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• af1d6eeb18 Drop frozen pocket-grid PLAN/SPEC; refine audit punch-list develop rdk 2026-05-20 19:42:47 +02:00
• 40d333f77f README: tighten 2.6 teaser; bump tested Java to 26 rdk 2026-05-20 18:06:00 +02:00
• 1473b3996f Bump version to 2.6-alpha untagged-1b101757d79da82148b3 2.6-alpha rdk 2026-05-20 13:15:37 +02:00
• a60cb33b60 README: add 2.6-alpha teaser to "What's new" rdk 2026-05-20 13:12:38 +02:00
• 41cdbe8773 Add post-2.5.1 audit punch-list to misc/dev rdk 2026-05-20 12:24:25 +02:00
• e3b551c902 Add second ChimeraX pocket-grid visualization screenshot rdk 2026-05-20 12:15:27 +02:00
• fab83cc11a Bump junit-jupiter to 6.1.0 rdk 2026-05-20 11:40:32 +02:00
• 84148eb95b Bump biojava to 7.2.5 (biojava-structure 7.2.5-rdk.1) rdk 2026-05-20 11:39:09 +02:00
• 550ab9e1a0 testsets.sh: add opt-in pocket_grid_long sweep rdk 2026-05-20 11:35:58 +02:00
• 46194b8bdc Add ChimeraX pocket-grid visualization screenshots rdk 2026-05-20 03:28:44 +02:00
• cbf4c3ffac testsets.sh: cover per-grid-point descriptors + aa_mapping smoke tests rdk 2026-05-20 03:06:50 +02:00
• 0afdbe7d65 Doc polish: em-dash sweep + pocket-{grid,descriptors} audit cleanup rdk 2026-05-20 02:57:25 +02:00
• e3af9106c6 Mark pocket-grid/descriptors docs as preview + capture future ideas rdk 2026-05-20 00:12:12 +02:00
• 556ea9faa8 Cleanup batch: BitSet reuse + idiom touches (no user-visible perf change) rdk 2026-05-19 19:59:29 +02:00
• 6c1e394ea5 Extract three framework helpers (centroid, schema, registry) rdk 2026-05-19 16:23:09 +02:00
• 6fad858bc6 Audit follow-ups: bug fix, doc refresh, exception taxonomy, test hardening rdk 2026-05-19 15:36:12 +02:00
• cb6f7f75eb Doc / comment refresh after the multi-column descriptor migration rdk 2026-05-19 14:41:03 +02:00
• 73e7c9df9a Per-pocket descriptors: multi-column interface + PrincipalMomentsDescriptor rdk 2026-05-19 14:34:33 +02:00
• 0e044f6bb3 Audit follow-ups: fill warning, NaN guard, test hardening + docs rdk 2026-05-19 13:29:10 +02:00
• 6888716aa0 Tests for pocket-grid-point descriptors + extract DescriptorListValidator rdk 2026-05-19 10:29:02 +02:00
• 1931ef1f93 Pocket-grid-point descriptors: framework + two VolSite descriptors rdk 2026-05-19 09:59:37 +02:00
• a3efd0840c Pocket-grid defensive guards + ChimeraX rank-gap fix rdk 2026-05-19 07:47:43 +02:00
• f06628dd63 Audit follow-ups: rename leftovers, doc fixes, numeric validation rdk 2026-05-19 07:24:16 +02:00
• 60220d7a57 Add pocket-grid + descriptors export with PyMOL / ChimeraX viz rdk 2026-05-19 03:03:33 +02:00
• 913e0b551e Expand rescoring docs for SwinSite, Seq2Pocket, and rescore_conservation rdk 2026-05-17 02:44:00 +02:00
• 0ef60da818 Guard pocket loaders against degenerate input rdk 2026-05-17 01:44:29 +02:00
• ddd5d8a11c Add Seq2PocketLoader for Seq2Pocket pocket predictions rdk 2026-05-16 12:40:36 +02:00
• e9641680c1 Silence javac deprecation/unchecked notes rdk 2026-05-15 16:15:26 +02:00
• c6ee163ece Audit cleanup: remove dead param, dead commented code, stale docs rdk 2026-05-15 09:34:28 +02:00
