Format code with Blackdeepsource-transform-b65b5545

1 files changed, 293 insertions, 117 deletions

diff --git a/plip/plipcmd.py b/plip/plipcmd.py
index e4c0815..b590d09 100644
--- a/plip/plipcmd.py
+++ b/plip/plipcmd.py
@@ -25,12 +25,14 @@ from plip.exchange.webservices import fetch_pdb
 from plip.structure.preparation import create_folder_if_not_exists, extract_pdbid
 from plip.structure.preparation import tilde_expansion, PDBComplex
 
-description = f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}" \
-              "is a command-line based tool to analyze interactions in a protein-ligand complex. " \
-              "If you are using PLIP in your work, please cite: " \
-              "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. " \
-              "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315" \
-              f"Supported and maintained by: {config.__maintainer__}"
+description = (
+    f"The Protein-Ligand Interaction Profiler (PLIP) {__version__}"
+    "is a command-line based tool to analyze interactions in a protein-ligand complex. "
+    "If you are using PLIP in your work, please cite: "
+    "Salentin,S. et al. PLIP: fully automated protein-ligand interaction profiler. "
+    "Nucl. Acids Res. (1 July 2015) 43 (W1): W443-W447. doi:10.1093/nar/gkv315"
+    f"Supported and maintained by: {config.__maintainer__}"
+)
 
 
 def threshold_limiter(aparser, arg):
@@ -40,13 +42,13 @@ def threshold_limiter(aparser, arg):
     return arg
 
 
-def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
+def process_pdb(pdbfile, outpath, as_string=False, outputprefix="report"):
     """Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
     if not as_string:
-        pdb_file_name = pdbfile.split('/')[-1]
-        startmessage = f'starting analysis of {pdb_file_name}'
+        pdb_file_name = pdbfile.split("/")[-1]
+        startmessage = f"starting analysis of {pdb_file_name}"
     else:
-        startmessage = 'starting analysis from STDIN'
+        startmessage = "starting analysis from STDIN"
     logger.info(startmessage)
     mol = PDBComplex()
     mol.output_path = outpath
@@ -68,10 +70,16 @@ def process_pdb(pdbfile, outpath, as_string=False, outputprefix='report'):
 
     if config.PYMOL or config.PICS:
         from plip.visualization.visualize import visualize_in_pymol
-        complexes = [VisualizerData(mol, site) for site in sorted(mol.interaction_sets)
-                     if not len(mol.interaction_sets[site].interacting_res) == 0]
+
+        complexes = [
+            VisualizerData(mol, site)
+            for site in sorted(mol.interaction_sets)
+            if not len(mol.interaction_sets[site].interacting_res) == 0
+        ]
         if config.MAXTHREADS > 1:
-            logger.info(f'generating visualizations in parallel on {config.MAXTHREADS} cores')
+            logger.info(
+                f"generating visualizations in parallel on {config.MAXTHREADS} cores"
+            )
             parfn = parallel_fn(visualize_in_pymol)
             parfn(complexes, processes=config.MAXTHREADS)
         else:
@@ -89,19 +97,22 @@ def download_structure(inputpdbid):
     Checks for validity of ID and handles error while downloading.
     Returns the path of the downloaded file."""
     try:
-        if len(inputpdbid) != 4 or extract_pdbid(inputpdbid.lower()) == 'UnknownProtein':
-            logger.error(f'invalid PDB-ID (wrong format): {inputpdbid}')
+        if (
+            len(inputpdbid) != 4
+            or extract_pdbid(inputpdbid.lower()) == "UnknownProtein"
+        ):
+            logger.error(f"invalid PDB-ID (wrong format): {inputpdbid}")
             sys.exit(1)
         pdbfile, pdbid = fetch_pdb(inputpdbid.lower())
-        pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
+        pdbpath = tilde_expansion("%s/%s.pdb" % (config.BASEPATH.rstrip("/"), pdbid))
         create_folder_if_not_exists(config.BASEPATH)
-        with open(pdbpath, 'w') as g:
+        with open(pdbpath, "w") as g:
             g.write(pdbfile)
-        logger.info(f'file downloaded as {pdbpath}')
+        logger.info(f"file downloaded as {pdbpath}")
         return pdbpath, pdbid
 
     except ValueError:  # Invalid PDB ID, cannot fetch from RCBS server
-        logger.error(f'PDB-ID does not exist: {inputpdbid}')
+        logger.error(f"PDB-ID does not exist: {inputpdbid}")
         sys.exit(1)
 
