AsIsStarts

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 OEShapeDatabase with the AsIs molecule starting orientation.

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 the molecule. The reason for this design decision is to not force an additional memory overhead for an already memory intensive OEShapeDatabase object.

Code

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

Download code

AsIsStartsExample.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
# provided to current licensees or subscribers of Cadence products or
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# subject to these terms. Cadence claims no rights to Customer's
# modifications. Modification of Sample Code is at Customer's sole and
# exclusive risk. Sample Code may require Customer to have a then
# current license or subscription to the applicable Cadence offering.
# THE SAMPLE CODE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
# EXPRESS OR IMPLIED.  OPENEYE DISCLAIMS ALL WARRANTIES, INCLUDING, BUT
# 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 sys
import os

from openeye import oechem
from openeye import oefastrocs

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.oeb> <queries> <hits.oeb>" % argv[0])
        return 0

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

    # read in database
    dbname = argv[1]

    if oechem.OEIsGZip(dbname):
        oechem.OEThrow.Fatal("%s is an unsupported database file format as it is gzipped.\n"
                             "Preferred formats are .oeb, .sdf or .oez", dbname)

    print("Opening database file %s ..." % dbname)
    dbase = oefastrocs.OEShapeDatabase()
    moldb = oechem.OEMolDatabase()

    if not moldb.Open(dbname):
        oechem.OEThrow.Fatal("Unable to open '%s'" % dbname)

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

    # customize search options
    opts = oefastrocs.OEShapeDatabaseOptions()
    opts.SetInitialOrientation(oefastrocs.OEFastROCSOrientation_AsIs)

    opts.SetLimit(50)
    opts.SetMaxConfs(5)
    opts.SetMaxOverlays(opts.GetNumInertialStarts() * opts.GetNumStarts())

    if opts.GetInitialOrientation() == oefastrocs.OEFastROCSOrientation_AsIs:
        numStarts = opts.GetNumStarts()
        numInertialStarts = opts.GetNumInertialStarts()
        oechem.OEThrow.Info("This example will use %u starts & %u inertial starts"
                            % (numStarts, numInertialStarts))

    qfname = 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)

    # write out everthing to a similary named file
    ofs = oechem.oemolostream()
    if not ofs.open(argv[3]):
        oechem.OEThrow.Fatal("Unable to open '%s'" % argv[3])
    oechem.OEWriteMolecule(ofs, query)

    print("Searching for %s" % qfname)
    for score in dbase.GetSortedScores(query, opts):
        print("Score for mol %u(conf %u) %f shape %f color" % (
               score.GetMolIdx(), score.GetConfIdx(),
               score.GetShapeTanimoto(), score.GetColorTanimoto()))
        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" % argv[3])

    return 0


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

See also

• OEFastROCSOrientation.AsIs