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0 pointsluthaf6y ago0 comments

What do you think is missing in the current offering (OpenBabel, RDKIT, maybe some other I am missing)?

Context: I do research in computational chemistry, and write an open source library for this, that could be used for cheminformatics too. I don't really know what is needed for this though, since I never touched cheminformatics.

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hobofan6y ago

I've dabbled a bit with OpenBabel and RDKIT, but I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy. I suspect that a big part of this could "just" be missing documentation / tutorials to get into it.

Maybe I'm just not deep enough into it, but from my impression so far especially when it comes to application-level software (in contrast to specialized research), OEChem and similar closed source libraries seem to be the most widely used ones, with nothing quite comparable available.

Context: Software Engineer that is also currently a biochemistry undergraduate.

luthafOP6y ago

> I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy.

Somehow the same for me, this is part of why I started my own project (http://chemfiles.org). I have the impression that for cheminformatics you want to see molecules as graphes, is this true or is a list of bonds enough for usual purposes?

I have heard of OEChem but never used it. I'll try to find some documentation to have a look.

hobofan6y ago

> I have the impression that for cheminformatics you want to see molecules as graphes

Yeah, that was my thinking.

I've also seen your work on lumol, so you seem to be one of the few people working in the field with Rust! I just recently started writing a SMILES parser in Rust[0], as a first step towards an in-memory graph representation of molecules. I have a first rough draft of that locally, though it's very rough and changing a lot, as I have to adjust it weekly as I'm basically learning the required theory at the same time :D

[0]: https://github.com/hobofan/smiles-parser

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hobofan6y ago

Context: Software Engineer that is also currently a biochemistry undergraduate.

luthafOP6y ago

> I found their interfaces especially for simple things (traversing atoms/bonds in a molecule) quite unwieldy.

I have heard of OEChem but never used it. I'll try to find some documentation to have a look.

hobofan6y ago

> I have the impression that for cheminformatics you want to see molecules as graphes

Yeah, that was my thinking.

[0]: https://github.com/hobofan/smiles-parser

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