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plinder-org / plinder

Protein Ligand INteraction Dataset and Evaluation Resource
https://plinder.sh
Apache License 2.0
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Crystal lattice contact counter #12

Closed OleinikovasV closed 2 months ago

OleinikovasV commented 2 months ago

Used PyMOL to detect lattice contacts that are within a cutoff to a ligand.

Currently, this requires installing a separate pymol environment.

Multiprocessed script that takes test split data and estimates the contacts for a given ligand system: detect for both total number of contacts from lattice to ligand, and total number of ligand atoms involved in the contacts.

Ideally, this should be done at the earlier stage of annotation, but currently may be too slow to run for the entire dataset.

Update: rebased onto main.

github-actions[bot] commented 2 months ago

Coverage report

This PR does not seem to contain any modification to coverable code.