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CaviTracer - refactor for enhanced accuracy and speed of channel identification to be competitive with established SOTA tools #2249

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Merged
karolamik13 merged 35 commits into from
Jul 20, 2026
+3,338 −718
Merged

CaviTracer - refactor for enhanced accuracy and speed of channel identification to be competitive with established SOTA tools #2249

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f473084
channels: homogeneous-ball atom substitution to approximate weighted …
briza81 Jul 7, 2026
4a3f588
channels: vectorize tessellation filtering and pathfinding by vectori…
briza81 Jul 7, 2026
0504b5b
channels: per-stage LOGGER timing in calcChannels with unified report…
briza81 Jul 7, 2026
d53d53f
channels: cleaning comments
briza81 Jul 7, 2026
7a86bdb
channels: add restrict_channels_to_start_point flag (default False) w…
briza81 Jul 7, 2026
17c1dcc
channels: restrict surface-erosion sphere_fit to the boundary shell i…
briza81 Jul 7, 2026
f30fcc7
channels: record per-channel cost (Dijkstra path weight) and curvatur…
briza81 Jul 7, 2026
4f2e013
channels: truncate channels at surface mouths to avoid their duplicat…
briza81 Jul 8, 2026
64271bd
channels: rename homogenize bool → diagram ("homogenized"/"simple"/"w…
briza81 Jul 9, 2026
540bba6
channels: bounded r2 surface peel (max_peel_depth) to strip the r1 "m…
briza81 Jul 9, 2026
1c9f29d
channels: update of calcChannels parameters pre-optimized to resemble…
briza81 Jul 9, 2026
63dfdd7
channels: update of style to better align with styleguide.rst by rena…
briza81 Jul 9, 2026
2cdbfa2
channels: cleaning unused imports
briza81 Jul 10, 2026
bab843e
channels: add diagram="weighted" (additively-weighted/Apollonius) Vor…
briza81 Jul 10, 2026
b9ca70d
channels: additively weighted VD are run in serial to avoid complicat…
briza81 Jul 13, 2026
a1a59f4
channels: local (enclosure-based) surface peel, removing the r1 depen…
briza81 Jul 13, 2026
5b1f3a3
channels: single sparsity, retire the inert one from calcSurfaceCavit…
briza81 Jul 14, 2026
5bd2cb7
channels: fix the peel eating wide pores, like porine. Default drops…
briza81 Jul 14, 2026
da909eb
channels: optimize the start_point seed instead of taking the nearest…
briza81 Jul 14, 2026
e1d5c52
channels: cache Voronoi clearances on the calculator as a single sour…
briza81 Jul 15, 2026
3dd61fe
channels: report the edge bottleneck radius, not circumcenter clearan…
briza81 Jul 15, 2026
ddaff8b
channels: cost the Dijkstra edges on the gate clearance, not the ente…
briza81 Jul 15, 2026
9e5311c
channels: match the volume tube at the gates — processChannel now inj…
briza81 Jul 15, 2026
c809ece
channels: measure cavity/mouth depth in geodesic Angstrom, not tetrah…
briza81 Jul 15, 2026
0afa489
channels: vectorize buildSparseGraph — build the weighted CSR adjacen…
briza81 Jul 15, 2026
7e97fed
channels: fix CONECT and same residue IDs in the combined channel PQR…
briza81 Jul 15, 2026
0d307c3
channels: add edge_cost='integral', a mesh-invariant clearance-profil…
briza81 Jul 16, 2026
b96635a
channels: fix docstring typos and wrapping
briza81 Jul 16, 2026
6862b7b
channels: extract sphereFit from deleteSimplices3d + documenting both
briza81 Jul 16, 2026
4be6430
Update channels.py
karolamik13 Jul 17, 2026
5d61cdf
CaviTracer - calcChannelSurfaceOverlaps() - improved with multiproc calc
karolamik13 Jul 17, 2026
3e91bdd
CaviTracer - calcSurfaceCavityOverlaps and channels docs
karolamik13 Jul 17, 2026
888bfd4
CaviTracer (#1 in TODO list; input atoms filtering) - _reportAtomsInp…
karolamik13 Jul 18, 2026
fae4cc6
CaviTracer - mainly docs improvements (vorpy, dash & cosmetic)
karolamik13 Jul 20, 2026
ea1c046
CaviTracer - typo found in showSurfaceCavities() func [fix]
karolamik13 Jul 20, 2026
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