Added metric rmsd_coverage for docking related benchmarks
Added unit tests
Checklist:
[x] Was this PR discussed in an issue? It is recommended to first discuss a new feature into a GitHub issue before opening a PR.
[x] Add tests to cover the fixed bug(s) or the newly introduced feature(s) (if appropriate).
[ ] Update the API documentation if a new function is added, or an existing one is deleted.
[x] Write concise and explanatory changelogs above.
[x] If possible, assign one of the following labels to the PR: feature, fix, chore, documentation or test (or ask a maintainer to do it for you).
The rmsd metrics are implemented based on the Posebuster codebase. A few modifications were made, replacing RDKit callables with equivalent Datamol functions. The RMSD calculation was also simplified to evaluate only the first conformer of the predicted molecule and to consider only heavy atoms.
Note: Posebusters provides a series of checkers, known as 'Posebuster Checkers,' to further filter out unwanted docked ligand conformers. To avoid over-complicating Polaris metrics module with case-specific metrics, users should apply these filters before uploading results to the Polaris hub.
Changelogs
rmsd_coveragefor docking related benchmarksChecklist:
feature,fix,chore,documentationortest(or ask a maintainer to do it for you).The rmsd metrics are implemented based on the Posebuster codebase. A few modifications were made, replacing RDKit callables with equivalent Datamol functions. The RMSD calculation was also simplified to evaluate only the first conformer of the predicted molecule and to consider only heavy atoms.
Note: Posebusters provides a series of checkers, known as 'Posebuster Checkers,' to further filter out unwanted docked ligand conformers. To avoid over-complicating Polaris metrics module with case-specific metrics, users should apply these filters before uploading results to the Polaris hub.