/usr/bin/plipcmd is in plip 1.3.5+dfsg-1.
This file is owned by root:root, with mode 0o755.
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"""
Protein-Ligand Interaction Profiler - Analyze and visualize protein-ligand interactions in PDB files.
plipcmd - Main script for PLIP command line execution.
"""
# Compatibility
from __future__ import print_function
from __future__ import absolute_import
# Own modules
from plip.modules.preparation import *
from plip.modules.visualize import visualize_in_pymol
from plip.modules.plipremote import VisualizerData
from plip.modules.report import StructureReport,__version__
from plip.modules import config
from plip.modules.mp import parallel_fn
from plip.modules.webservices import check_pdb_status, fetch_pdb
# Python standard library
import sys
import argparse
from argparse import ArgumentParser
import time
import multiprocessing
import json
# External libraries
import lxml.etree as et
descript = "Protein-Ligand Interaction Profiler (PLIP) v%s " \
"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" % __version__
def threshold_limiter(aparser, arg):
arg = float(arg)
if arg <= 0:
aparser.error("All thresholds have to be values larger than zero.")
return arg
def process_pdb(pdbfile, outpath):
"""Analysis of a single PDB file. Can generate textual reports XML, PyMOL session files and images as output."""
startmessage = '\nStarting analysis of %s\n' % pdbfile.split('/')[-1]
write_message(startmessage)
write_message('='*len(startmessage)+'\n')
mol = PDBComplex()
mol.output_path = outpath
mol.load_pdb(pdbfile)
# #@todo Offers possibility for filter function from command line (by ligand chain, position, hetid)
for ligand in mol.ligands:
mol.characterize_complex(ligand)
create_folder_if_not_exists(outpath)
# Generate the report files
streport = StructureReport(mol)
config.MAXTHREADS = min(config.MAXTHREADS, len(mol.interaction_sets))
######################################
# PyMOL Visualization (parallelized) #
######################################
if config.PYMOL or config.PICS:
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:
write_message('\nGenerating visualizations in parallel on %i cores ...' % config.MAXTHREADS)
parfn = parallel_fn(visualize_in_pymol)
parfn(complexes, processes=config.MAXTHREADS)
else:
[visualize_in_pymol(plcomplex) for plcomplex in complexes]
if config.XML: # Generate report in xml format
streport.write_xml()
if config.TXT: # Generate report in txt (rst) format
streport.write_txt()
def download_structure(inputpdbid):
"""Given a PDB ID, downloads the corresponding PDB structure.
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':
sysexit(3, 'Invalid PDB ID (Wrong format)\n')
pdbfile, pdbid = fetch_pdb(inputpdbid.lower())
pdbpath = tilde_expansion('%s/%s.pdb' % (config.BASEPATH.rstrip('/'), pdbid))
create_folder_if_not_exists(config.BASEPATH)
with open(pdbpath, 'w') as g:
g.write(pdbfile)
write_message('file downloaded as %s\n\n' % pdbpath)
return pdbpath, pdbid
except ValueError: # Invalid PDB ID, cannot fetch from RCBS server
sysexit(3, 'Invalid PDB ID (Entry does not exist)\n')
def remove_duplicates(slist):
"""Checks input lists for duplicates and returns
a list with unique entries"""
unique = list(set(slist))
difference = len(slist) - len(unique)
if difference == 1:
write_message("Removed one duplicate entry from input list.\n")
if difference > 1:
write_message("Removed %i duplicate entries from input list.\n" % difference)
return unique
def main(inputstructs, inputpdbids):
"""Main function. Calls functions for processing, report generation and visualization."""
pdbid, pdbpath = None, None
# #@todo For multiprocessing, implement better stacktracing for errors
# Print title and version
title = "* Protein-Ligand Interaction Profiler v%s *" % __version__
write_message('\n' + '*' * len(title) + '\n')
write_message(title)
write_message('\n' + '*' * len(title) + '\n\n')
if inputstructs is not None: # Process PDB file(s)
num_structures = len(inputstructs)
inputstructs = remove_duplicates(inputstructs)
for inputstruct in inputstructs:
if os.path.getsize(inputstruct) == 0:
sysexit(2, 'Empty PDB file\n') # Exit if input file is empty
if num_structures > 1:
basename = inputstruct.split('.')[-2].split('/')[-1]
config.OUTPATH = '/'.join([config.BASEPATH, basename])
process_pdb(inputstruct, config.OUTPATH)
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()])
process_pdb(pdbpath, config.OUTPATH)
if (pdbid is not None or inputstructs is not None) and config.BASEPATH is not None:
if config.BASEPATH in ['.', './']:
write_message('\nFinished analysis. Find the result files in the working directory.\n\n')
else:
write_message('\nFinished analysis. Find the result files in %s\n\n' % config.BASEPATH)
if __name__ == '__main__':
##############################
# Parse command line arguments
##############################
parser = ArgumentParser(prog="PLIP", description=descript)
pdbstructure = parser.add_mutually_exclusive_group(required=True) # Needs either PDB ID or file
pdbstructure.add_argument("-f", "--file", dest="input", nargs="+")
pdbstructure.add_argument("-i", "--input", dest="pdbid", nargs="+")
parser.add_argument("-o", "--out", dest="outpath", default="./")
parser.add_argument("-v", "--verbose", dest="verbose", default=False, help="Set verbose 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 into with covalent bonds but treat them as single ligands"
"fot 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("--debug", dest="debug", default=False,
help="Turn on DEBUG mode with extended log.",
action="store_true")
parser.add_argument("--nofix", dest="nofix", default=False,
help="Turns off fixing of PDB files.",
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")
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")
# 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')]
for t in thresholds:
parser.add_argument('--%s' % t.name, dest=t.name, type=lambda val: threshold_limiter(parser, val),
help=argparse.SUPPRESS)
arguments = parser.parse_args()
config.VERBOSE = True if (arguments.verbose or arguments.debug) else False
config.DEBUG = True if arguments.debug else False
config.MAXTHREADS = arguments.maxthreads
config.XML = arguments.xml
config.TXT = arguments.txt
config.PICS = arguments.pics
config.PYMOL = arguments.pymol
config.OUTPATH = arguments.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
config.PEPTIDES = arguments.peptides
config.INTRA = arguments.intra
config.NOFIX = arguments.nofix
config.KEEPMOD = arguments.keepmod
config.DNARECEPTOR = arguments.dnareceptor
# 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 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
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.")
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.")
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.")
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
main(expanded_path, arguments.pdbid) # Start main script
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