Source code for schrodinger.application.phase.packages.mmp3dscreener

"""
This module contains the MMP3DScreener class, which performs flexible
shape-based screens of a 3D matched molecular pairs database with queries
supplied as SMILES strings.
"""

import os

from schrodinger import structure
from schrodinger.infra import phase


class MMP3DScreener:
    """
    Performs flexible shape-based screens of a 3D matched molecular pairs
    database with queries supplied as SMILES strings.
    """

    def __init__(self, mmp3d_db_path, conf_options=None):
        """
        Constructor that takes a Maestro file containing a 3D MMP database and
        conformer generation options. Default conformer generation options are
        used if conf_options is omitted.

        :param mmp3d_db_path: Path to 3D MMP database file
        :type mmp3d_db_path: str

        :param conf_options: Conformer generation options
        :type conf_options: phase.PhpConfOptions
        """

        self._validateDb(mmp3d_db_path)
        self._mmp3d_db_path = mmp3d_db_path
        self._conf_options = conf_options or phase.PhpConfOptions()

    def screen(self, smiles, title=None):
        """
        Generator that performs a flexible 3D screen against each pair of
        structures in the MMP database. Each call to this function returns
        a 3D shape-based alignment of the query to the next MMP, with the
        shape similarity stored in the property phase.PHASE_DUAL_SHAPE_SIM.

        :param smiles: SMILES string of the query
        :type smiles: str

        :param title: Title for all returned structures
        :type title: str

        :return: The best alignment to each MMP in the database
        :rtype: structure.Structure
        """

        st = structure.SmilesStructure(smiles).get3dStructure(
            require_stereo=False)
        if title:
            st.title = title
        aligner = phase.PhpShapeTripletAligner(st.handle, self._conf_options)
        with structure.StructureReader(self._mmp3d_db_path) as reader:
            for st1 in reader:
                st2 = next(reader)
                try:
                    st_aligned = structure.Structure(
                        aligner.alignToPair(st1.handle, st2.handle))
                    yield st_aligned
                except (RuntimeError, phase.PhpException) as e:
                    triplet = f'{smiles} to MMP {st1.title}, {st2.title}'
                    print("Skipping alignment of %s: %s" % (triplet, e))

    def _validateDb(self, mmp3d_db_path):
        """
        Ensures that the provided MMP 3D database is a Maestro file and that
        it exists.

        :param mmp3d_db_path: Path to 3D MMP database file
        :type mmp3d_db_path: str

        :raise OSError: If mmp3d_db_path is not a Maestro file or is not found
        """

        file_format = phase.get_phase_file_format(mmp3d_db_path)
        if file_format != phase.PhpFileFormat_PHP_FORMAT_MAE:
            raise OSError("Illegal MMP 3D database file name: \"%s\"" %
                          mmp3d_db_path)
        if not os.path.isfile(mmp3d_db_path):
            raise OSError("MMP 3D database file \"%s\" not found" %
                          mmp3d_db_path)