Implicit Mills Dean No Rings

Return the results for a database for each query sorted by their rank in that search. Attaches the shape Tanimoto as SD data. Demonstrates the usage of the ImplicitMillsDeanNoRings subtype of the OEColorForceField class. This will ignore rings when calculating color score.

Note

The OEShapeDatabase does not store molecular information, only coordinate information from each conformer. If the original molecule is required for output it is the responsibility of the programmer to maintain the relationship of the OEShapeDatabase indices to molecule. The reason for this design decision is to not force a additional memory overhead for an already memory intensive OEShapeDatabase object.

Code

prompt> ImplicitMillsDeanNoRingsExample.py <database> [<queries> ... ]

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ImplicitMillsDeanNoRingsExample.py

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
# All rights reserved.
# TERMS FOR USE OF SAMPLE CODE The software below ("Sample Code") is
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# subject to these terms. Cadence claims no rights to Customer's
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# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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# NOT LIMITED TO, WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
# PARTICULAR PURPOSE AND NONINFRINGEMENT. In no event shall Cadence be
# liable for any damages or liability in connection with the Sample Code
# or its use.

import os
import sys

from openeye import oechem
from openeye import oefastrocs
from openeye import oeshape

oepy = os.path.join(os.path.dirname(__file__), "..", "python")
sys.path.insert(0, os.path.realpath(oepy))


def main(argv=[__name__]):
    if len(argv) < 3:
        oechem.OEThrow.Usage("%s <database> [<queries> ... ]" % argv[0])

    if not oefastrocs.OEFastROCSIsGPUReady():
        oechem.OEThrow.Info("No supported GPU available!")
        return 0

    dbname = argv[1]
    # read in database
    ifs = oechem.oemolistream()
    if not ifs.open(dbname):
        oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)

    print("Opening database file %s ..." % dbname)
    timer = oechem.OEWallTimer()
    cff = oeshape.OEColorForceField()
    cff.Init(oeshape.OEColorFFType_ImplicitMillsDeanNoRings)
    dbase = oefastrocs.OEShapeDatabase(cff)
    moldb = oechem.OEMolDatabase()
    if not moldb.Open(ifs):
        oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)

    dots = oechem.OEThreadedDots(10000, 200, "conformers")
    if not dbase.Open(moldb, dots):
        oechem.OEThrow.Fatal("Unable to initialize OEShapeDatabase on '%s'" % dbname)

    dots.Total()
    print("%f seconds to load database" % timer.Elapsed())

    opts = oefastrocs.OEShapeDatabaseOptions()

    for qfname in argv[2:]:
        # read in query
        qfs = oechem.oemolistream()
        if not qfs.open(qfname):
            oechem.OEThrow.Fatal("Unable to open '%s'" % qfname)

        query = oechem.OEGraphMol()
        if not oechem.OEReadMolecule(qfs, query):
            oechem.OEThrow.Fatal("Unable to read query from '%s'" % qfname)

        ext = oechem.OEGetFileExtension(qfname)
        base = qfname[:-(len(ext) + 1)]

        # write out everthing to a similary named file
        ofs = oechem.oemolostream()
        ofname = base + "_results." + ext
        if not ofs.open(ofname):
            oechem.OEThrow.Fatal("Unable to open '%s'" % argv[4])

        print("Searching for %s" % qfname)
        numhits = moldb.NumMols()
        opts.SetLimit(numhits)

        for score in dbase.GetSortedScores(query, opts):
            dbmol = oechem.OEMol()
            molidx = score.GetMolIdx()
            if not moldb.GetMolecule(dbmol, molidx):
                print("Unable to retrieve molecule '%u' from the database" % molidx)
                continue

            mol = oechem.OEGraphMol(dbmol.GetConf(oechem.OEHasConfIdx(score.GetConfIdx())))

            oechem.OESetSDData(mol, "ShapeTanimoto", "%.4f" % score.GetShapeTanimoto())
            oechem.OESetSDData(mol, "ColorTanimoto", "%.4f" % score.GetColorTanimoto())
            oechem.OESetSDData(mol, "TanimotoCombo", "%.4f" % score.GetTanimotoCombo())
            score.Transform(mol)

            oechem.OEWriteMolecule(ofs, mol)
        print("Wrote results to %s" % ofname)

    return 0


if __name__ == '__main__':
    sys.exit(main(sys.argv))