OE3DMolStyle hierarchy between molecule, conformers, and atoms

A program that shows how the style hierarchy in OE3DMolStyle is inherited between molecules, conformer, and atoms. The style applied to the main molecule will be the top level style. The style applied to each conformer will take priority over any overlapping style options between the two. The style applied to each atom will take priority over both the conformers and the molecule. The output file will have a molecule style of: Wireframe, blue, yellow molecular surface, and no hydrogens. The first conformer will have a style that indludes: CPK, blue, yellow molecular surface, and polar hydrogens. The second conformer will have the same style as the molecule. The first atom on the first conformer will have a style that includes: Stick, white, no surface, and polar hydrogens. The first atom on the second conformer will have a style that includes: Stick, white, no surface, and no hydrogens. The second atom on the first conformer will have a style that includes: CPK, pink, blue molecular surface, and polar H.

Example

prompt> styleHierarchy.py input.oeb output.oeb

Code

Download code

styleHierarchy.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

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

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

    ofs = oechem.oemolostream()
    if not ofs.open(argv[2]):
        oechem.OEThrow.Fatal("Unable to open %s for writing" % argv[2])

    for mol in ifs.GetOEMols():
        mol.NewConf(mol)
        mol.NewConf(mol)

        molSty = oechem.OE3DMolStyle()
        molSty.SetAtomStyle(oechem.OEAtomStyle_Wireframe)
        molSty.SetAtomColorer(oechem.OEMolStyleColorer(oechem.OEBlue))
        molSty.SetSurfaceColorer(oechem.OEMolStyleColorer(oechem.OEYellow))
        molSty.SetHydrogenVisibility(oechem.OEHydrogenVisibility_Off)
        molSty.SetSurfaceType(oechem.OESurfaceType_Molecular)

        confSty = oechem.OE3DMolStyle()
        confSty.SetAtomStyle(oechem.OEAtomStyle_CPK)
        confSty.SetHydrogenVisibility(oechem.OEHydrogenVisibility_Polar)

        atomSty = oechem.OE3DMolStyle()
        atomSty.SetAtomStyle(oechem.OEAtomStyle_Stick)
        atomSty.SetAtomColorer(oechem.OEMolStyleColorer(oechem.OEWhite))
        atomSty.SetSurfaceType(oechem.OESurfaceType_Off)

        atomSty2 = oechem.OE3DMolStyle()
        atomSty2.SetAtomColorer(oechem.OEMolStyleColorer(oechem.OEPink))

        oechem.OESetStyle(mol, molSty)

        molConf1 = mol.GetConf(oechem.OEHasConfIdx(0))
        oechem.OESetStyle(molConf1, confSty)

        molAtom1 = mol.GetAtom(oechem.OEHasAtomIdx(0))
        oechem.OESetStyle(molAtom1, atomSty)

        molAtom2 = mol.GetAtom(oechem.OEHasAtomIdx(1))
        oechem.OESetStyle(molAtom2, atomSty2)

        if not oechem.OEHasStyle(mol):
            oechem.OEThrow.Fatal("OE3DMolStyle was not applied to the OEMol")

        oechem.OEWriteMolecule(ofs, mol)
        

#    for conf in mol.GetConfs():
#        tempConfSty = oechem.OE3DMolStyle()
#        tempConfSty = oechem.OEGetStyle(conf)
#        print(tempConfSty.GetString())

#    for atom in mol.GetAtoms():
#        tempAtomSty = oechem.OE3DMolStyle()
#        tempAtomSty = oechem.OEGetStyle(atom)
#        print(tempAtomSty.GetString())

#    tempMolSty = oechem.OE3DMolStyle()
#    tempMolSty = oechem.OEGetStyle(mol)
#    print(tempMolSty.GetString())

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

#This is a complicated example of adding multiple OE3DMolStyles to the connfomer, atoms, and molecule
#The mol will have a style that includes: Wireframe, blue, yellow molecular surface, no hydrogens
#The first conf will have a style that indludes: CPK, blue, yellow molecular surface, polar hydrogens
#The second conf will have the same style of the mol
#The first atom on the first conf will have a style that includes: Stick, white, no surface, polar hydrogens
#The first atom on the second conf will have a style that includes: Stick, white, no surface, no hydrogens
#The second atom on the first conf will have a style that includes: CPK, pink, blue molecular surface, polar H
#This shows the hierarchy of how the stle moves from mol to conf to atom
#The top level is always the mol, but the style in a conf will take priority
#The atom will have the style from the mol and conf, but if a OE3DMolStyle is added to an atom then it will take priority 