Depicting Tripos Atom Types

Problem

You want to depict the Tripos atom types on your molecule. See example in Figure 1.

../_images/triposatom2img.png — **Figure 1. Example of depicting Tripos atom types**

Ingredients

OEChem TK - cheminformatics toolkit
OEDepict TK - molecule depiction toolkit

Difficulty Level

Solution

The OEDepict TK allows you to display any atom property as a string next to the atomic label on your molecular diagram. First you have to create a class derived from the OEDisplayAtomPropBase abstract base class of which __call__ method returns the type string of an atom.

class TriposTypeLabel(oedepict.OEDisplayAtomPropBase):
    def __init__(self):
        oedepict.OEDisplayAtomPropBase.__init__(self)

    def __call__(self, atom):
        return atom.GetType()

    def CreateCopy(self):
        copy = TriposTypeLabel()
        return copy.__disown__()

Before depicting the molecule, you have to call the OETriposAtomTypeNames function that sets the atom name property of each atom to be the Tripos type (see line 3 in the code below).

Then the TriposTypeLabel class, defined above, can be used to customize the molecule depiction. When a OE2DMolDisplay object is constructed to depict a molecule, it takes an OE2DMolDisplayOptions object that stores all the options that determine how a molecule is depicted. By default, no atom property label is rendered next to the atoms. This default behavior can be overwritten by calling the OE2DMolDisplayOptions.SetAtomPropertyFunctor method (see line 6 in the code below).

When you render the molecule the Tripos atom type label will be depicted next to the atom. See example in Figure 1.

def DepictMoleculeWithTriposAtomTypes(image, mol):

    oechem.OETriposAtomTypeNames(mol)

    opts = oedepict.OE2DMolDisplayOptions(image.GetWidth(), image.GetHeight(), oedepict.OEScale_AutoScale)
    opts.SetAtomPropertyFunctor(TriposTypeLabel())

    disp = oedepict.OE2DMolDisplay(mol, opts)
    oedepict.OERenderMolecule(image, disp)

Discussion

Similarly, you can also display bond property information on your molecule image. You can find examples in the Displaying Bond Properties section of the OEDepict TK manual.