Hi RDKitters,

I have a question not really specific to RDKit but I am sure that some of you already faced this problem.


Regarding some specific types of chiralities (not on carbons), I can manage chiralities from RS(=O)R' or R[N+]R'R''R''' compounds. But I do not know what is the best solution to manage compounds like the following :

1- Compounds with axial chirality e.g. binap compounds

(https://en.wikipedia.org/wiki/Axial_chirality)

2- Metallic complexes, in particular Pt complexes with 6 non equivalents bonds e.g. satraplatin

(https://en.wikipedia.org/wiki/Satraplatin)

My question is : what is the best format to store the structure and the chiral information of those structures? How do you manage them?

Of course, we should be able to regenerate the right structure from the chosen format.

In a step further, the file should be readable for (sub)structure searches [no failure when rdkit read the molecule].

At best the chirality should be questionable. Thus how to configure the HasSubstructureMatch in order to match the right chirality?

For satraplatin we can use chiral bonds that can be saved in .mol but not in smiles. For binap, the classical bold bond is saved as chiral bond in .mol and not saved in smiles.

Thanks for all the work done on RDKit,

Cheers,

Lionel


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