Dear Stéphane,
I am not sure if there's a direct way to achieve bonds highlighting. You
can highlight them manually by:
mol = Chem.MolFromSmiles('c1cc(C(=O)O)c(OC(=O)C)cc1')
patt = Chem.MolFromSmarts('C(=O)O')
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 = Draw.rdMolDraw2D.MolDraw2DSVG(500, 500)
Draw.rdMolDraw2D.PrepareAndDrawMolecule(d, mol,
highlightAtoms=hit_ats,highlightBonds=hit_bonds)
Note that this will highlight only a single match of the substructure and
not all matches, for that, use GetSubstructMatches and modify the code
accordingly.
You may see the documentation for the given example:
https://www.rdkit.org/docs/GettingStartedInPython.html#drawing-molecules
I hope this helps,
Best regards,
Omar
On Mon, Jan 25, 2021 at 5:17 PM BOURG Stephane <stephane.bo...@cnrs.fr>
wrote:
> Dear all,
>
>
>
> Within rdkit '2020.03.6' the following code in a jupyter notebook goves
> the first image below :
>
>
>
> from rdkit import Chem
>
> from rdkit.Chem.Draw import IPythonConsole
>
>
>
> m = Chem.MolFromSmiles('c1cc(C(=O)O)c(OC(=O)C)cc1')
>
> substructure = Chem.MolFromSmarts('C(=O)O')
>
> print(m.GetSubstructMatches(substructure))
>
> m
>
>
>
>
>
> The same code with rdkit 2020.09.3 doesn’t highlight the bond.
>
>
>
> What should I correct to highlight the bonds ?
>
>
>
> Many thanks
>
>
>
>
>
> Stéphane BOURG, Ph. D.
>
> Equipe Bioinformatique Structurale et Chémoinformatique (SBC)
>
>
>
> Institut de Chimie Organique et Analytique (ICOA)
>
> UMR CNRS-Université d’Orléans 7311
>
> Pôle de Chimie
>
> Rue de Chartres – BP 6759
>
> 45 067 Orléans Cedex 2
>
>
>
> Tél : +33 (0)2 38 49 45 89
>
> E-mail : stephane.bo...@cnrs.fr
>
>
>
>
> _______________________________________________
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> Rdkit-discuss@lists.sourceforge.net
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