If I use this package, which set of metrics will it report?

atomicarchitects / molmetrics

Metrics for assessing 3D molecular structures.

MIT License

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If I use this package, which set of metrics will it report? #1

Open chaitjo opened 1 month ago

chaitjo commented 1 month ago

In the Symphony paper, validity and uniqueness metrics have been reported via 3 different methods.

If I use molmetrics, which of the numbers could I compare apples-to-apples with?

Is my understanding correct:

If saved with xyz format --> xyz2mol
If saved with any of the other formats (mol, pdb, sdf) --> OpenBabel
EDM lookup table is not implemented

PS. Thanks for a handy package!

ameya98 commented 1 month ago

Currently, the code exists for all 3 (this repo was directly lifted from the Symphony repo) but I need to figure out the best API to expose these metrics nicely. Right now, the RDKit metrics (computed using xyz2mol) work (as seen in the example). I will add the openbabel and EDM stuff soon. Note that the RDKit version also affects the results: https://github.com/atomicarchitects/symphony/issues/118 Please feel free to suggest more metrics to add!