diff --git a/scripts/mdpow-ghyd b/scripts/mdpow-ghyd index 8df75197..51bf4466 100755 --- a/scripts/mdpow-ghyd +++ b/scripts/mdpow-ghyd @@ -183,7 +183,7 @@ if __name__ == "__main__": parser.add_option('-p', '--plotfile', dest="plotfile", help="plot dV/dlambda to FILE; use png or pdf suffix to " "determine the file type. 'auto' generates a pdf file " - "DIRECTORY/dVdl__.pdf and 'None' disables it [%default]", + "DIRECTORY/dVdl__.pdf and 'none' disables it [%default]", metavar="FILE") parser.add_option('-e', '--energies', dest="energyfile", help="append solvation free energies to FILE [%default]", diff --git a/scripts/mdpow-pcw b/scripts/mdpow-pcw index 4a1d47a8..a38e095b 100755 --- a/scripts/mdpow-pcw +++ b/scripts/mdpow-pcw @@ -193,7 +193,7 @@ if __name__ == "__main__": parser.add_argument('--plotfile', dest="plotfile", default='none', help="plot dV/dlambda to FILE; use png or pdf suffix to " "determine the file type. 'auto' generates a pdf file " - "DIRECTORY/dVdl_MOLID_pcw.pdf and 'none' disables it " + "DIRECTORY/dVdl__pcw.pdf and 'none' disables it " "The plot function is only available for mdpow estimator," "and is disabled when using alchemlyb estimators.", metavar="FILE") diff --git a/scripts/mdpow-pow b/scripts/mdpow-pow index 4081f3f8..d010b8c8 100755 --- a/scripts/mdpow-pow +++ b/scripts/mdpow-pow @@ -193,22 +193,22 @@ if __name__ == "__main__": parser.add_argument('--plotfile', dest="plotfile", default='none', help="plot dV/dlambda to FILE; use png or pdf suffix to " "determine the file type. 'auto' generates a pdf file " - "DIRECTORY/dVdl_MOLID_pcw.pdf and 'none' disables it " - "The plot function is only available for mdpow estimator," + "DIRECTORY/dVdl__pow.pdf and 'none' disables it. " + "The plot function is only available for mdpow estimator, " "and is disabled when using alchemlyb estimators.", metavar="FILE") parser.add_argument('-o', '--outfile', dest="outfile", default="pow.txt", - help="append one-line results summary to FILE ", + help="append one-line results summary to FILE", metavar="FILE") parser.add_argument('-e', '--energies', dest="energyfile", default="energies.txt", - help="append solvation free energies to FILE ", + help="append solvation free energies to FILE", metavar="FILE") parser.add_argument('--estimator', dest="estimator", default='alchemlyb', choices=['mdpow', 'alchemlyb'], - help="choose the estimator to be used, alchemlyb or mdpow estimators") + help="choose the estimator implementation to be used, alchemlyb or mdpow estimators") parser.add_argument('--method', dest="method", default='MBAR', choices=['TI', 'MBAR', 'BAR'], - help="choose the method to calculate free energy ",) + help="choose the estimator method to calculate free energy",) parser.add_argument('--force', dest='force', default=False, action="store_true", help="force rereading all data ") @@ -216,26 +216,26 @@ if __name__ == "__main__": SIs.add_argument('--SI', dest='SI', action="store_true", default=True, help="enable statistical inefficiency (SI) analysis. " - "Statistical inefficiency analysis is performed by default when using" + "Statistical inefficiency analysis is performed by default when using " "alchemlyb estimators and is always disabled when using mdpow estimator.") SIs.add_argument('--no-SI', dest='noSI', action="store_true", default=False, help="disable statistical inefficiency analysis. " - "Statistical inefficiency analysis is performed by default when using" + "Statistical inefficiency analysis is performed by default when using " "alchemlyb estimators and is disabled when using mdpow estimator. ") parser.add_argument('-s', '--stride', dest="stride", type=int, default=1, - help="use every N-th datapoint from the original dV/dlambda data. ", + help="use every N-th datapoint from the original dV/dlambda data.", metavar="N") parser.add_argument('--start', dest="start", type=int, default=0, - help="start point for the data used from the original dV/dlambda data. ") + help="start point for the data used from the original dV/dlambda data.") parser.add_argument('--stop', dest="stop", type=int, default=None, - help="stop point for the data used from the original dV/dlambda data. ",) + help="stop point for the data used from the original dV/dlambda data.") parser.add_argument('--ignore-corrupted', dest="permissive", action="store_true", default=False, help="skip lines in the md.xvg files that cannot be parsed. " "WARNING: Other lines in the file might have been corrupted in " "such a way that they appear correct but are in fact wrong. " - "WRONG RESULTS CAN OCCUR! USE AT YOUR OWN RISK ") + "WRONG RESULTS CAN OCCUR! USE AT YOUR OWN RISK.") opts = parser.parse_args() if len(opts.directory) > 1 and not opts.plotfile.lower() in ('none', 'auto'): diff --git a/scripts/mdpow-solvationenergy b/scripts/mdpow-solvationenergy index 529eee69..d06d9a60 100755 --- a/scripts/mdpow-solvationenergy +++ b/scripts/mdpow-solvationenergy @@ -223,8 +223,8 @@ if __name__ == "__main__": parser.add_argument('--plotfile', dest="plotfile", default='none', help="plot dV/dlambda to FILE; use png or pdf suffix to " "determine the file type. 'auto' generates a pdf file " - "DIRECTORY/dVdl__.pdf and 'none' disables it " - "The plot function is only available for mdpow estimator," + "DIRECTORY/dVdl__.pdf and 'none' disables it. " + "The plot function is only available for mdpow estimator, " "and is disabled when using alchemlyb estimators.", metavar="FILE") parser.add_argument('--solvent', '-S', dest='solvent', default='water', @@ -249,12 +249,12 @@ if __name__ == "__main__": SIs.add_argument('--SI', dest='SI', action="store_true", default=True, help="enable statistical inefficiency (SI) analysis. " - "Statistical inefficiency analysis is performed by default when using" + "Statistical inefficiency analysis is performed by default when using " "alchemlyb estimators and is always disabled when using mdpow estimator.") SIs.add_argument('--no-SI', dest='noSI', action="store_true", default=False, help="disable statistical inefficiency analysis. " - "Statistical inefficiency analysis is performed by default when using" + "Statistical inefficiency analysis is performed by default when using " "alchemlyb estimators and is disabled when using mdpow estimator. ") parser.add_argument('-s', '--stride', dest="stride", type=int, default=1, help="use every N-th datapoint from the original dV/dlambda data. ",