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2de315e9e0
- Rename PocketCriterium to PocketCriterion (fix Latin spelling) - Revert getLigandAtoms() back to getAtoms() in BindingSite interface - Rename getCentroidForEval() to getCenterForEval() - Rename explicitCentroid to explicitCenter in ResidueSite - Rename SiteCentroidMethod values: explicit_centroid->explicit, sas_points_center_of_mass->sas_points_centroid - Rename site_centroid_method param to site_eval_center_method - Ligand.getCentroid() now delegates to getCenterForEval()
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 |