John Mayfield
John Mayfield
> The file was read from V3000 and written to V2000 by ChemAxon. Why not read the V3000 directly?
Note it does give you back a query atom container... ```java public static void main(String[] args) throws CDKException { String ctfile = "\n" + " Mrv2204 10172221282D \n" + "\n"...
It is sometimes possible to convert queries into molecules but we hesitate to do this automatically since it can introduce errors.
> That doesn't make things easier, does it...? If you try to treat a query as molecule you're going to have a bad time. It's simply the limit of what...
> I definitely want to drop those query molecules within my processing pipeline. However, at the moment, they crash the flow of the pipeline by raising an exception and I...
But yes running CdkAtomTypeMatcher on a query should throw a better error!
See also: https://nextmovesoftware.com/blog/2022/04/08/cxsmiles-gotchas-part-1-bond-indexes/
> 🤨 Sorry for to escape the ``@OH`` tag which is used of [Octahedral](https://en.wikipedia.org/wiki/Octahedral_molecular_geometry) geometry
Rebased, Obviously this would target 2024_03 at best.
No rush, I fudge it in the reaction extractor anyways :-). Just thought a useful addition/relaxation.