Cleanup branch - Githubissues

OleinikovasV commented 1 month ago

Documentation cleanup:

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
adding descriptions for user-facing annotations to pydantic.Field(description="")
renaming for consistency: ligand_num_missing_neighboring_ppi_residues -> ligand_num_missing_ppi_interface_residues
...

Commented out fixes - require another index rerun:

github-actions[bot] commented 1 month ago

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core
__init__.py
src/plinder/data
__init__.py
final_structure_qc.py
get_system_annotations.py
splits.py					256
src/plinder/data/pipeline
config.py
io.py
utils.py
src/plinder/data/structure
atoms.py
src/plinder/data/utils/annotations
aggregate_annotations.py					425-427, 436, 1080
get_ligand_validation.py					69
interaction_utils.py
ligand_utils.py
protein_utils.py					104
rdkit_utils.py					297-298, 347-352, 358, 514-541
save_utils.py
src/plinder/eval/docking
utils.py
Project Total