Custom Color FF Prep

Caches custom color atoms onto molecules. The output must be OEB. OEShapeDatabase, ShapeDatabaseServer.py, and ShapeDatabaseClient.py will honor cached color atoms if present on the molecules. Make sure the script is run on both the database and the query molecules before running a search.

Code

prompt> CustomColorFFPrep.py <input> <output.oeb>

Download code

CustomColorFFPrep.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.

# Cache custom color atoms onto a molecule to be used by FastROCS

import os
import sys

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

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

COLOR_FORCE_FIELD = """#
TYPE negative
#
#
PATTERN negative [-]
PATTERN negative [OD1+0]-[!#7D3]~[OD1+0]
PATTERN negative [OD1+0]-[!#7D4](~[OD1+0])~[OD1+0]
#
#
INTERACTION negative negative attractive gaussian weight=1.0 radius=1.0
"""


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

    # input - preserve rotor-offset-compression
    ifs = oechem.oemolistream()
    ihand = ifs.GetBinaryIOHandler()
    ihand.Clear()
    oechem.OEInitHandler(ihand, oechem.OEBRotCompressOpts(), oechem.OEBRotCompressOpts())

    ifname = argv[1]
    if not ifs.open(ifname):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % argv[1])

    # output
    ofname = argv[2]
    oformt = oechem.OEGetFileType(oechem.OEGetFileExtension(ofname))
    if oformt != oechem.OEFormat_OEB:
        oechem.OEThrow.Fatal("Output file format much be OEB")

    ofs = oechem.oemolostream()
    if not ofs.open(ofname):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % ofname)

    iss = oechem.oeisstream(COLOR_FORCE_FIELD)
    cff = oeshape.OEColorForceField()
    if not cff.Init(iss):
        oechem.OEThrow.Fatal("Unable to initialize OEColorForceField")

    dots = oechem.OEDots(10000, 200, "molecules")
    for mol in ifs.GetOEMols():
        oefastrocs.OEPrepareFastROCSMol(mol, cff)

        oechem.OEWriteMolecule(ofs, mol)

        dots.Update()

    dots.Total()
    ofs.close()

    print("Indexing %s" % ofname)
    if not oechem.OECreateMolDatabaseIdx(ofname):
        oechem.OEThrow.Fatal("Failed to index %s" % argv[2])

    return 0


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