• 9fd7ffe0db Bump gradle wrapper 9.5.0->9.5.1, slf4j 2.0.17->2.0.18, parquet-floor 1.65->1.69 rdk 2026-05-15 02:57:07 +02:00
• c78519c98e Cofactor smoke harness, CDK VdW workaround, analyze-cofactors fixes cofactors rdk 2026-05-15 00:35:08 +02:00
• 79cda78473 Add cofactor-as-protein-surface feature (Issue #79 part 2) rdk 2026-05-14 07:58:14 +02:00
• b2a23179f1 Bump groovy 5.0.5->5.0.6, log4j 2.25.4->2.26.0, zstd-jni 1.5.7-7->1.5.7-8 rdk 2026-05-12 01:56:07 +02:00
• 0e8bb0cb33 Add SwinSiteLoader for SwinSite pocket predictions rdk 2026-05-08 01:05:15 +02:00
• 59bc84c265 Mention pocket column alongside score in export-points docs rdk 2026-05-07 03:21:27 +02:00
• f5ad22f604 Document 2.6 evaluation-metric fixes and note ligand-detection breaking change rdk 2026-05-06 14:46:06 +02:00
• 15349bb48f Add pocket rank column to points export, fix overlap labeling rdk 2026-05-06 14:08:29 +02:00
• ee8ff7b471 Bump Gradle wrapper 9.4.1->9.5.0 rdk 2026-04-30 12:07:55 +02:00
• 9fe0e28bc0 Bump gradle-versions-plugin 0.53.0->0.54.0, commons-io 2.21.0->2.22.0, guava 33.5.0->33.6.0, gson 2.13.2->2.14.0, parquet-floor 1.64->1.65 rdk 2026-04-29 22:33:45 +02:00
• c143e0fa9c Fix ConcavityLoader to bind prediction to queryProtein rdk 2026-04-29 00:41:01 +02:00
• 42dfe7fd6f Fix PUResNet pocket loader to handle shifted insertion codes rdk 2026-04-28 22:25:44 +02:00
• 43b1f7dcf1 Fix pocket centroid calculation in ConcavityLoader and PUResNetLoader rdk 2026-04-03 19:30:27 +02:00
• 994ad45238 Bump groovy 5.0.4->5.0.5, log4j 2.25.3->2.25.4 rdk 2026-04-01 22:25:51 +02:00
• 17a4304d29 Add rg, n_unp_pockets, n_unp_pockets_multichain fields to AhojSiteInfo rdk 2026-04-01 12:44:10 +02:00
• 858ba45fe7 Refactor AhojUbsSiteParser to use CSV library and add AhojSiteInfo data class rdk 2026-04-01 10:22:43 +02:00
• 6cf293478a Add atom hybridization feature (one-hot sp2/sp3) rdk 2026-03-21 21:55:00 +01:00
• 1997ab948e switch CI Java distribution from temurin to oracle rdk 2026-03-21 18:42:22 +01:00
• 1c636757d6 update CI Java version matrix: drop 23/24, add 26 rdk 2026-03-21 17:54:56 +01:00
• b58726c27e bump arrow and parquet-floor dependencies rdk 2026-03-21 17:52:37 +01:00
• 0a51f504d0 bump gradle rdk 2026-03-21 16:04:31 +01:00
• a66bea74be Add eval_output_prediction_files param to output per-protein prediction CSVs in eval commands rdk 2026-03-17 18:59:13 +01:00
• faddcfb70f Lazy-init EnergyCalculator and LJEnergyCalculator in energy features 2.6.0-dev.7 rdk 2026-03-16 07:55:16 +01:00
• 48cb681aaa Refactor DSO/DSWO: replace Tuple2 with OverlapCounts, cache counts instead of Atoms, simplify CdkUtils rdk 2026-03-16 03:20:48 +01:00
• 5b4613c3a4 Extract FpocketAdHocHelper, add run_fpocket_ad_hoc param for eval-rescore and rescore commands rdk 2026-03-16 03:20:41 +01:00
• ba53b97e90 Add per-method CSVs and grouped summary to binding-site-centers, add DataTable filter/distinctValues/formatGroupedSummaryTable rdk 2026-03-16 01:06:44 +01:00
• 91987129fe Bump version to 2.6.0-dev.7 rdk 2026-03-15 21:37:05 +01:00
• 8852739016 Add DCC_4 protein-centric success rate metrics rdk 2026-03-15 21:35:53 +01:00
