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Move argparse sub-command to group.

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This commit is contained in:
Nathan Baker
2020-05-12 14:27:46 -07:00
parent 847004a2d6
commit 387d0a5664
1 changed files with 63 additions and 64 deletions
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127
propka/lib.py
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@@ -138,7 +138,7 @@ def parse_res_string(res_str):
return chain, resnum, inscode
def build_parser(parser_=None):
def build_parser(parser=None):
"""Build an argument parser for PROPKA.
Args:
@@ -148,75 +148,74 @@ def build_parser(parser_=None):
Returns:
ArgumentParser object.
"""
if parser_ is not None:
subparsers = parser_.add_subparsers(title="PROPKA sub-command group")
parser = subparsers.add_parser("PROPKA", help="PROPKA invocation options")
if parser is not None:
group = parser.add_argument_group(title="PROPKA invoation options")
else:
parser = argparse.ArgumentParser(description=("PROPKA predicts the pKa values of ionizable "
"groups in proteins and protein-ligand "
"complexes based in the 3D structure"),
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
# This is duck-typing at its finest
group = parser
group.add_argument("input_pdb", help="read data from <filename>")
parser.add_argument("-f", "--file", action="append", dest="filenames",
help="read data from <filename>, i.e. <filename> is added to arguments")
parser.add_argument("-r", "--reference", dest="reference", default="neutral",
help=("setting which reference to use for stability calculations "
"[neutral/low-pH]"))
parser.add_argument("-c", "--chain", action="append", dest="chains",
help=('creating the protein with only a specified chain. Specify '
'" " for chains without ID [all]'))
parser.add_argument("-i", "--titrate_only", dest="titrate_only",
help=('Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"'))
parser.add_argument("-t", "--thermophile", action="append", dest="thermophiles",
help=("defining a thermophile filename; usually used in "
"'alignment-mutations'"))
parser.add_argument("-a", "--alignment", action="append", dest="alignment",
help=("alignment file connecting <filename> and <thermophile> "
"[<thermophile>.pir]"))
parser.add_argument("-m", "--mutation", action="append", dest="mutations",
help=("specifying mutation labels which is used to modify "
"<filename> according to, e.g. N25R/N181D"))
parser.add_argument("-v", "--version", dest="version_label", default="Jan15",
help="specifying the sub-version of propka [Jan15/Dec19]")
parser.add_argument("-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%default]")
parser.add_argument("-z", "--verbose", dest="verbosity", action="store_const",
const=2, help="output debugging information")
parser.add_argument("-q", "--quiet", dest="verbosity", action="store_const",
const=0, default=1, help="inhibit printing to stdout")
parser.add_argument("-o", "--pH", dest="pH", type=float, default=7.0,
help="setting pH-value used in e.g. stability calculations [7.0]")
parser.add_argument("-w", "--window", dest="window", nargs=3, type=float,
default=(0.0, 14.0, 1.0),
help=("setting the pH-window to show e.g. stability profiles "
"[0.0, 14.0, 1.0]"))
parser.add_argument("-g", "--grid", dest="grid", nargs=3, type=float,
default=(0.0, 14.0, 0.1),
help=("setting the pH-grid to calculate e.g. stability "
"related properties [0.0, 14.0, 0.1]"))
parser.add_argument("--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
parser.add_argument("--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]")
parser.add_argument("-d", "--display-coupled-residues", dest="display_coupled_residues",
action="store_true", help=("Displays alternative pKa values due "
"to coupling of titratable groups"))
parser.add_argument("-l", "--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file",
action="store_true", default=False,
help=("Reuses the ligand mol2 files allowing the user to alter "
"ligand bond orders"))
parser.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False)
parser.add_argument("--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)",
default=False)
parser.add_argument("input_pdb",
help="read data from <filename>")
if parser_ is not None:
return parser_
group.add_argument("-f", "--file", action="append", dest="filenames", default=[],
help="read data from <filename>, i.e. <filename> is added to arguments")
group.add_argument("-r", "--reference", dest="reference", default="neutral",
help=("setting which reference to use for stability calculations "
"[neutral/low-pH]"))
group.add_argument("-c", "--chain", action="append", dest="chains",
help=('creating the protein with only a specified chain. Specify '
'" " for chains without ID [all]'))
group.add_argument("-i", "--titrate_only", dest="titrate_only",
help=('Treat only the specified residues as titratable. Value should '
'be a comma-separated list of "chain:resnum" values; for example: '
'-i "A:10,A:11"'))
group.add_argument("-t", "--thermophile", action="append", dest="thermophiles",
help=("defining a thermophile filename; usually used in "
"'alignment-mutations'"))
group.add_argument("-a", "--alignment", action="append", dest="alignment",
help=("alignment file connecting <filename> and <thermophile> "
"[<thermophile>.pir]"))
group.add_argument("-m", "--mutation", action="append", dest="mutations",
help=("specifying mutation labels which is used to modify "
"<filename> according to, e.g. N25R/N181D"))
group.add_argument("-v", "--version", dest="version_label", default="Jan15",
help="specifying the sub-version of propka [Jan15/Dec19]")
group.add_argument("-p", "--parameters", dest="parameters",
default=pkg_resources.resource_filename(__name__, "propka.cfg"),
help="set the parameter file [%(default)s]")
group.add_argument("-z", "--verbose", dest="verbosity", action="store_const",
const=2, help="output debugging information")
group.add_argument("-q", "--quiet", dest="verbosity", action="store_const",
const=0, default=1, help="inhibit printing to stdout")
group.add_argument("-o", "--pH", dest="pH", type=float, default=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,
default=(0.0, 14.0, 1.0),
help=("setting the pH-window to show e.g. stability profiles "
"[0.0, 14.0, 1.0]"))
group.add_argument("-g", "--grid", dest="grid", nargs=3, type=float,
default=(0.0, 14.0, 0.1),
help=("setting the pH-grid to calculate e.g. stability "
"related properties [0.0, 14.0, 0.1]"))
group.add_argument("--mutator", dest="mutator",
help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
group.add_argument("--mutator-option", dest="mutator_options", action="append",
help="setting property for mutator [e.g. type=\"side-chain\"]")
group.add_argument("-d", "--display-coupled-residues", dest="display_coupled_residues",
action="store_true", help=("Displays alternative pKa values due "
"to coupling of titratable groups"))
group.add_argument("-l", "--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file",
action="store_true", default=False,
help=("Reuses the ligand mol2 files allowing the user to alter "
"ligand bond orders"))
group.add_argument("-k", "--keep-protons", dest="keep_protons", action="store_true",
help="Keep protons in input file", default=False)
group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
help="Protonate all atoms (will not influence pKa calculation)",
default=False)
return parser