 
@@ -111,9 +122,9 @@ def remove_duplicates(slist):
     unique = list(set(slist))
     difference = len(slist) - len(unique)
     if difference == 1:
-        logger.info('removed one duplicate entry from input list')
+        logger.info("removed one duplicate entry from input list")
     if difference > 1:
-        logger.info(f'Removed {difference} duplicate entries from input list')
+        logger.info(f"Removed {difference} duplicate entries from input list")
     return unique
 
 
@@ -122,9 +133,9 @@ def run_analysis(inputstructs, inputpdbids):
     pdbid, pdbpath = None, None
     # @todo For multiprocessing, implement better stacktracing for errors
     # Print title and version
-    logger.info(f'Protein-Ligand Interaction Profiler (PLIP) {__version__}')
-    logger.info(f'brought to you by: {config.__maintainer__}')
-    logger.info(f'please cite: https://www.doi.org/10.1093/nar/gkv315')
+    logger.info(f"Protein-Ligand Interaction Profiler (PLIP) {__version__}")
+    logger.info(f"brought to you by: {config.__maintainer__}")
+    logger.info(f"please cite: https://www.doi.org/10.1093/nar/gkv315")
     output_prefix = config.OUTPUTFILENAME
 
     if inputstructs is not None:  # Process PDB file(s)
@@ -132,114 +143,258 @@ def run_analysis(inputstructs, inputpdbids):
         inputstructs = remove_duplicates(inputstructs)
         read_from_stdin = False
         for inputstruct in inputstructs:
-            if inputstruct == '-':
+            if inputstruct == "-":
                 inputstruct = sys.stdin.read()
                 read_from_stdin = True
                 if config.RAWSTRING:
                     if sys.version_info < (3,):
-                        inputstruct = bytes(inputstruct).decode('unicode_escape')
+                        inputstruct = bytes(inputstruct).decode("unicode_escape")
                     else:
-                        inputstruct = bytes(inputstruct, 'utf8').decode('unicode_escape')
+                        inputstruct = bytes(inputstruct, "utf8").decode(
+                            "unicode_escape"
+                        )
             else:
                 if os.path.getsize(inputstruct) == 0:
-                    logger.error('empty PDB file')
+                    logger.error("empty PDB file")
                     sys.exit(1)
                 if num_structures > 1:
-                    basename = inputstruct.split('.')[-2].split('/')[-1]
-                    config.OUTPATH = '/'.join([config.BASEPATH, basename])
-                    output_prefix = 'report'
-            process_pdb(inputstruct, config.OUTPATH, as_string=read_from_stdin, outputprefix=output_prefix)
+                    basename = inputstruct.split(".")[-2].split("/")[-1]
+                    config.OUTPATH = "/".join([config.BASEPATH, basename])
+                    output_prefix = "report"
+            process_pdb(
+                inputstruct,
+                config.OUTPATH,
+                as_string=read_from_stdin,
+                outputprefix=output_prefix,
+            )
     else:  # Try to fetch the current PDB structure(s) directly from the RCBS server
         num_pdbids = len(inputpdbids)
         inputpdbids = remove_duplicates(inputpdbids)
         for inputpdbid in inputpdbids:
             pdbpath, pdbid = download_structure(inputpdbid)
             if num_pdbids > 1:
-                config.OUTPATH = '/'.join([config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()])
-                output_prefix = 'report'
+                config.OUTPATH = "/".join(
+                    [config.BASEPATH, pdbid[1:3].upper(), pdbid.upper()]
+                )
+                output_prefix = "report"
             process_pdb(pdbpath, config.OUTPATH, outputprefix=output_prefix)
 
     if (pdbid is not None or inputstructs is not None) and config.BASEPATH is not None:
-        if config.BASEPATH in ['.', './']:
-            logger.info('finished analysis, find the result files in the working directory')
+        if config.BASEPATH in [".", "./"]:
+            logger.info(
+                "finished analysis, find the result files in the working directory"
+            )
         else:
-            logger.info(f'finished analysis, find the result files in {config.BASEPATH}')
+            logger.info(
+                f"finished analysis, find the result files in {config.BASEPATH}"
+            )
 
