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fixing typos (#176)
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* Update mdpow-solvationenergy

* Update mdpow-pow

* made description of plot filename consistent between scripts

Co-authored-by: Bogdan I. Iorga <[email protected]>
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@orbeckst @iorga
orbeckst and iorga authored Aug 4, 2021
1 parent 87d1117 commit a31003c
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Showing 4 changed files with 18 additions and 18 deletions.
2 changes: 1 addition & 1 deletion scripts/mdpow-ghyd
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Original file line number Diff line number Diff line change
Expand Up @@ -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_<molname>_<solvent>.pdf and 'None' disables it [%default]",
"DIRECTORY/dVdl_<molname>_<solvent>.pdf and 'none' disables it [%default]",
metavar="FILE")
parser.add_option('-e', '--energies', dest="energyfile",
help="append solvation free energies to FILE [%default]",
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2 changes: 1 addition & 1 deletion scripts/mdpow-pcw
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Expand Up @@ -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_<molname>_pcw.pdf and 'none' disables it "
"The plot function is only available for mdpow estimator,"
"and is disabled when using alchemlyb estimators.",
metavar="FILE")
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24 changes: 12 additions & 12 deletions scripts/mdpow-pow
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Original file line number Diff line number Diff line change
Expand Up @@ -193,49 +193,49 @@ 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_<molname>_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 ")
SIs = parser.add_mutually_exclusive_group()
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'):
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8 changes: 4 additions & 4 deletions scripts/mdpow-solvationenergy
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Original file line number Diff line number Diff line change
Expand Up @@ -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_<molname>_<solvent>.pdf and 'none' disables it "
"The plot function is only available for mdpow estimator,"
"DIRECTORY/dVdl_<molname>_<solvent>.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',
Expand All @@ -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. ",
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