Basic example of setting up an OE3DMolStyle on a molecule

A program that is an example for setting an OE3DMolStyle to a OEMolBase. The style being apply will label and color atoms by element. The atoms will be displayed in ball and stick format. The protein structures will be displayed as ribbons and colored based off residue. Hydrogen visibility is set to polar, and the interaction style is set to Inter molecular hydrogen bonds.

Example

prompt> basicStyle.py input.oeb output.oeb

Code

Download code

basicStyle.py

#!/usr/bin/env python
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import sys
from openeye import oechem

def main(argv=[__name__]):
         
    if len(argv) != 3:
        oechem.OEThrow.Usage("%s <infile>" % 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():
        molSty = oechem.OE3DMolStyle()
        protCol = oechem.OEMolStyleColorer(oechem.OEAtomColorScheme_Residue)
        atomCol = oechem.OEMolStyleColorer(oechem.OEAtomColorScheme_Element, oechem.OEWhite)
        atomCol.AddColor(6, oechem.OEGreen)
        atomCol.AddColor(7, oechem.OERed)
        atomCol.AddColor(8, oechem.OEBlue)
        

        molSty.SetAtomColorer(atomCol)
        molSty.SetProteinColorer(protCol)
        molSty.SetProteinStyle(oechem.OEProteinStyle_Ribbons)
        molSty.SetAtomLabelType(oechem.OEAtomLabelScheme_Element)
        molSty.SetAtomStyle(oechem.OEAtomStyle_BallAndStick)
        molSty.SetHydrogenVisibility(oechem.OEHydrogenVisibility_Polar)
        molSty.SetInteractionStyle(oechem.OEInteractionStyle_IntermolecularHBonds)

        oechem.OESetStyle(mol, molSty)

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

        oechem.OEWriteMolecule(ofs, mol)
        

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