 
-if __name__ == '__main__':
+if __name__ == "__main__":
     """Parse command line arguments and start main script for analysis."""
     parser = ArgumentParser(prog="PLIP", description=description)
-    pdbstructure = parser.add_mutually_exclusive_group(required=True)  # Needs either PDB ID or file
+    pdbstructure = parser.add_mutually_exclusive_group(
+        required=True
+    )  # Needs either PDB ID or file
     # '-' as file name reads from stdin
-    pdbstructure.add_argument("-f", "--file", dest="input", nargs="+", help="Set input file, '-' reads from stdin")
+    pdbstructure.add_argument(
+        "-f",
+        "--file",
+        dest="input",
+        nargs="+",
+        help="Set input file, '-' reads from stdin",
+    )
     pdbstructure.add_argument("-i", "--input", dest="pdbid", nargs="+")
-    outputgroup = parser.add_mutually_exclusive_group(required=False)  # Needs either outpath or stdout
+    outputgroup = parser.add_mutually_exclusive_group(
+        required=False
+    )  # Needs either outpath or stdout
     outputgroup.add_argument("-o", "--out", dest="outpath", default="./")
-    outputgroup.add_argument("-O", "--stdout", dest="stdout", action="store_true", default=False,
-                             help="Write to stdout instead of file")
-    parser.add_argument("--rawstring", dest="use_raw_string", default=False, action="store_true",
-                        help="Use Python raw strings for stdout and stdin")
-    parser.add_argument("-v", "--verbose", dest="verbose", default=False, help="Turn on verbose mode",
-                        action="store_true")
-    parser.add_argument("-q", "--quiet", dest="quiet", default=False, help="Turn on quiet mode", action="store_true")
-    parser.add_argument("-s", "--silent", dest="silent", default=False, help="Turn on silent mode", action="store_true")
-    parser.add_argument("-p", "--pics", dest="pics", default=False, help="Additional pictures", action="store_true")
-    parser.add_argument("-x", "--xml", dest="xml", default=False, help="Generate report file in XML format",
-                        action="store_true")
-    parser.add_argument("-t", "--txt", dest="txt", default=False, help="Generate report file in TXT (RST) format",
-                        action="store_true")
-    parser.add_argument("-y", "--pymol", dest="pymol", default=False, help="Additional PyMOL session files",
-                        action="store_true")
-    parser.add_argument("--maxthreads", dest="maxthreads", default=multiprocessing.cpu_count(),
-                        help="Set maximum number of main threads (number of binding sites processed simultaneously)."
-                             "If not set, PLIP uses all available CPUs if possible.",
-                        type=int)
-    parser.add_argument("--breakcomposite", dest="breakcomposite", default=False,
-                        help="Don't combine ligand fragments with covalent bonds but treat them as single ligands for the analysis.",
-                        action="store_true")
-    parser.add_argument("--altlocation", dest="altlocation", default=False,
-                        help="Also consider alternate locations for atoms (e.g. alternate conformations).",
-                        action="store_true")
-    parser.add_argument("--nofix", dest="nofix", default=False,
-                        help="Turns off fixing of PDB files.",
-                        action="store_true")
-    parser.add_argument("--nofixfile", dest="nofixfile", default=False,
-                        help="Turns off writing files for fixed PDB files.",
-                        action="store_true")
-    parser.add_argument("--nopdbcanmap", dest="nopdbcanmap", default=False,
-                        help="Turns off calculation of mapping between canonical and PDB atom order for ligands.",
-                        action="store_true")
-    parser.add_argument("--dnareceptor", dest="dnareceptor", default=False,
-                        help="Uses the DNA instead of the protein as a receptor for interactions.",
-                        action="store_true")
-    parser.add_argument("--name", dest="outputfilename", default="report",
-                        help="Set a filename for the report TXT and XML files. Will only work when processing single structures.")
-    ligandtype = parser.add_mutually_exclusive_group()  # Either peptide/inter or intra mode
-    ligandtype.add_argument("--peptides", "--inter", dest="peptides", default=[],
-                            help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts",
-                            nargs="+")
-    ligandtype.add_argument("--intra", dest="intra", help="Allows to define one chain to analyze intra-chain contacts.")
-    parser.add_argument("--keepmod", dest="keepmod", default=False,
-                        help="Keep modified residues as ligands",
-                        action="store_true")
-    parser.add_argument("--nohydro", dest="nohydro", default=False,
-                        help="Do not add polar hydrogens in case your structure already contains hydrogens.",
-                        action="store_true")
+    outputgroup.add_argument(
+        "-O",
+        "--stdout",
+        dest="stdout",
+        action="store_true",
+        default=False,
+        help="Write to stdout instead of file",
+    )
+    parser.add_argument(
+        "--rawstring",
+        dest="use_raw_string",
+        default=False,
+        action="store_true",
+        help="Use Python raw strings for stdout and stdin",
+    )
+    parser.add_argument(
+        "-v",
+        "--verbose",
+        dest="verbose",
+        default=False,
+        help="Turn on verbose mode",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-q",
+        "--quiet",
+        dest="quiet",
+        default=False,
+        help="Turn on quiet mode",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-s",
+        "--silent",
+        dest="silent",
+        default=False,
