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':
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))
create_folder_if_not_exists(config.BASEPATH)
with open(pdbpath, 'w') as g:
g.write(pdbfile)
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}')
sys.exit(1)
def 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
# '-' as file name 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.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 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=
"Treat nucleic acids as part of the receptor structure (together with any present protein) instead of as a ligand.",
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")
parser.add_argument(
"--model",
dest="model",
default=1,
type=int,
help="Model number to be used for multi-model structures.")
# 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()
# configure log levels
config.VERBOSE = True if arguments.verbose else False
config.QUIET = True if arguments.quiet else False
config.SILENT = True if arguments.silent else False
if config.VERBOSE:
logger.setLevel(logging.DEBUG)
elif config.QUIET:
logger.setLevel(logging.WARN)
elif config.SILENT:
logger.setLevel(logging.CRITICAL)
else:
logger.setLevel(config.DEFAULT_LOG_LEVEL)
config.MAXTHREADS = arguments.maxthreads
config.XML = arguments.xml
config.TXT = arguments.txt
config.PICS = arguments.pics
config.PYMOL = arguments.pymol
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.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.NOFIXFILE = arguments.nofixfile
config.NOPDBCANMAP = arguments.nopdbcanmap
config.KEEPMOD = arguments.keepmod
config.DNARECEPTOR = arguments.dnareceptor
config.OUTPUTFILENAME = arguments.outputfilename
config.NOHYDRO = arguments.nohydro
config.MODEL = arguments.model
# Make sure we have pymol with --pics and --pymol
if config.PICS or config.PYMOL:
try:
import pymol
except ImportError:
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 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
run_analysis(expanded_path, arguments.pdbid) # Start main script