Replace optparse with argparse.

Optparse is deprecated.  Argparse will allow tighter integration with
PDB2PQR/APBS.

propka/lib.py

@@ -4,6 +4,8 @@ from __future__ import print_function
 import sys
 import pkg_resources
 import logging
+import argparse
+
 
 logger = logging.getLogger("propka")
 stdout_handler = logging.StreamHandler(sys.stdout)
@@ -136,9 +138,95 @@ def parse_res_string(res_str):
     return chain, resnum, inscode
 
 
+def build_parser(parser_=None):
+    """Build an argument parser for PROPKA.
+
+    Args:
+        parser_:  existing parser.  If this is not None, then the PROPKA parser will
+                 be created as a subparser to this existing parser.  Otherwise, a 
+                 new parser will be created.
+    Returns:
+        ArgumentParser object.
+    """
+    if parser_ is not None:
+        subparsers = parser_.add_subparsers(title="PROPKA sub-command group",
+                                            dest="propka_group", action="store_true")
+        parser = subparsers.add_parser("PROPKA", help="PROPKA invocation options",
+                                       dest="propka", action="store_true")
+    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.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>")
+    return parser
+
+
 def loadOptions(*args):
     """
-    Load the arguments parser with options. Note that verbosity is set as soon as this function is invoked.
+    Load the arguments parser with options. Note that verbosity is set as soon
+    as this function is invoked.
+
+    Returns:
+        argparse namespace
     """
     from optparse import OptionParser
 
@@ -149,68 +237,17 @@ def loadOptions(*args):
     parser = OptionParser(usage)
 
     # loading the parser
-    parser.add_option("-f", "--file", action="append", dest="filenames",
+    parser = build_parser()
-           help="read data from <filename>, i.e. <filename> is added to arguments")
-    parser.add_option("-r", "--reference", dest="reference", default="neutral",
-           help="setting which reference to use for stability calculations [neutral/low-pH]")
-    parser.add_option("-c", "--chain", action="append", dest="chains",
-           help='creating the protein with only a specified chain. Specify " " for chains without ID [all]')
-    parser.add_option("-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_option("-t", "--thermophile", action="append", dest="thermophiles",
-           help="defining a thermophile filename; usually used in 'alignment-mutations'")
-    parser.add_option("-a", "--alignment", action="append", dest="alignment",
-           help="alignment file connecting <filename> and <thermophile> [<thermophile>.pir]")
-    parser.add_option("-m", "--mutation", action="append", dest="mutations",
-           help="specifying mutation labels which is used to modify <filename> according to, e.g. N25R/N181D")
-    parser.add_option("-v", "--version", dest="version_label", default="Jan15",
-           help="specifying the sub-version of propka [Jan15/Dec19]")
-    parser.add_option("-p", "--parameters",dest="parameters", default=pkg_resources.resource_filename(__name__, "propka.cfg"),
-           help="set the parameter file [%default]")
-    parser.add_option("-z", "--verbose", dest="verbosity", action="store_const", const=2,
-           help="output debugging information")
-    parser.add_option("-q", "--quiet", dest="verbosity", action="store_const", const=0, default=1,
-                      help="inhibit printing to stdout")
-    parser.add_option("-o", "--pH", dest="pH", type="float", default=7.0,
-           help="setting pH-value used in e.g. stability calculations [7.0]")
-    parser.add_option("-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_option("-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_option("--mutator", dest="mutator",
-           help="setting approach for mutating <filename> [alignment/scwrl/jackal]")
-    parser.add_option("--mutator-option", dest="mutator_options", action="append",
-           help="setting property for mutator [e.g. type=\"side-chain\"]")
-
-    parser.add_option("-d","--display-coupled-residues", dest="display_coupled_residues", action="store_true",
-           help="Displays alternative pKa values due to coupling of titratable groups")
-    parser.add_option("-l","--reuse-ligand-mol2-files", dest="reuse_ligand_mol2_file", action="store_true",
-           help="Reuses the ligand mol2 files allowing the user to alter ligand bond orders", default=False)
-    parser.add_option("-k","--keep-protons", dest="keep_protons", action="store_true",
-           help="Keep protons in input file", default=False)
-    parser.add_option("--protonate-all", dest="protonate_all", action="store_true",
-           help="Protonate all atoms (will not influence pKa calculation)", default=False)
-
 
     # parsing and returning options and arguments
     if len(args) == 0:
         # command line
-        options, args = parser.parse_args()
+        options = parser.parse_args()
     else:
-        options, args = parser.parse_args(list(args))
+        options = parser.parse_args(list(args))
 
     # adding specified filenames to arguments
-    if options.filenames:
+    options.filenames.append(options.input_pdb)
-      for filename in options.filenames:
-        args.append(filename)
-
-    # checking at early stage that there is at least one pdbfile to work with. The error message is misleading
-    # if one is using the python interface via Molecular_container.
-    if len(args) == 0:
-      info("No pdbfile provided")
-      #sys.exit(9)
 
     # Convert titrate_only string to a list of (chain, resnum) items:
     if options.titrate_only is not None:
@@ -236,10 +273,7 @@ def loadOptions(*args):
         logger.warning("Invalid verbosity level, using default")
 
     # done!
-    return options, args
+    return options
-
-
-
 
 
 def makeTidyAtomLabel(name,element):

propka/run.py

@@ -1,13 +1,18 @@
 # entry point for propka script
-
+import logging
 import propka.lib, propka.molecular_container
 
+
+_LOGGER = logging.getLogger("PROPKA")
+
+
 def main():
     """
     Reads in structure files, calculates pKa values, and prints pKa files
     """
     # loading options, flaggs and arguments
-    options, pdbfiles = propka.lib.loadOptions()
+    options = propka.lib.loadOptions()
+    pdbfiles = options.filenames
 
     for pdbfile in pdbfiles:
         my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
@@ -25,7 +30,10 @@ def single(pdbfile, optargs=None):
        single("protein.pdb", optargs=["--mutation=N25R/N181D", "-v", "--pH=7.2"])
     """
     optargs = optargs if optargs is not None else []
-    options, ignored_pdbfiles = propka.lib.loadOptions(*optargs)
+    options = propka.lib.loadOptions(*optargs)
+    pdbfile = options.filenames.pop(0)
+    if len(options.filenames) > 0:
+        _LOGGER.warning("Ignoring filenames: %s", options.filenames)
 
     my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)
     my_molecule.calculate_pka()

scripts/propka31.py

@@ -16,7 +16,8 @@ def main():
     Reads in structure files, calculates pKa values, and prints pKa files
     """
     # loading options, flaggs and arguments
-    options, pdbfiles = propka.lib.loadOptions()
+    options = propka.lib.loadOptions()
+    pdbfiles = options.filenames
 
     for pdbfile in pdbfiles:
         my_molecule = propka.molecular_container.Molecular_container(pdbfile, options)