def dispatch(args): if args['--targetsfile']: with open(args['--targetsfile'], 'r') as targetsfile: targets = [ line.strip() for line in targetsfile.readlines() if line[0] != '#' ] elif args['--targets']: targets = args['--targets'].split(',') else: targets = False if args['--templatesfile']: with open(args['--templatesfile'], 'r') as templatesfile: templates = [ line.strip() for line in templatesfile.readlines() if line[0] != '#' ] elif args['--templates']: templates = args['--templates'].split(',') else: templates = False if args['--model_seqid_cutoff']: model_seqid_cutoff = float(args['--model_seqid_cutoff']) else: model_seqid_cutoff = False if args['--gpupn']: gpupn = int(args['--gpupn']) else: gpupn = 1 sim_length = eval_quantity_string(args['--simlength']) if args['--verbose']: loglevel = 'debug' else: loglevel = 'info' if args['--api_params']: api_params = parse_api_params_string(args['--api_params']) else: api_params = {} ensembler.refinement.refine_explicit_md( openmm_platform=args['--openmm_platform'], gpupn=gpupn, sim_length=sim_length, process_only_these_targets=targets, process_only_these_templates=templates, model_seqid_cutoff=model_seqid_cutoff, retry_failed_runs=args['--retry_failed_runs'], write_solvated_model=args['--write_solvated_model'], ff=args['--ff'], water_model=args['--water_model'], verbose=args['--verbose'], **api_params)
def dispatch(args): if args['--targetsfile']: with open(args['--targetsfile'], 'r') as targetsfile: targets = [line.strip() for line in targetsfile.readlines() if line[0] != '#'] elif args['--targets']: targets = args['--targets'].split(',') else: targets = False if args['--templatesfile']: with open(args['--templatesfile'], 'r') as templatesfile: templates = [line.strip() for line in templatesfile.readlines() if line[0] != '#'] elif args['--templates']: templates = args['--templates'].split(',') else: templates = False if args['--template_seqid_cutoff']: template_seqid_cutoff = float(args['--template_seqid_cutoff']) else: template_seqid_cutoff = False if args['--gpupn']: gpupn = int(args['--gpupn']) else: gpupn = 1 sim_length = eval_quantity_string(args['--simlength']) if args['--verbose']: loglevel = 'debug' else: loglevel = 'info' if args['--api_params']: api_params = parse_api_params_string(args['--api_params']) else: api_params = {} ensembler.refinement.refine_explicit_md( openmm_platform=args['--openmm_platform'], gpupn=gpupn, sim_length=sim_length, process_only_these_targets=targets, process_only_these_templates=templates, template_seqid_cutoff=template_seqid_cutoff, retry_failed_runs=args['--retry_failed_runs'], write_solvated_model=args['--write_solvated_model'], ff=args['--ff'], water_model=args['--water_model'], verbose=args['--verbose'], **api_params )
def test_eval_quantity_string(): quantity = eval_quantity_string('2 picoseconds') assert quantity == 2 * unit.picosecond
def test_eval_quantity_string(): assert eval_quantity_string("2 picoseconds") == 2 * unit.picoseconds assert eval_quantity_string("2picoseconds") == 2 * unit.picoseconds assert eval_quantity_string("2 / picoseconds") == 2 / unit.picoseconds assert eval_quantity_string("2 nanosecond") == 2 * unit.nanoseconds
def test_eval_quantity_string(): assert eval_quantity_string('2 picoseconds') == 2 * unit.picoseconds assert eval_quantity_string('2picoseconds') == 2 * unit.picoseconds assert eval_quantity_string('2 / picoseconds') == 2 / unit.picoseconds assert eval_quantity_string('2 nanosecond') == 2 * unit.nanoseconds