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MobleyLab / chemper

Repository for Chemical Perception Sampling Tools
MIT License
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Add Aromaticity support to chemper #46

Closed bannanc closed 5 years ago

bannanc commented 5 years ago

After discussions around aromaticity models today, I realized it might be a good idea to add aromaticity model selection support to chemper.

This isn't an urgent problem because right now you could just use your toolkit externally using these steps:

  1. Create molecule in OE or RDK
  2. Specify aromaticity using OE or RDK
  3. Feed your molecule into chemper to do your clustering.

This is the order I will use for testing chemper with SMIRNOFF for now. However, in the long run it would be nice to also be able to have the order:

  1. Create your chemper Mol through OE, RDK, input molecule
  2. Apply new aromaticity model

You could imagine this being useful in testing how the aromaticity model affected creating SMIRKS patterns for clusters.

bannanc commented 5 years ago

MDL support was added in PR #58, to the best of my knowledge that is the only model we know for sure they both support, so that is the only one I will include for now.