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_parse_api_params_string():
params_dict = parse_api_params_string(
'{"a": 3.2 / picoseconds, "b": "x", "c": 2.4}')
assert params_dict == {'a': 3.2 / unit.picosecond, 'b': 'x', 'c': 2.4}
def test_parse_api_params_string():
parsed = parse_api_params_string('{"a": 3 / picoseconds, "b": "x", "c": 2.4}')
assert parsed == {"a": 3 / unit.picoseconds, "b": "x", "c": 2.4}
def test_parse_api_params_string():
params_dict = parse_api_params_string('{"a": 3.2 / picoseconds, "b": "x", "c": 2.4}')
assert params_dict == {'a': 3.2 / unit.picosecond, 'b': 'x', 'c': 2.4}
