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CaviTracer - Optimization - #2241

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MatthewLicht wants to merge 16 commits into

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MatthewLicht:ct_dev

Open

CaviTracer - Optimization #2241
MatthewLicht wants to merge 16 commits into
prody:main from
MatthewLicht:ct_dev

Commits

Commits on Jun 26, 2026

changes sum to the builtin sum to prevent issue with numpy depreciation of np.sum(generator)
MatthewLicht MatthewLicht
committed
d6c025b
changed calcChannels to match new calculator functions
MatthewLicht MatthewLicht
committed
f02cb20
added calcChannelsMultipleAtomGroups which runs calcChannels for multiple unrelated atomgroups
MatthewLicht MatthewLicht
committed
0a88ea1
updated calcChannelsMultipleFrames to use multiprocessing POOL
MatthewLicht MatthewLicht
committed
2665d4a
updated Channel class to be compatible with functions using multiprocressing Poolsuch as _ag_worker and _frame_worker
MatthewLicht MatthewLicht
committed
b64bfcc
vectorized sphere_fit and delete_simplices3d so that spherefit is calculated for all relevant tetrahedra in the vector, rather than a for loop
MatthewLicht MatthewLicht
committed
ec6abb8
updated delete_section for faster mask creation and filtering
MatthewLicht MatthewLicht
committed
3928489
updated surface_layer to take advantage of contiguousarrays and views
MatthewLicht MatthewLicht
committed
236b013
updated dijkstra to use scipy algorithms and to build paths as nodes and branches
MatthewLicht MatthewLicht
committed
eb72e3b
added centers and radii to process_channel outputs to match changes to Channel class
MatthewLicht MatthewLicht
committed
4b82727
added calc_circumcenters function to ChannelCalculator class
MatthewLicht MatthewLicht
committed
e52a47e
added normalModeCavityAnalysis
MatthewLicht MatthewLicht
committed
8893430
removed normalModeCavityAnalysis, needed updating
MatthewLicht MatthewLicht
committed
0ba87b1
added additional error handling for multiprocessing
MatthewLicht MatthewLicht
committed
6632c29

Commits on Jul 5, 2026

removed unnecessary import and altered formatting for legibility
MatthewLicht MatthewLicht
committed
e3618d5

Commits on Jul 6, 2026

resolved formatting issues
MatthewLicht MatthewLicht
committed
d9b95d0