Source code for ample.util.scwrl_util

"""
@author: jmht
"""

import glob
import os
import logging

from ample.util import ample_util, pdb_edit

logger = logging.getLogger(__name__)


[docs]class Scwrl(object):
    def __init__(self, scwrl_exe=None, workdir=None):
        self.workdir = workdir
        if self.workdir is None:
            self.workdir = os.getcwd()
        if not ample_util.is_exe(scwrl_exe):
            raise RuntimeError("scwrl_exe {0} cannot be found.".format(scwrl_exe))
        self.scwrl_exe = scwrl_exe

[docs]    def add_sidechains(self, pdbin=None, pdbout=None, sequence=None, hydrogens=False, strip_oxt=False):
        """Add the specified sidechains to the pdb"""

        _pdbout = pdbout
        if strip_oxt:
            _pdbout = pdbout + "_OXT"

        cmd = [self.scwrl_exe, "-i", pdbin, "-o", _pdbout]

        # Not needed by default
        if sequence is not None:
            sequenceFile = os.path.join(self.workdir, "sequence.file")
            with open(sequenceFile, 'w') as w:
                w.write(sequence + os.linesep)
            cmd += ["-s", sequenceFile]

        # Don't output hydrogens
        if not hydrogens:
            cmd += ['-h']

        logfile = os.path.abspath("scwrl.log")
        retcode = ample_util.run_command(cmd, logfile=logfile)

        if retcode != 0:
            raise RuntimeError("Error running Scwrl - please check the logfile: {0}".format(logfile))
        else:
            os.unlink(logfile)

        if strip_oxt:
            # Remove all OXT atoms
            pdb_edit.strip(_pdbout, pdbout, atom_types=['OXT'])
            os.unlink(_pdbout)

        return os.path.abspath(pdbout)

[docs]    def process_directory(self, in_dir, out_dir, strip_oxt=False, prefix="scwrl"):
        logger.info('Adding sidechains with SCWRL to models in directory: {0}'.format(in_dir))
        self.process_models(glob.glob(os.path.join(in_dir, '*.pdb')), out_dir, strip_oxt=strip_oxt, prefix=prefix)
        return

[docs]    def process_models(self, models, out_dir, strip_oxt=False, prefix="scwrl"):
        logger.info('Adding sidechains with SCWRL to models')
        out_pdbs = []
        for i, pdb in enumerate(models):
            out_pdbs.append(
                self.add_sidechains(
                    pdbin=pdb, pdbout=ample_util.filename_append(pdb, prefix, directory=out_dir), strip_oxt=strip_oxt
                )
            )
        logger.info('Processed {0} models with SCWRL into directory: {1}'.format(i + 1, out_dir))
        return out_pdbs