+        help="Turn on silent mode",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-p",
+        "--pics",
+        dest="pics",
+        default=False,
+        help="Additional pictures",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-x",
+        "--xml",
+        dest="xml",
+        default=False,
+        help="Generate report file in XML format",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-t",
+        "--txt",
+        dest="txt",
+        default=False,
+        help="Generate report file in TXT (RST) format",
+        action="store_true",
+    )
+    parser.add_argument(
+        "-y",
+        "--pymol",
+        dest="pymol",
+        default=False,
+        help="Additional PyMOL session files",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--maxthreads",
+        dest="maxthreads",
+        default=multiprocessing.cpu_count(),
+        help="Set maximum number of main threads (number of binding sites processed simultaneously)."
+        "If not set, PLIP uses all available CPUs if possible.",
+        type=int,
+    )
+    parser.add_argument(
+        "--breakcomposite",
+        dest="breakcomposite",
+        default=False,
+        help="Don't combine ligand fragments with covalent bonds but treat them as single ligands for the analysis.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--altlocation",
+        dest="altlocation",
+        default=False,
+        help="Also consider alternate locations for atoms (e.g. alternate conformations).",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--nofix",
+        dest="nofix",
+        default=False,
+        help="Turns off fixing of PDB files.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--nofixfile",
+        dest="nofixfile",
+        default=False,
+        help="Turns off writing files for fixed PDB files.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--nopdbcanmap",
+        dest="nopdbcanmap",
+        default=False,
+        help="Turns off calculation of mapping between canonical and PDB atom order for ligands.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--dnareceptor",
+        dest="dnareceptor",
+        default=False,
+        help="Uses the DNA instead of the protein as a receptor for interactions.",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--name",
+        dest="outputfilename",
+        default="report",
+        help="Set a filename for the report TXT and XML files. Will only work when processing single structures.",
+    )
+    ligandtype = (
+        parser.add_mutually_exclusive_group()
+    )  # Either peptide/inter or intra mode
+    ligandtype.add_argument(
+        "--peptides",
+        "--inter",
+        dest="peptides",
+        default=[],
+        help="Allows to define one or multiple chains as peptide ligands or to detect inter-chain contacts",
+        nargs="+",
+    )
+    ligandtype.add_argument(
+        "--intra",
+        dest="intra",
+        help="Allows to define one chain to analyze intra-chain contacts.",
+    )
+    parser.add_argument(
+        "--keepmod",
+        dest="keepmod",
+        default=False,
+        help="Keep modified residues as ligands",
+        action="store_true",
+    )
+    parser.add_argument(
+        "--nohydro",
+        dest="nohydro",
+        default=False,
+        help="Do not add polar hydrogens in case your structure already contains hydrogens.",
+        action="store_true",
+    )
     # Optional threshold arguments, not shown in help
-    thr = namedtuple('threshold', 'name type')
-    thresholds = [thr(name='aromatic_planarity', type='angle'),
-                  thr(name='hydroph_dist_max', type='distance'), thr(name='hbond_dist_max', type='distance'),
-                  thr(name='hbond_don_angle_min', type='angle'), thr(name='pistack_dist_max', type='distance'),
-                  thr(name='pistack_ang_dev', type='other'), thr(name='pistack_offset_max', type='distance'),
-                  thr(name='pication_dist_max', type='distance'), thr(name='saltbridge_dist_max', type='distance'),
-                  thr(name='halogen_dist_max', type='distance'), thr(name='halogen_acc_angle', type='angle'),
-                  thr(name='halogen_don_angle', type='angle'), thr(name='halogen_angle_dev', type='other'),
-                  thr(name='water_bridge_mindist', type='distance'), thr(name='water_bridge_maxdist', type='distance'),
-                  thr(name='water_bridge_omega_min', type='angle'), thr(name='water_bridge_omega_max', type='angle'),
-                  thr(name='water_bridge_theta_min', type='angle')]
+    thr = namedtuple("threshold", "name type")
+    thresholds = [
+        thr(name="aromatic_planarity", type="angle"),
+        thr(name="hydroph_dist_max", type="distance"),
+        thr(name="hbond_dist_max", type="distance"),
+        thr(name="hbond_don_angle_min", type="angle"),
+        thr(name="pistack_dist_max", type="distance"),
+        thr(name="pistack_ang_dev", type="other"),
+        thr(name="pistack_offset_max", type="distance"),
+        thr(name="pication_dist_max", type="distance"),
+        thr(name="saltbridge_dist_max", type="distance"),
+        thr(name="halogen_dist_max", type="distance"),
+        thr(name="halogen_acc_angle", type="angle"),
+        thr(name="halogen_don_angle", type="angle"),
+        thr(name="halogen_angle_dev", type="other"),
+        thr(name="water_bridge_mindist", type="distance"),
+        thr(name="water_bridge_maxdist", type="distance"),
+        thr(name="water_bridge_omega_min", type="angle"),
+        thr(name="water_bridge_omega_max", type="angle"),
+        thr(name="water_bridge_theta_min", type="angle"),
+    ]
     for t in thresholds:
-        parser.add_argument('--%s' % t.name, dest=t.name, type=lambda val: threshold_limiter(parser, val),
-                            help=argparse.SUPPRESS)
+        parser.add_argument(
+            "--%s" % t.name,
+            dest=t.name,
+            type=lambda val: threshold_limiter(parser, val),
+            help=argparse.SUPPRESS,
+        )
 
