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cb6f7f75eb
- Params.groovy: pocket_descriptors javadoc now lists all 7 shipped
descriptors (was: 6); softens the "essentially free" rationale to
acknowledge principal_moments' small eigendecomposition cost.
- PocketDescriptorsTest.groovy: class javadoc "six shipped descriptors"
→ "seven", names principal_moments alongside the rest.
- export-pocket-descriptors.md: "6 base shipped descriptors use this
adapter" → "6 of 7 use the adapter; principal_moments (multi-column)
implements PocketDescriptor directly". Removes a misleading count.
- export-pocket-{grid,descriptors}.md: default-list rationale no longer
claims adding descriptors is "essentially free" — clarifies that
grid-derived scalars are cheap once the grid is built but
principal_moments adds a small per-pocket compute on top, still
negligible vs the grid build.
Caught by deep audit of 60220d7a..73e7c9df focused on doc/comment drift
after the recent multi-column interface migration.
Documentation
This directory contains documentation and tutorials for P2Rank. Note that the coverage is spotty and incomplete -- not all features and workflows are documented here.
Usage
| File | Description |
|---|---|
| rescoring.md | Rescoring predictions from other pocket prediction methods (Fpocket, Pocketeer, etc.) |
| export-points.md | Exporting SAS points with feature vectors and predicted ligandability scores |
| aa-mapping.md | Non-canonical amino acid residue mapping to standard residues |
| hidden-commands.md | Miscellaneous hidden commands and analysis tools |
| random-examples.md | Assorted command-line examples for prediction and evaluation |
Training
| File | Description |
|---|---|
| training-tutorial.md | Training and evaluating custom models, crossvalidation, grid optimization |
| feature-setup.md | Feature vector configuration and introduction to adding new features |
| new-feature-evaluation-tutorial.md | Implementing a new feature and evaluating its contribution to prediction |
| hyperparameter-optimization-tutorial.md | Grid and Bayesian optimization of algorithm parameters |
| training-score-transformers.md | Training probability and z-score transformers for pocket and residue scores |