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Analyzed about 15 hours ago. based on code collected 1 day ago.

Commit Message	Contributor	Files Modified	Lines Added	Lines Removed	Code Location	Date
Aug 17, 2025 — Aug 17, 2026 Showing page 1 of 348 Search / Filter on:
Merge pull request #2264 from kontheodosiadis/main	Karolina Mikulska-Ruminska	More...				5 days ago
Added two new functions for tracking the clusters in the trajectory	kontheodosiadis	More...				5 days ago
Merge pull request #2258 from jamesmkrieger/clustenm-multistart	James Krieger	More...				5 days ago
Added warning for cluster ID 0 handling	kontheodosiadis	More...				6 days ago
Fixed colormap bug on showReachabilityPlot	kontheodosiadis	More...				6 days ago
Matplotlib fallback for Seaborn histograms	kontheodosiadis	More...				6 days ago
Revert changes to interactions.py	kontheodosiadis	More...				6 days ago
Fixed int appearence on showClusterStatisticsTable - General minor fixes and changes	kontheodosiadis	More...				6 days ago
CaviTracer - changes in showFrequentObjectResidues() [James K suggestion]	karolamik13	More...				7 days ago
Changes accoridng to James K. suggestions	karolamik13	More...				7 days ago
Merge pull request #2266 from karolamik13/prody__main	Karolina Mikulska-Ruminska	More...				7 days ago
CaviTracer - scanSurfaceCavityParameters()	karolamik13	More...				7 days ago
CaviTracer - improvements for showFrequentObjectResidues()	karolamik13	More...				7 days ago
Fixed title bug in showPairwiseRMSDHeatmap	kontheodosiadis	More...				7 days ago
CaviTracer - showFrequentObjectResidues()	karolamik13	More...				7 days ago
CaviTracer - calcFrequentObjectResidues() for channels, pores and surface cavities	karolamik13	More...				8 days ago
CaviTracer - multiprocessing in calcSurfaceCavitiesMultipleFrames()	karolamik13	More...				8 days ago
Created rmsd_clustering module - Relocated functions - Cleaned up Redundant Code	kontheodosiadis	More...				8 days ago
Merge pull request #2263 from briza81/CaviTracer-parameters-update	Karolina Mikulska-Ruminska	More...				9 days ago
New clustering function - DBSCAN, OPTICS for Reachability Plot	kontheodosiadis	More...				12 days ago
CaviTracer: removing fogotten comments	briza81	More...				14 days ago
CaviTracer: per-object output files are now named with Path.with_name(), not str.replace() to avoid cases wehn separate channel/cavity files were named by filename.replace('.pqr','_chl0.pqr'), which rewrites every occurrence of the extension anywhere in the path. An output directory called run.pqr/ was renamed along with the file, so the write failed after the combined file had already been produced; a name carrying no extension matched neither replace, so every object overwrote the previous one and the combined file with it; and a name holding both extensions was numbered twice. The new _numberedPath() helper numbers the file's own name only and leaves the directories alone.	briza81	More...				14 days ago
CaviTracer: lining distance is now measured from the object surface, not its centre. Previously, distA was measured from the probe centre, but the probe is a sphere whose radius varies along the object, so the reach past the wall was distA - r: a second shell was collected where an object is narrow and the wall was missed entirely where it is wide. The criterion is now \|v - x\| <= r + distA, and distA defaults to 2.5, which keeps channel reports close to their previous size; the distance still runs to the atom centre, so a touching atom sits at about one van der Waals radius. Channel and pore radii come from the radius spline, which also removes repetitive analysis of PDB file with each channel, making it about five times faster. Cavity vertices carry no radius, so the inscribed radius is recomputed against the atoms the tessellation used (water excluded); hence a vertex cannot lie inside one of those atoms, so a negative radius is reported as a mismatch between the cavities and the atoms given, rather than clamped away. + Minor refactors.	briza81	More...				14 days ago
CaviTracer: channel/pore/cavity lining is now read per residue, not per CA atom. Previously, since nucleic acids, ligands, cofactors and ions have no CA, they were dropped from the lining reports entirely, and a channel lined by no protein raised AttributeError (e.g. on ribosome). Residues now come from the hierarchical view. Water is excluded unless include_water=True,. one_letter_aa translates only amino acids and nucleotides. Labels carry the chain (ASP108:A) unless include_chain=False, without which a residue number is not an identifier in an oligomer. An object with no lining is reported as "channelN: None" rather than skipped.	briza81	More...				14 days ago
New clustering functions - Hierarchical, KMedoids	kontheodosiadis	More...				14 days ago
CaviTracer: several advanced/unusuall arguments are now keyword-only they were move out of the calcChannels signature into **kwargs, listed in a CHANNELS_ADVANCED_OPTIONS table inside the function. They are settings a normal run never touches, and the signature is long enough already. Unknown keywords raise TypeError instead of being ignored, so a misspelled option is reported rather than silently falling back to its default. All these args options remain documented among the arguments, under a note that they are accepted as keywords only.	briza81	More...				14 days ago
CaviTracer: small typo in variable name	briza81	More...				14 days ago
Cavitracer: channel truncation at surface is now unconditional, as the channels slithering on surface are clear artifacts, no need for switch that would enable thier production	briza81	More...				14 days ago
Cavitracer - changeing r1 and r2 parameter names to surf_radius and inner_radius for ease of use	briza81	More...				14 days ago
Merge pull request #2229 from jamesmkrieger/jamesk/bio_phylo_imports	James Krieger	More...				20 days ago

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