Refactoring eval for better usability

[Ninjani]

• [X] Clean up metrics and names: now uses ["lddt_pli", "bisy_rmsd", "lddt_lp"] as the ligand scores
• [X] Make eval use PlinderSystem
• [X] Refactor and test plinder_evaluate, plinder_stratify and plinder_plot
• [X] QOL function evaluate which can be run as:

  from plinder.eval.docking.write_scores import evaluate
  system_id = "1a3b__1__1.B__1.D"
  evaluate(
  model_system_id=f"pred_{system_id}_rank1",
  reference_system_id=system_id,
  receptor_file=None, # Rigid re-docking, uses the receptor cif file of the reference system
  ligand_files=[Path(f"tests/test_data/eval/predicted_poses/{system_id}/rank1.sdf")],
  flexible=False, # if True then returns protein scores (lddt, bb_lddt etc.)
  posebusters=False, # if True then returns posebusters boolean scores
  posebusters_full=False, # if True then returns posebusters full report
  )

• [X] Allow scoring non-PLINDER systems as reference (not yet exposed in plinder_evaluate)
• [X] Update dataset/evaluation.md docs

[github-actions[bot]]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/index
utils.py
src/plinder/core/scores
query.py
src/plinder/core/system
system.py					13, 292-293, 307-308
src/plinder/core/utils
cpl.py
gcs.py
unpack.py
src/plinder/data
clusters.py
databases.py
docs.py
final_structure_qc.py
get_system_annotations.py
save_linked_structures.py					15, 316, 342
src/plinder/data/pipeline
config.py
io.py
mpqueue.py
tasks.py
src/plinder/data/structure
atoms.py
src/plinder/data/utils
diffdock_utils.py
src/plinder/data/utils/annotations
aggregate_annotations.py
ligand_utils.py
protein_utils.py
src/plinder/eval/docking
make_plots.py					84-85, 264, 275
stratify_test_set.py					321, 333
utils.py					80, 86, 211-214, 357-362
write_scores.py					56-86, 133, 274, 292
Project Total

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