Clean up line breaks in lib.py
See https://github.com/jensengroup/propka-3.1/issues/43
This commit is contained in:
Nathan Baker
146
propka/lib.py
146
propka/lib.py
@@ -157,7 +157,8 @@ def parse_res_string(res_str):
|
||||
try:
|
||||
chain, resnum_str = res_str.split(":")
|
||||
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:
|
||||
resnum = int(resnum_str)
|
||||
except ValueError:
|
||||
@@ -185,73 +186,96 @@ def build_parser(parser=None):
|
||||
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)
|
||||
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>")
|
||||
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(
|
||||
"-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]")
|
||||
try:
|
||||
group.add_argument("--log-level", choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
|
||||
help="logging level verbosity", default="INFO")
|
||||
group.add_argument(
|
||||
"--log-level",
|
||||
choices=["DEBUG", "INFO", "WARNING", "ERROR", "CRITICAL"],
|
||||
help="logging level verbosity", default="INFO")
|
||||
except argparse.ArgumentError:
|
||||
# It is possible that --log-level has already been set by APBS
|
||||
pass
|
||||
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("-q", "--quiet", action="store_const", const="WARNING",
|
||||
dest="log_level", help="suppress non-warning messages")
|
||||
group.add_argument("--protonate-all", dest="protonate_all", action="store_true",
|
||||
help="Protonate all atoms (will not influence pKa calculation)",
|
||||
default=False)
|
||||
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(
|
||||
"-q", "--quiet", action="store_const", const="WARNING",
|
||||
dest="log_level", help="suppress non-warning messages")
|
||||
group.add_argument(
|
||||
"--protonate-all", dest="protonate_all", action="store_true",
|
||||
help="Protonate all atoms (will not influence pKa calculation)",
|
||||
default=False)
|
||||
return parser
|
||||
|
||||
|
||||
|
||||
Reference in New Issue
Block a user