Make Robust Loader

[yusuf1759]

• [x] - Add Flexible Structure Abstraction
• [x] - Add utility to load biotite array
• [x] - Add utility to load rdkit mol
• [ ] - Add utility to crop apo and pred to match holo sequence range
• [x] - Add masks for missing protein coordinates or mismatched sequence (between the inference and holo)
• [x] - Add mappings for ligand inference/input SMILES and the resolved structure

[github-actions[bot]]

Coverage report

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File	Statements	Missing	Coverage	Coverage (new stmts)	Lines missing
src/plinder/core/index
system.py					13, 40, 73-74, 110, 209-210, 255-258, 270-279, 297-321, 335-336, 350-351, 389-403, 422, 433
src/plinder/core/loader
dataset.py					3-91
featurizer.py					1-102
transforms.py					1-20
utils.py					1-210
src/plinder/core/structure
atoms.py					85, 99-101, 128-132, 134, 153-156, 160, 211-241, 256-279, 285-289, 293-295, 299, 305-306, 312, 320-337, 345-346, 355-356, 364-375, 382-389
contacts.py					112-113, 207, 220, 226-232, 258-261
diffdock_utils.py					26, 32, 38-43, 58-79, 86-93, 96-98, 102-121, 127-169, 173-188, 372-375, 379-446, 450-464, 476-520
models.py
structure.py					37, 63-73, 82, 86-89, 162, 172, 178-181, 198-206, 210, 212, 214, 237-238, 241-262, 279-281, 290-310, 316-319, 329-390, 393-394, 406, 408, 449-455, 460-463, 468-473, 480-491, 498-504, 519, 524-533, 538-543, 548-553, 563-573, 578-579, 584-590, 595-596, 612-618, 623-625, 630-632, 637-639, 644-650, 655-658, 663-669, 674-678, 683-687, 692-696, 701-705, 711-716, 720
superimpose.py					92, 104-107, 115, 138
surgery.py					19-30, 38-48, 54-86, 97, 118-129
vendored.py					30-32, 36-38, 44-53, 70-72, 77-87, 96, 103-104, 124-127, 140, 161-162, 167-173, 179-184, 194-284, 342, 352, 384, 470-472, 483-503, 515, 517, 531-551, 558-578, 613-638, 671-688, 694-707, 763-798, 817-826, 842-844, 862-865, 885-903
src/plinder/core/utils
constants.py
dataclass.py					10-18, 29-74
load_systems.py					8
src/plinder/data
save_linked_structures.py
src/plinder/data/common
constants.py					3-7
log.py
src/plinder/data/structure
atoms.py					5-7
contacts.py					5-7
src/plinder/data/utils
diffdock_utils.py					15
src/plinder/data/utils/annotations
interface_gap.py
rdkit_utils.py
src/plinder/eval/docking
utils.py
Project Total

The report is truncated to 25 files out of 31. To see the full report, please visit the workflow summary page.

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