Re: [Rdkit-discuss] How many bonds of a Type in a molecule

[Jan H. J. <jhj...@ch...>]

mol.GetSubstructMatches(Chem.MolFromSmarts(‘[*]=[*]’))

Should find all double bonds between non-aromatic atoms. If you want to include those Chem.Kekulize(mol) first.

On 8 Dec 2020, at 15.01, José Emilio Sánchez Aparicio <Jos...@ua...<mailto:Jos...@ua...>> wrote:

Dear all,

I need to find how many bonds of a certain type are in a molecule. For example, for DOUBLE bonds, I would do:

bond_number = 0
for bond in mol.GetBonds():
    if bond.GetType() == Chem.BondType.DOUBLE:
        bond_number += 1

However, searching for faster manners to do this, I found "rdqueries". For example, to find how many atoms of Carbon there are in a molecule, you could do:

q = rdqueries.AtomNumEqualsQueryAtom(6)
carbon_number = len(mol.GetAtomsMatchingQuery(q))

I'm wondering if some of you know the equivalent in "rdqueries" to find the number of bonds that match a type.

Many thanks in advance. Best,

José-Emilio Sánchez
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