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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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Xstal lattice contact counter #13

Closed OleinikovasV closed 2 months ago

OleinikovasV commented 3 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, fixed git config (previously commits were attributed to non-existing account)

github-actions[bot] commented 3 months ago

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FileStatementsMissingCoverageCoverage
(new stmts)		Lines missing
  src/plinder/core
  __init__.py
  src/plinder/data
  __init__.py
  src/plinder/data/common
  constants.py
  src/plinder/eval/docking
  utils.py
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OleinikovasV commented 3 months ago

image

6lu7 is a good test case - my pymol script detects 2 contacted ligand atoms - with 3 contacted atoms in a symmetry mate when using 5 A cutoff

OleinikovasV commented 2 months ago

Stale branch - crystal contacts have been implemented via gemmi - see https://github.com/plinder-org/plinder/pull/14 , thus this PR is redundant