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plinder-org / plinder

Protein Ligand INteraction Dataset and Evaluation Resource
https://plinder.sh
Apache License 2.0
163 stars 9 forks source link

Cleanup again #53

Closed OleinikovasV closed 1 month ago

OleinikovasV commented 2 months ago

This branch applies and further extends the features from a stale PR https://github.com/plinder-org/plinder/pull/23

Includes: documentation automation via DocBaseModel and document_properties_to_tsv adding descriptions for user-facing annotations to pydantic.Field(description="") update ligand classification logic for is_other bugfix: for some ligands is_lipinski and is_fragment was wrongly False when the value is 0 and not None update: is_ion or is_artifact is no longer annotated as ligand types (is_lipinski, etc) fix: num_unresolved_heavy_atoms inconsistency when residue is not defined in ost renaming for consistency: Kinase name -> kinase_name renaming for consistency: ligand_num_missing_neighboring_ppi_residues -> ligand_num_missing_ppi_interface_residues

... Commented out #TODO about future fixes - require another index rerun:

fix: matched_smiles function to replace PLIP's resolved_smiles fix: entry resolution for cryo-em

github-actions[bot] commented 2 months ago

Coverage report

Click to see where and how coverage changed

FileStatementsMissingCoverageCoverage
(new stmts)		Lines missing
  src/plinder/core/index
  utils.py 170-175, 177-178, 180-181
  src/plinder/core/loader
  loader.py 6, 123-128
  src/plinder/core/scores
  links.py 44-45, 47-48, 65-66
  query.py
  src/plinder/core/split
  plot.py
  utils.py
  src/plinder/core/system
  system.py 244-249, 271
  src/plinder/core/utils
  cpl.py 114
  unpack.py 114
  src/plinder/data
  final_structure_qc.py 144-145, 151-152, 154
  save_linked_structures.py 249, 259-260, 266, 274, 287-314
  splits.py
  src/plinder/data/pipeline
  pipeline.py 341-345, 349, 356-360, 369-374, 378-389, 393-394
  tasks.py 1013, 1022-1025, 1044-1070, 1079-1090, 1101-1125
  utils.py 479-500, 509, 590, 605-610, 621-651, 662-686, 706, 712, 725-732, 759-767, 791-797
  src/plinder/data/structure
  atoms.py
  src/plinder/data/utils/annotations
  aggregate_annotations.py 385, 505, 539, 552, 1184, 1445, 1454-1475
  get_ligand_validation.py
  interaction_utils.py
  ligand_utils.py
  protein_utils.py
  rdkit_utils.py 297-298, 347-352, 358, 514-541
  utils.py 51, 53
  src/plinder/eval/docking
  utils.py 317, 332, 337-338
  write_scores.py 51-73
Project Total  

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