Apply ChEMBL solubility transformations

A utility that reads an input set of structures and outputs transformed structures along with annotations containing of the original data based on the matched pairs discovered from indexing solubility data from the [ChEMBL24-2018] data set.

See also

• OEApplyChEMBL24SolubilityTransforms function

Command Line Interface

prompt> ChEMBLsolubility.py input.sdf output.sdf

Code

Download code

ChEMBLsolubility.py

#!/usr/bin/env python
# (C) 2022 Cadence Design Systems, Inc. (Cadence) 
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#############################################################################
# Utility to apply ChEMBL24 solubility transforms to an input set of structures
# ---------------------------------------------------------------------------
# ChEMBLsolubility.py [-i] input_mols [-o] output_mols
#                     [ -verbose ] [ -context [0|2] ] [ -minpairs # ]
#
# input_mols: filename of molecules to transform based on analysis
# output_mols: filename to collect transformed molecules
# [-verbose]: optional flag to request verbose progress
# [-context #]: optional flag to request a specific chemistry context
# [-minpairs #]: optional flag to request a minimum number of pairs to apply transforms
#############################################################################
from openeye import oechem
from openeye import oemedchem
import sys

############################################################
InterfaceData = """
!BRIEF [-i] <infile1> [-o] <infile2> [ -verbose ] [ -context [0|2]] [ -minpairs # ]
!PARAMETER -i
  !ALIAS -in
  !ALIAS -input
  !TYPE string
  !REQUIRED true
  !BRIEF Input file name
  !KEYLESS 1
!END
!PARAMETER -o
  !ALIAS -out
  !ALIAS -output
  !TYPE string
  !REQUIRED true
  !BRIEF Output file name
  !KEYLESS 2
!END
!PARAMETER -verbose
  !ALIAS -v
  !TYPE bool
  !DEFAULT false
  !BRIEF Verbose output
!END
!PARAMETER -context
  !ALIAS -c
  !TYPE string
  !DEFAULT 0
  !BRIEF Chemistry context for output
!END
!PARAMETER -minpairs 2
   !TYPE int
   !DEFAULT 0
   !BRIEF require at least -minpairs to apply the transformations (default: all)
!END
"""


def main(argv=[__name__]):
    itf = oechem.OEInterface(InterfaceData, argv)

    verbose = itf.GetBool("-verbose")

    # input structure(s) to transform
    ifsmols = oechem.oemolistream()
    if not ifsmols.open(itf.GetString("-i")):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % itf.GetString("-i"))

    # save output structure(s) to this file
    ofs = oechem.oemolostream()
    if not ofs.open(itf.GetString("-o")):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % itf.GetString("-o"))

    # request a specific context for the transform activity, here 0-bonds
    chemctxt = oemedchem.OEMatchedPairContext_Bond0
    askcontext = itf.GetString("-context")[:1]
    if askcontext == '0':
        chemctxt = oemedchem.OEMatchedPairContext_Bond0
    elif askcontext == '2':
        chemctxt = oemedchem.OEMatchedPairContext_Bond2
    else:
        oechem.OEThrow.Fatal("Invalid context specified: " +
                             askcontext + ", only 0|2 allowed")

    minpairs = itf.GetInt("-minpairs")
    if minpairs > 1 and verbose:
        print('Requiring at least {0:d} matched pairs to apply transformations'.format(minpairs))

    irec = 0
    ocnt = 0
    ototal = 0
    for mol in ifsmols.GetOEGraphMols():
        irec += 1
        oechem.OEDeleteEverythingExceptTheFirstLargestComponent(mol)
        iter = oemedchem.OEApplyChEMBL24SolubilityTransforms(mol, chemctxt, minpairs)
        if not iter.IsValid():
            name = mol.GetTitle()
            if not mol.GetTitle():
                name = 'record ' + str(irec)
            oechem.OEThrow.Warning("%s: did not produce any output" % name)
            continue
        ocnt = 0
        for outmol in iter:
            ocnt += 1
            oechem.OEWriteMolecule(ofs, outmol)
        if not ocnt:
            print('Record', irec, 'No output generated')
            print(oechem.OEMolToSmiles(mol))
        else:
            ototal += ocnt
            if verbose:
                print('Record:', "{0:4d}".format(irec),
                      'transformation count=', "{0:6d}".format(ocnt),
                      'total mols=', "{0:7d}".format(ototal))

    if not irec:
        oechem.OEThrow.Fatal('No records in input structure file to transform')

    if not ocnt:
        oechem.OEThrow.Warning('No transformed structures generated')

    print("Input molecules={0:d} output molecules={1:d}".format(irec, ototal))

    return 0


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