def get_arg_parser():
"""Returns the custom argument parser for this script"""
parser = fe.FEArgumentParser(
description="High level script that attempts to use data from multiple"
" calculations to provide free energies of solvation and "
"binding. Also calculates cycle closures for all data. "
"Assumes standard ProtoMS naming conventions for data "
"output directories. Data should be organised such that "
"each transformation between two ligands should have a "
"single master directory containing output directories "
"for each simulation state (e.g. master/out1_free). Master"
"directories should be passed to the -d flag. "
"Reported free energies are averages "
"over all repeats found. Reported errors are single "
"standard errors calculated from repeats.",
parents=[fe.get_alchemical_arg_parser()],
conflict_handler='resolve')
parser.add_argument(
'-d',
'--directories',
nargs='+',
required=True,
help="Location of folders containing ProtoMS output directories.")
parser.add_argument(
"-s",
"--signs",
nargs='+',
type=str,
choices=('+', '-'),
help="List of '+' or '-' characters, one for each directory provided "
"to the -d flag. Indicates the sign that should be used for each "
"free energy difference when calculating cycle closures.",
required=True)
parser.add_argument('--estimators',
nargs='+',
default=['ti', 'mbar', 'bar'],
choices=['ti', 'mbar', 'bar', 'gcap'],
help="Choose estimators")
parser.add_argument('-v',
'--volume',
type=float,
default=None,
help="Volume of GCMC region")
# use mutually exclusive group for these as we need one and only one
group = parser.add_mutually_exclusive_group(required=True)
group.add_argument(
"--dualtopology",
action='store_true',
default=False,
help="Indicates data is for a dual topology calculation.")
group.add_argument(
"--singletopology",
type=str,
choices=('comb', 'sep'),
help="Indicates data is for a single topology calculation. "
"Option comb indicates a single step calculation. "
"Option sep indicates separate steps for van der Waals "
" and electrostatics components.")
return parser
def get_arg_parser():
"""Returns the custom argument parser for this script"""
parser = fe.FEArgumentParser(
description="Calculate individual contributions of different terms "
"to the total free energy difference. Although terms are "
"guaranteed to be additive with TI, the decomposition "
"is not strictly well defined. That said, it can be "
"illustrative to consider the dominant contributions of "
"a calculation.",
parents=[fe.get_alchemical_arg_parser()])
parser.add_argument(
"-b", "--bound", nargs="+", action='append',
help="Output directory(s) of additional bound phase calculation(s). "
"Using this flag causes data loaded via -d to be considered as "
"solvent phase data. All data is then combined to provide a "
"decomposition of the binding free energy. Behaves identically "
"to -d in treatment of repeats and calculation legs.",
clashes=['gas'])
parser.add_argument(
"-g", "--gas", nargs="+", action='append',
help="As -b except data loaded via this flag is treated as gas phase "
"data to provide to provide a decomposed solvation free energy.",
clashes=['bound'])
parser.add_argument(
"--dualtopology", action='store_true', default=False,
help="Indicates provided data is from a dual topology calculation. "
"Attempts to consolidate terms, for clarity, from ligands that "
"can have opposite signs and large magnitudes. Please note that "
"standard errors calculated with this approach are no longer "
"rigorous and can be spuriously large.")
parser.add_argument("--pmf", action='store_true', default=False,
help="Plot the Potential of Mean Force for all terms.")
parser.add_argument("--full", action='store_false', default=True,
help="Prevents printing out of zero contribution energies.")
return parser
def get_arg_parser():
"""Add custom argument parser for this script"""
parser = fe.FEArgumentParser(
description="Calculate water binding free energies using Grand "
"Canonical Integration.",
parents=[fe.get_gci_arg_parser()],
conflict_handler='resolve')
return parser
def get_arg_parser():
"""Add custom options for this script"""
parser = fe.FEArgumentParser(
description="Calculate water binding free energies using Grand "
"Canonical Integration and incorporating rigorous "
"corrections for long-range electrostatics and "
"dispersion. Reweighting is carried out using both "
"an umbrella sampling result and MBAR.",
parents=[fe.get_gci_arg_parser()], conflict_handler='resolve')
parser.add_argument(
'-f', '--filename', default='results_inst',
help="Name of file containing simulation energies with short cutoff."
" Default=results_inst")
parser.add_argument(
'-ln', '--longname', default='results_long',
help="Name of file containing simulation energies with long cutoff."
" Default=results_long")
return parser
def get_arg_parser():
"""Returns the custom argument parser for this script"""
parser = fe.FEArgumentParser(
description="Calculate free energy differences using a range of"
" estimators",
parents=[fe.get_alchemical_arg_parser()])
parser.add_argument('--pmf',
action='store_true',
default=False,
help="Make graph of potential of mean force",
clashes=('test_convergence', 'test_equilibration'))
parser.add_argument(
'--test-equilibration',
default=None,
type=float,
help="Perform free energy calculations 10 times using varying "
"proportions of the total data set provided. Data used will "
"range from 100%% of the dataset down to the proportion "
"provided to this argument",
clashes=('test_convergence', 'lower_bound'))
parser.add_argument(
'--test-convergence',
default=None,
type=float,
help="Perform free energy calculations 10 times using varying "
"proportions of the total data set provided. Data used will "
"range from 100%% of the dataset up to the proportion "
"provided to this argument")
parser.add_argument(
'--estimators',
nargs='+',
default=['ti', 'mbar', 'bar'],
choices=['ti', 'mbar', 'bar', 'gcap'],
help="Choose free energy estimator to use. By default TI, BAR and MBAR"
" are used. Note that the GCAP estimator assumes a different file"
" structure and ignores the --subdir flag.")
parser.add_argument('-v',
'--volume',
type=float,
default=None,
help="Volume of GCMC region")
return parser
def get_arg_parser():
"""Returns the custom argument parser for this script"""
parser = fe.FEArgumentParser(
description="Calculate free energy differences using a range of"
" estimators",
parents=[fe.get_alchemical_arg_parser()])
parser.add_argument('-v',
'--volume',
type=float,
default=None,
help="Volume of GCMC region")
parser.add_argument(
'--estimators',
nargs='+',
default=['ti', 'mbar', 'bar'],
choices=['ti', 'mbar', 'bar'],
help="Choose free energy estimator to use. By default TI, BAR and MBAR"
" are used. Note that the GCAP estimator assumes a different file"
" structure and ignores the --subdir flag.")
return parser