def prepare_database(database,
atomtypes_filename,
parameters,
mol2_directory,
verbose=False):
"""
Wrapper function to prepare the database for sampling
"""
#TODO: fix this. Right now it inserts the path for the parent directory to access atomtyping.py
cwd = os.getcwd()
sys.path.insert(0, os.path.dirname(cwd))
from atomtyping import type_atoms
database_prepped = load_database(database, mol2_directory, verbose=verbose)
database_with_systems = create_openmm_systems(database_prepped,
verbose=verbose)
database_atomtyped = type_atoms(database_with_systems,
atomtypes_filename,
verbose=verbose)
gen_simulation_data_parallel = partial(generate_simulation_data,
database_atomtyped, parameters)
pool = Pool(32)
sim_results = pool.map(gen_simulation_data_parallel,
database_atomtyped.keys())
database_simulated = {}
#create a new database with the results of the simulation
for result in sim_results:
database_simulated[result[0]] = result[1]
return database_simulated
def prepare_database(database, atomtypes_filename,parameters, mol2_directory, verbose=False):
"""
Wrapper function to prepare the database for sampling
"""
database_prepped = load_database(database, mol2_directory, verbose=verbose)
database_with_systems = create_openmm_systems(database_prepped, verbose=verbose)
database_atomtyped = type_atoms(database_with_systems, atomtypes_filename, verbose=verbose)
database_simulated = generate_simulation_data(database_atomtyped, parameters)
return database_simulated
def prepare_database(database,
atomtypes_filename,
parameters,
mol2_directory,
verbose=False):
"""
Wrapper function to prepare the database for sampling
"""
database_prepped = load_database(database, mol2_directory, verbose=verbose)
database_with_systems = create_openmm_systems(database_prepped,
verbose=verbose)
database_atomtyped = type_atoms(database_with_systems,
atomtypes_filename,
verbose=verbose)
database_simulated = generate_simulation_data(database_atomtyped,
parameters)
return database_simulated
def prepare_database(database, atomtypes_filename, parameters, mol2_directory, verbose=False):
"""
Wrapper function to prepare the database for sampling
"""
# TODO: fix this. Right now it inserts the path for the parent directory to access atomtyping.py
cwd = os.getcwd()
sys.path.insert(0, os.path.dirname(cwd))
from atomtyping import type_atoms
database_prepped = load_database(database, mol2_directory, verbose=verbose)
database_with_systems = create_openmm_systems(database_prepped, verbose=verbose)
database_atomtyped = type_atoms(database_with_systems, atomtypes_filename, verbose=verbose)
gen_simulation_data_parallel = partial(generate_simulation_data, database_atomtyped, parameters)
pool = Pool(32)
sim_results = pool.map(gen_simulation_data_parallel, database_atomtyped.keys())
database_simulated = {}
# create a new database with the results of the simulation
for result in sim_results:
database_simulated[result[0]] = result[1]
return database_simulated
