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Clean up line breaks in lib.py

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See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
2020-05-25 19:09:11 -07:00
parent e5dedc1786
commit 5242366006
1 changed files with 85 additions and 61 deletions
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70
propka/lib.py
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@@ -157,7 +157,8 @@ def parse_res_string(res_str):
try: try:
chain, resnum_str = res_str.split(":") chain, resnum_str = res_str.split(":")
except ValueError: except ValueError:
raise ValueError("Invalid residue string (must contain 2 colon-separated values)") raise ValueError("Invalid residue string (must contain 2 "
"colon-separated values)")
try: try:
resnum = int(resnum_str) resnum = int(resnum_str)
except ValueError: except ValueError:
@@ -185,71 +186,94 @@ def build_parser(parser=None):
if parser is not None: if parser is not None:
group = parser.add_argument_group(title="PROPKA invoation options") group = parser.add_argument_group(title="PROPKA invoation options")
else: else:
parser = argparse.ArgumentParser(description=("PROPKA predicts the pKa values of ionizable " parser = argparse.ArgumentParser(
description=("PROPKA predicts the pKa values of ionizable "
"groups in proteins and protein-ligand " "groups in proteins and protein-ligand "
"complexes based in the 3D structure"), "complexes based in the 3D structure"),
formatter_class=argparse.ArgumentDefaultsHelpFormatter) formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# This is duck-typing at its finest # This is duck-typing at its finest
group = parser group = parser
group.add_argument("input_pdb", help="read data from <filename>") group.add_argument("input_pdb", help="read data from <filename>")
group.add_argument("-f", "--file", action="append", dest="filenames", default=[], group.add_argument(
"-f", "--file", action="append", dest="filenames", default=[],
help="read data from <filename>, i.e. <filename> is added to arguments") help="read data from <filename>, i.e. <filename> is added to arguments")
group.add_argument("-r", "--reference", dest="reference", default="neutral", group.add_argument(
"-r", "--reference", dest="reference", default="neutral",
help=("setting which reference to use for stability calculations " help=("setting which reference to use for stability calculations "
"[neutral/low-pH]")) "[neutral/low-pH]"))
group.add_argument("-c", "--chain", action="append", dest="chains", group.add_argument(
"-c", "--chain", action="append", dest="chains",
help=('creating the protein with only a specified chain. Specify ' help=('creating the protein with only a specified chain. Specify '
'" " for chains without ID [all]')) '" " for chains without ID [all]'))
group.add_argument("-i", "--titrate_only", dest="titrate_only", group.add_argument(
"-i", "--titrate_only", dest="titrate_only",
help=('Treat only the specified residues as titratable. Value should ' help=('Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: ' 'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"')) '-i "A:10,A:11"'))
group.add_argument("-t", "--thermophile", action="append", dest="thermophiles", group.add_argument(
"-t", "--thermophile", action="append", dest="thermophiles",
help=("defining a thermophile filename; usually used in " help=("defining a thermophile filename; usually used in "
"'alignment-mutations'")) "'alignment-mutations'"))
group.add_argument("-a", "--alignment", action="append", dest="alignment", group.add_argument(
"-a", "--alignment", action="append", dest="alignment",
help=("alignment file connecting <filename> and <thermophile> " help=("alignment file connecting <filename> and <thermophile> "
"[<thermophile>.pir]")) "[<thermophile>.pir]"))
group.add_argument("-m", "--mutation", action="append", dest="mutations", group.add_argument(
"-m", "--mutation", action="append", dest="mutations",
help=("specifying mutation labels which is used to modify " help=("specifying mutation labels which is used to modify "
"<filename> according to, e.g. N25R/N181D")) "<filename> according to, e.g. N25R/N181D"))
group.add_argument("-v", "--version", dest="version_label", default="Jan15", group.add_argument(
"-v", "--version", dest="version_label", default="Jan15",
help="specifying the sub-version of propka [Jan15/Dec19]") help="specifying the sub-version of propka [Jan15/Dec19]")
group.add_argument("-p", "--parameters", dest="parameters", group.add_argument(
"-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"), default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%(default)s]") help="set the parameter file [%(default)s]")
try: try:
group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"], group.add_argument(
"--log-level",
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
help="logging level verbosity", default="INFO") help="logging level verbosity", default="INFO")
except argparse.ArgumentError: except argparse.ArgumentError:
# It is possible that --log-level has already been set by APBS # It is possible that --log-level has already been set by APBS
pass pass
group.add_argument("-o", "--pH", dest="pH", type=float, default=7.0, group.add_argument(
"-o", "--pH", dest="pH", type=float, default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]") help="setting pH-value used in e.g. stability calculations [7.0]")
group.add_argument("-w", "--window", dest="window", nargs=3, type=float, group.add_argument(
"-w", "--window", dest="window", nargs=3, type=float,
default=(0.0, 14.0, 1.0), default=(0.0, 14.0, 1.0),
help=("setting the pH-window to show e.g. stability profiles " help=("setting the pH-window to show e.g. stability profiles "
"[0.0, 14.0, 1.0]")) "[0.0, 14.0, 1.0]"))
group.add_argument("-g", "--grid", dest="grid", nargs=3, type=float, group.add_argument(
"-g", "--grid", dest="grid", nargs=3, type=float,
default=(0.0, 14.0, 0.1), default=(0.0, 14.0, 0.1),
help=("setting the pH-grid to calculate e.g. stability " help=("setting the pH-grid to calculate e.g. stability "
"related properties [0.0, 14.0, 0.1]")) "related properties [0.0, 14.0, 0.1]"))
group.add_argument("--mutator", dest="mutator", group.add_argument(
"--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]") help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
group.add_argument("--mutator-option", dest="mutator_options", action="append", group.add_argument(
"--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]") help="setting property for mutator [e.g. type=\"side-chain\"]")
group.add_argument("-d", "--display-coupled-residues", dest="display_coupled_residues", group.add_argument(
action="store_true", help=("Displays alternative pKa values due " "-d", "--display-coupled-residues", dest="display_coupled_residues",
action="store_true",
help=("Displays alternative pKa values due "
"to coupling of titratable groups")) "to coupling of titratable groups"))
group.add_argument("-l", "--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file", group.add_argument(
"-l", "--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file",
action="store_true", default=False, action="store_true", default=False,
help=("Reuses the ligand mol2 files allowing the user to alter " help=("Reuses the ligand mol2 files allowing the user to alter "
"ligand bond orders")) "ligand bond orders"))
group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true", group.add_argument(
"-k", "--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False) help="Keep protons in input file", default=False)
group.add_argument("-q", "--quiet", action="store_const", const="WARNING", group.add_argument(
"-q", "--quiet", action="store_const", const="WARNING",
dest="log_level", help="suppress non-warning messages") dest="log_level", help="suppress non-warning messages")
group.add_argument("--protonate-all", dest="protonate_all", action="store_true", group.add_argument(
"--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)", help="Protonate all atoms (will not influence pKa calculation)",
default=False) default=False)
return parser return parser