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authordeepsource-autofix[bot] <62050782+deepsource-autofix[bot]@users.noreply.github.com>2020-07-07 14:55:17 +0000
committerGitHub <noreply@github.com>2020-07-07 14:55:17 +0000
commit0d135d611506e81d322596c7827b08bbfd3b7c08 (patch)
treea281b8e1f140ad3de77d818747fce03bcfa5b77b /plip/plipcmd.py
parent7059ee2a4ced23e467741cc846eb185886ffca38 (diff)
Format code with Blackdeepsource-transform-b65b5545
Diffstat (limited to 'plip/plipcmd.py')
-rw-r--r--plip/plipcmd.py410
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