Major refactor

[OleinikovasV]

Scoping branch to reduce external dependencies to reduce support conflicts.
Eliminates explicit use of

• mmcif --> biotite
• gemmi --> biotite
• openbabel --> rdkit
• networkx --> networkit
• plip --> peppr
• ost (only used in eval) --> biotite
• posebusters (only eval)

Adds:

• peppr

Bugfixes:

• System ID 8q5i__1__1.GA__1.ZB missing DNA complex #61
• PyTorch wheel in requirements_data.txt requires Python 3.12 but environment.yml specifies Python 3.10 #117
• ligand_binding_affinity values are incorrectly parsed! #94

[github-actions]

Coverage report

Click to see where and how coverage changed

File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/index
system.py					324, 335-336, 347-355, 366-367, 384-395
src/plinder/core/split
plot.py					742
src/plinder/core/structure
atoms.py					234
diffdock_utils.py					101-122
smallmols_utils.py					179-180, 297
structure.py					635-637, 642-644
vendored.py					47-52, 493-495
src/plinder/data
clusters.py					315-316, 349-353
final_structure_qc.py					94-95, 118-126, 147-148, 150, 154-155, 373-375
save_linked_structures.py					29-38, 43-50, 77-117, 287-289
src/plinder/data/pipeline
io.py					134-142
mpqueue.py					82-85
transform.py					135-140, 152-154, 164-172, 180-193, 203, 225
utils.py					633-638, 651-662, 671-676, 683-694
src/plinder/data/utils/annotations
aggregate_annotations.py					588-592, 1034-1035, 1094, 1106-1108, 1115, 1245, 1338
cif_utils.py					54, 57, 74, 203, 206, 241, 257, 270-271, 349, 353-355, 439, 444-446, 453, 499, 529, 536, 538-540, 562, 579, 664-666, 693-698, 710, 725, 728-729
get_similarity_scores.py					632-641, 678-687
interaction_utils.py					46-48, 53, 62, 132-133, 294-295, 303-304, 320-321, 330, 341-342, 361-362, 394-395, 413-414
interface_gap.py					133-134, 159
ligand_utils.py					69, 80, 109-111, 119, 135, 163, 169-179, 302, 304, 306, 309-311, 439, 787-792, 942-943, 962, 978-981, 1019, 1024, 1030-1031, 1045-1046, 1083, 1151, 1153, 1177-1181, 1386-1387, 1396-1404
mmpdb_utils.py
protein_utils.py					54, 61, 64, 124-147, 160, 224-229, 234-235, 306-307, 310, 315, 344
save_utils.py					52, 59-60, 62, 108-112, 132
src/plinder/eval/docking
stratify_test_set.py					357
utils.py					512-537
Project Total

The report is truncated to 25 files out of 33. To see the full report, please visit the workflow summary page.

This report was generated by python-coverage-comment-action