Intro to the molecule enumerator | RDKit blog

[utterances-bot]

Intro to the molecule enumerator | RDKit blog

Using some advanced query features

https://greglandrum.github.io/rdkit-blog/tutorial/substructure/2021/05/13/intro-to-the-molecule-enumerator.html

[coleb]

Very cool! Which GUI sketchers let chemists generate these V3000 or CXSMILES variants?

[greglandrum]

@coleb: I use Marvin Sketch for just about everything, but I've also tested with the V3000 output from Biovia Draw and that works fine.
I haven't tried with ChemDraw yet since I don't have that installed on my main windows laptop

[BernalFA]

Great Post. But I have an older version of rdkit. How could I update it? Should I re-install it?

[greglandrum]

@BernalFA: please direct RDKit questions to the github discussions page: https://github.com/rdkit/rdkit/discussions

[ShangChien]

this approach is very powerful ! !
But is it possible to generate a new molecule by acene two aromatic molecules?

[greglandrum]

@ShangChien : I don't think so. If I understand the question correctly that is something you would want to use with the RDKit's chemical reaction functionality: https://www.rdkit.org/docs/GettingStartedInPython.html#chemical-reactions

[alvesvm]

Is there a way that RDKit can read R groups from V3000 or CXSMILES? It seems that in the current version, we can vary position of one group, but not different groups.

[greglandrum]

@alvesvm the RDKit does not support the RGFile format, but should otherwise support V3000 mol or SDF reasonably well. If this isn't what you mean, can you provide an example?

I believe that the code does allow having multiple positition-variation bonds.

[alvesvm]

@greglandrum I was able to use multiple position-variation bonds, but I can add only one group in each variation bond. The Markush Enumerator from ChemAxon can generate the analogs using this example. However, I get this error in RDKit:

`---------------------------------------------------------------------------
ArgumentError Traceback (most recent call last)
~\AppData\Local\Temp/ipykernel_3332/3442741229.py in
----> 1 combined_bundle = rdMolEnumerator.Enumerate(markush_mol)
2 align_bundle_coords(combined_bundle)
3 MolsToGridImage(combined_bundle,subImgSize=(300,250))

ArgumentError: Python argument types in
rdkit.Chem.rdMolEnumerator.Enumerate(NoneType)
did not match C++ signature:
Enumerate(class RDKit::ROMol mol, struct RDKit::MolEnumerator::MolEnumeratorParams enumParams)
Enumerate(class RDKit::ROMol mol, unsigned int maxPerOperation=0)`

[greglandrum]

Yeah, that's an RGroups file, which the RDKit does not currently support

[alvesvm]

Thank you for clarifying that.