RDKit rdMolDraw2D.PrepareAndDrawMolecule

Cheminformatics Tutorials - Herong's Tutorial Examples

∟Molecule Substructure Search with RDKit

∟RDKit rdMolDraw2D.PrepareAndDrawMolecule - Substructure Highlight

This section provides a tutorial example on how to highlight a substructure in a molecule with m.GetSubstructMatch(s) and rdMolDraw2D.PrepareAndDrawMolecule() methods in RDKit library.

If you want to highlight a substructure in a molecule, you can use:

"l = m.GetSubstructMatch(s)" to get a list of matching atoms in the molecule.
"rdMolDraw2D.PrepareAndDrawMolecule()" to prepare highlights on matching atoms and their bonds and draw the molecule.

Here is an example of from the "Getting Started with the RDKit in Python" guide at https://www.rdkit.org/docs/GettingStartedInPython.html.

from rdkit.Chem.Draw import rdMolDraw2D
smi = 'c1cc(F)ccc1Cl'
mol = Chem.MolFromSmiles(smi)
patt = Chem.MolFromSmarts('ClccccF')
hit_ats = list(mol.GetSubstructMatch(patt))
hit_bonds = []
for bond in patt.GetBonds():
   aid1 = hit_ats[bond.GetBeginAtomIdx()]
   aid2 = hit_ats[bond.GetEndAtomIdx()]
   hit_bonds.append(mol.GetBondBetweenAtoms(aid1,aid2).GetIdx())
d = rdMolDraw2D.MolDraw2DCairo(300, 300)
rdMolDraw2D.PrepareAndDrawMolecule(d, mol, highlightAtoms=hit_ats,
                                  highlightBonds=hit_bonds)
d.FinishDrawing()
p = d.GetDrawingText()

from IPython.display import Image
i = Image(p)
display(i)