Assigning Charges

The following code example shows how to assign partial charges. The program reads all of the molecules in the input file, assigns partial charges to each based on the selected method (the default is -method mmff94), and writes each charged molecule to the output file.

Command Line Interface

A description of the command line interface can be obtained by executing the program with the –help argument.

prompt> python assigncharges.py --help

will generate the following output:

Simple parameter list

 Charging options
   -method : which set of charges to apply

 input/output options
   -in : Input molecule
   -out : Output molecule (usually an oeb)

Code

Download code

assigncharges.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
# SaaS offerings (each a "Customer").
# Customer is hereby permitted to use, copy, and modify the Sample Code,
# 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
from openeye import oechem
from openeye import oequacpac


def AssignChargesByName(mol, name):
    if name == "noop":
        return oequacpac.OEAssignCharges(mol, oequacpac.OEChargeEngineNoOp())
    elif name == "mmff" or name == "mmff94":
        return oequacpac.OEAssignCharges(mol, oequacpac.OEMMFF94Charges())
    elif name == "am1bcc":
        return oequacpac.OEAssignCharges(mol, oequacpac.OEAM1BCCCharges())
    elif name == "am1bccnosymspt":
        optimize = True
        symmetrize = True
        return oequacpac.OEAssignCharges(mol,
                                         oequacpac.OEAM1BCCCharges(not optimize, not symmetrize))
    elif name == "amber" or name == "amberff94":
        return oequacpac.OEAssignCharges(mol, oequacpac.OEAmberFF94Charges())
    elif name == "am1bccelf10":
        return oequacpac.OEAssignCharges(mol, oequacpac.OEAM1BCCELF10Charges())
    return False


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

    if not oechem.OEParseCommandLine(itf, argv):
        oechem.OEThrow.Fatal("Unable to interpret command line!")

    ifs = oechem.oemolistream()

    inputFile = itf.GetString("-in")
    if not ifs.open(inputFile):
        oechem.OEThrow.Fatal("Unable to open %s for reading" % inputFile)

    ofs = oechem.oemolostream()

    outFile = itf.GetString("-out")
    if not ofs.open(outFile):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % outFile)

    chargeName = itf.GetString("-method")

    mol = oechem.OEMol()
    while oechem.OEReadMolecule(ifs, mol):
        if not AssignChargesByName(mol, chargeName):
            oechem.OEThrow.Warning("Unable to assign %s charges to mol %s"
                                   % (chargeName, mol.GetTitle()))
        oechem.OEWriteMolecule(ofs, mol)

    ifs.close()
    ofs.close()

#############################################################################
# INTERFACE
#############################################################################


InterfaceData = '''
!BRIEF AssignCharges.py [-options] <inmol> [<outmol>]

!CATEGORY "input/output options :"
   !PARAMETER -in
      !ALIAS -i
      !TYPE string
      !BRIEF Input molecule
      !VISIBILITY simple
      !REQUIRED true
      !KEYLESS 1
   !END

   !PARAMETER -out
      !ALIAS -o
      !TYPE string
      !DEFAULT oeassigncharges.oeb.gz
      !BRIEF Output molecule (usually an oeb)
      !VISIBILITY simple
      !REQUIRED false
      !KEYLESS 2
   !END
!END

!CATEGORY "Charging options :"
   !PARAMETER -method
      !TYPE string
      !LEGAL_VALUE noop
      !LEGAL_VALUE mmff
      !LEGAL_VALUE mmff94
      !LEGAL_VALUE am1bcc
      !LEGAL_VALUE am1bccnosymspt
      !LEGAL_VALUE amber
      !LEGAL_VALUE amberff94
      !LEGAL_VALUE am1bccelf10
      !DEFAULT mmff94
      !BRIEF which set of charges to apply
      !SIMPLE true
      !REQUIRED false
   !END
!END
'''

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

See also

• OEAssignCharges function