     arguments = parser.parse_args()
 
@@ -264,8 +419,11 @@ if __name__ == '__main__':
     config.STDOUT = arguments.stdout
     config.RAWSTRING = arguments.use_raw_string
     config.OUTPATH = arguments.outpath
-    config.OUTPATH = tilde_expansion("".join([config.OUTPATH, '/'])
-                                     if not config.OUTPATH.endswith('/') else config.OUTPATH)
+    config.OUTPATH = tilde_expansion(
+        "".join([config.OUTPATH, "/"])
+        if not config.OUTPATH.endswith("/")
+        else config.OUTPATH
+    )
     config.BASEPATH = config.OUTPATH  # Used for batch processing
     config.BREAKCOMPOSITE = arguments.breakcomposite
     config.ALTLOC = arguments.altlocation
@@ -283,28 +441,46 @@ if __name__ == '__main__':
         try:
             import pymol
         except ImportError:
-            logger.error('PyMOL is required for the --pics and --pymol option')
+            logger.error("PyMOL is required for the --pics and --pymol option")
             sys.exit(1)
     # Assign values to global thresholds
     for t in thresholds:
         tvalue = getattr(arguments, t.name)
         if tvalue is not None:
-            if t.type == 'angle' and not 0 < tvalue < 180:  # Check value for angle thresholds
-                parser.error("Threshold for angles need to have values within 0 and 180.")
-            if t.type == 'distance':
+            if (
+                t.type == "angle" and not 0 < tvalue < 180
+            ):  # Check value for angle thresholds
+                parser.error(
+                    "Threshold for angles need to have values within 0 and 180."
+                )
+            if t.type == "distance":
                 if tvalue > 10:  # Check value for angle thresholds
-                    parser.error("Threshold for distances must not be larger than 10 Angstrom.")
-                elif tvalue > config.BS_DIST + 1:  # Dynamically adapt the search space for binding site residues
+                    parser.error(
+                        "Threshold for distances must not be larger than 10 Angstrom."
+                    )
+                elif (
+                    tvalue > config.BS_DIST + 1
+                ):  # Dynamically adapt the search space for binding site residues
                     config.BS_DIST = tvalue + 1
             setattr(config, t.name.upper(), tvalue)
     # Check additional conditions for interdependent thresholds
     if not config.HALOGEN_ACC_ANGLE > config.HALOGEN_ANGLE_DEV:
-        parser.error("The halogen acceptor angle has to be larger than the halogen angle deviation.")
+        parser.error(
+            "The halogen acceptor angle has to be larger than the halogen angle deviation."
+        )
     if not config.HALOGEN_DON_ANGLE > config.HALOGEN_ANGLE_DEV:
-        parser.error("The halogen donor angle has to be larger than the halogen angle deviation.")
+        parser.error(
+            "The halogen donor angle has to be larger than the halogen angle deviation."
+        )
     if not config.WATER_BRIDGE_MINDIST < config.WATER_BRIDGE_MAXDIST:
-        parser.error("The water bridge minimum distance has to be smaller than the water bridge maximum distance.")
+        parser.error(
+            "The water bridge minimum distance has to be smaller than the water bridge maximum distance."
+        )
     if not config.WATER_BRIDGE_OMEGA_MIN < config.WATER_BRIDGE_OMEGA_MAX:
-        parser.error("The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle")
-    expanded_path = tilde_expansion(arguments.input) if arguments.input is not None else None
+        parser.error(
+            "The water bridge omega minimum angle has to be smaller than the water bridge omega maximum angle"
+        )
+    expanded_path = (
+        tilde_expansion(arguments.input) if arguments.input is not None else None
+    )
     run_analysis(expanded_path, arguments.pdbid)  # Start main script