steps,
saving_path)
task.run()
comm.Barrier()
except KeyboardInterrupt:
log.info("Caught interrupt...")
log.info("bye.")
def run_simulation(parser):
"""Main program, includes MPI directives"""
try:
comm = MPI.COMM_WORLD
parser = CommandLineParser()
args = parser.args
# Read setup and add it to the actual args object
setup = get_setup_from_file(args.setup_file)
for k, v in setup.iteritems():
setattr(args, k, v)
minion_id = comm.rank
if minion_id == 0:
info_file = create_simulation_info_file(args)
log.info("simulation parameters saved to %s" % info_file)
comm.Barrier()
# Read input structures
receptor = read_input_structure(args.receptor_pdb, args.noxt)
ligand = read_input_structure(args.ligand_pdb, args.noxt)
# CRITICAL to not break compatibility with previous results
receptor.move_to_origin()
ligand.move_to_origin()
if args.use_anm:
try:
receptor.n_modes = read_nmodes("%s%s" % (DEFAULT_REC_NM_FILE, NUMPY_FILE_SAVE_EXTENSION) )
except:
log.warning("No ANM found for receptor molecule")
receptor.n_modes = None
try:
ligand.n_modes = read_nmodes("%s%s" % (DEFAULT_LIG_NM_FILE, NUMPY_FILE_SAVE_EXTENSION) )
except:
log.warning("No ANM found for ligand molecule")
ligand.n_modes = None
starting_points_files = load_starting_positions(args.swarms, args.glowworms, args.use_anm,
args.anm_rec, args.anm_lig)
comm.Barrier()
num_workers = comm.size
for worker_id in xrange(num_workers):
if worker_id == minion_id:
starting_points_files = glob.glob('init/initial_positions*.dat')
scoring_functions, adapters = set_scoring_function(parser, receptor, ligand, minion_id)
for id_swarm in xrange(parser.args.swarms):
if worker_id == (id_swarm % num_workers):
print 'GSO cluster %d - Minion %d' % (id_swarm, minion_id)
gso = set_gso(parser.args.glowworms, adapters, scoring_functions,
starting_points_files[id_swarm],
parser.args.gso_seed, parser.args.translation_step,
parser.args.rotation_step, parser.args.configuration_file,
parser.args.use_anm, parser.args.nmodes_step,
parser.args.anm_rec, parser.args.anm_lig,
parser.args.local_minimization)
saving_path = "%s%d" % (DEFAULT_SWARM_FOLDER, id_swarm)
task = GSOClusterTask(id_swarm, gso, parser.args.steps, saving_path)
task.run()
comm.Barrier()
except KeyboardInterrupt:
log.info("Caught interrupt...")
log.info("bye.")
# Ligand
parser.add_argument("ligand_structures", help="ligand structures: PDB file or list of PDB files",
type=valid_file, metavar="ligand_structure")
# Lightdock output file
parser.add_argument("lightdock_output", help="lightdock output file",
type=valid_file, metavar="lightdock_output")
# Number of glowworms
parser.add_argument("glowworms", help="number of glowworms", type=valid_integer_number)
# Optional, setup file
parser.add_argument("--setup", "-setup", "-s", help="Simulation setup file",
dest="setup_file", metavar="setup_file", type=valid_file, default=None)
args = parser.parse_args()
# Load setup configuration if provided
setup = get_setup_from_file(args.setup_file) if args.setup_file else None
num_anm_rec = DEFAULT_NMODES_REC
num_anm_lig = DEFAULT_NMODES_LIG
if setup and setup['use_anm']:
num_anm_rec = setup['anm_rec']
num_anm_lig = setup['anm_lig']
# Receptor
structures = []
for structure in get_lightdock_structures(args.receptor_structures):
log.info("Reading %s receptor PDB file..." % structure)
atoms, residues, chains = parse_complex_from_file(structure)
structures.append({'atoms': atoms, 'residues': residues, 'chains': chains, 'file_name': structure})
log.info("%s atoms, %s residues read." % (len(atoms), len(residues)))
receptor = Complex.from_structures(structures)
