示例#1
0
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)
示例#2
0
文件: plipcmd.py 项目: kalinni/plip
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