def run_validation():
"""Run all validation tests.
This is probably best done by running the different validation set
singularly since the optimal number of GPUs depends on the protocol.
"""
for yank_script_filepath in glob.glob(os.path.join('..', '*', '*.yaml')):
print('Running {}...'.format(os.path.basename(yank_script_filepath)))
yaml_builder = YamlBuilder(yank_script_filepath)
yaml_builder.run_experiments()
def run_yank(job_id, n_jobs):
openmm_system_dir = os.path.join('..', 'openmmfiles')
pdb_dir = os.path.join('..', 'pdbfiles')
yank_script_template_filepath = 'yank_template.yaml'
# Read in YANK template script.
with open(yank_script_template_filepath, 'r') as f:
script_template = f.read()
# Load cached status calculations.
molecules_done = read_status()
# Find all molecules to run.
molecules_files_pattern = os.path.join(pdb_dir, '*_vacuum.pdb')
molecule_ids = [os.path.basename(molecule_file)[:-11]
for molecule_file in glob.glob(molecules_files_pattern)]
# Sort molecules so that parallel nodes won't make the same calculation.
molecule_ids = sorted(molecule_ids)
# Create YANK input files.
for i, molecule_id in enumerate(molecule_ids):
# Check if the job is assigned to this script and/or if we
# have already completed this.
if (i % n_jobs != job_id - 1 or
molecule_id in molecules_done):
print_and_flush('Node {}: Skipping {}'.format(job_id, molecule_id))
continue
# Output file paths.
vacuum_filename = molecule_id + '_vacuum'
solvated_filename = molecule_id + '_solvated'
vacuum_pdb_filepath = os.path.join(pdb_dir, vacuum_filename + '.pdb')
solvated_pdb_filepath = os.path.join(pdb_dir, solvated_filename + '.pdb')
vacuum_xml_filepath = os.path.join(openmm_system_dir, vacuum_filename + '.xml')
solvated_xml_filepath = os.path.join(openmm_system_dir, solvated_filename + '.xml')
# Create yank script.
phase1_path = str([solvated_xml_filepath, solvated_pdb_filepath])
phase2_path = str([vacuum_xml_filepath, vacuum_pdb_filepath])
script = script_template.format(experiment_dir=molecule_id,
phase1_path=phase1_path, phase2_path=phase2_path)
# Run YANK.
print_and_flush('Node {}: Running {}'.format(job_id, molecule_id))
yaml_builder = YamlBuilder(script)
yaml_builder.run_experiments()
# Update completed molecules.
update_status(molecule_id)
