Major refactor

[OleinikovasV]

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
• crystal contact detection within asymmetric units
• resolve sdf issue v2000 vs v3000 for dative bonds

Closes:

• Possibility of using plinder codebase to perform splitting for other datasets #102
• Updated Dataset #119

Features:

• Allows parsing any cif files with Entry.from_custom_cif_file
• add test for from_custom_cif_file from RNP
• Better handling of counts for pocket residues, interactions etc only considering proper ligands
• Release date fix (needs data regen)
• install cleanly to macOS
• upgrade to new posebusters
• upgrade base to python 3.12
• clean up docs

Other changes:

• Changing License to Apache-2.0
• Redefined systems: merging upon shared pocket residues (min 3), only artifacts added by 4A cutoff (like before), any polymer < 12 units is considered ligand (based on mmseqs search limit)

[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, 347-356, 367-368, 385-396
utils.py
src/plinder/core/structure
atoms.py					244
contacts.py
diffdock_utils.py					101-122
smallmols_similarity.py
smallmols_utils.py					206, 218-219, 227, 248-249, 303-304, 366
src/plinder/data
clusters.py					12, 78, 315-316, 349-353
final_structure_qc.py					94-95, 118-126, 147-148, 150, 154-155, 373-375
get_system_annotations.py
save_linked_structures.py					30-39, 44-51, 78-118, 288-290
src/plinder/data/pipeline
config.py
io.py					112, 134-142
transform.py					135-189, 197-207, 217, 239
utils.py					159-160, 585-590, 640-645, 658-669, 678-683, 690-701
src/plinder/data/utils/annotations
aggregate_annotations.py					289-293, 550, 592-596, 1046-1047, 1055, 1109, 1121-1123, 1133, 1326, 1455, 1494, 1505-1506, 1698-1699
cif_utils.py					59, 62, 72, 89, 245, 255, 293, 309, 322-323, 401, 405-407, 491, 496-498, 551, 581, 588, 590-592, 614, 631, 780, 783-784, 851-852, 880-891, 903
get_ligand_validation.py
get_similarity_scores.py					82-100, 340-345, 363-369, 388-426, 501-526, 603-612, 649-658, 741-748, 845-847
interaction_utils.py					47-49, 54, 133-134, 252-254, 297-298, 306-307, 323-324, 344-345, 364-365, 397-398, 416-417
interface_gap.py					133-134, 159
ligand_utils.py					62, 65-70, 112, 147-149, 152, 184-194, 317, 319, 321, 324-326, 454, 488-493, 565-566, 805-810, 962-964, 973-974, 993, 1009-1012, 1056, 1069, 1092-1093, 1133, 1206, 1208, 1232-1236, 1441-1442, 1451-1459
protein_utils.py					54, 61, 64, 87, 137, 167, 223-228, 233-234, 305-306, 309, 343
save_utils.py					45-46, 50-54, 100-104, 124
src/plinder/eval/docking
utils.py					512-537
Project Total

The report is truncated to 25 files out of 41. To see the full report, please visit the workflow summary page.

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