• a814157e2b Minor cleanups: fix typos, normalize loop syntax and imports in Evaluation rdk 2026-03-15 21:32:23 +01:00
• f3616da217 Unify Protein.sites to contain all binding sites, add predictedPocket to BindingSite interface rdk 2026-03-15 21:25:49 +01:00
• 829cf9b8be Return typed result objects from calcConservationStats and calcOverlapStatsForPockets rdk 2026-03-15 20:28:51 +01:00
• 8a516228e1 Fix @CompileStatic errors in Evaluation: destructuring assignment, int-to-Double casts rdk 2026-03-15 19:59:15 +01:00
• 5ac9aab18a Refactor Evaluation: simplify avg/div methods, use Function instead of Closure, extract writeScoresToFileIfRequested rdk 2026-03-15 19:27:15 +01:00
• 20236ef092 Refactor conservation/chains analysis, add @CompileStatic to Evaluation, rename criterium to criterion rdk 2026-03-15 17:59:53 +01:00
• d9de1fba7e Add contact_atoms_centroid site evaluation center method for ligand-defined sites rdk 2026-03-15 17:09:04 +01:00
• 49a8430a7d Add binding-site-centers command, refactor center methods, consolidate error reporting rdk 2026-03-14 18:22:47 +01:00
• 0e0cb47907 Add ca_atoms_centroid site evaluation center method with tests rdk 2026-03-14 15:57:41 +01:00
• 1ecb29f876 Add load_ligands_from_separate_files param for loading ligands from individual ligand_* files rdk 2026-03-13 18:21:26 +01:00
• 0b5b61304d Add legacy conservation file name format fallback (e.g. 2ed4_A.) rdk 2026-03-13 17:22:27 +01:00
• e7fc457f6a Fix ligand detection for BioJava GroupType misclassifications 2.6.0-dev.6 rdk 2026-03-10 14:34:28 +01:00
• d78f80ee73 Extract writeCases() method, rename sites.csv to observed_sites.csv rdk 2026-03-10 03:24:44 +01:00
• 838b0a697f Fix integer division bug in DSO criterion and clean up rdk 2026-03-10 02:27:11 +01:00
• 2de315e9e0 Rename API: PocketCriterium->PocketCriterion, getLigandAtoms->getAtoms, centroid->center rdk 2026-03-10 02:02:47 +01:00
• 412c590dcb Fix CSV spacing consistency: remove padding and trailing spaces rdk 2026-03-09 13:32:51 +01:00
• fdebd71daf Add example Jupyter notebook for analyzing P2Rank output rdk 2026-03-09 12:05:00 +01:00
• 61b8863c27 Simplify CSV output formatting and add null guard in CsvRow rdk 2026-03-09 11:17:59 +01:00
• 42ad4dfe9f Move centerOfMass and calculateCentroid to PerfUtils to avoid array allocation rdk 2026-03-09 02:22:48 +01:00
• d9b34ffbde Bump version to 2.6.0-dev.5 and update dependencies rdk 2026-03-07 23:14:06 +01:00
• af2f68e7b9 Add sites.csv to eval output and rename getAtoms() to getLigandAtoms() in BindingSite rdk 2026-03-07 22:53:03 +01:00
• 228cd1ab18 Fix review issues: stale comments, null centroid in closestPocket, docs rdk 2026-03-07 20:35:01 +01:00
• 60225e3f1f Add null guards for centroids in DCC and DCA criteria rdk 2026-03-05 05:06:22 +01:00
• 7adb080022 Write error files to outdir in finalizeDatasetResult rdk 2026-03-05 04:16:44 +01:00
• ed8e9cabe9 Add configurable site centroid method and SAS-as-atoms option for evaluation rdk 2026-03-05 02:16:55 +01:00
• ea0968816b Render predicted pocket and explicit site centroids in PyMOL renderer rdk 2026-03-04 21:37:56 +01:00
• 22ac1e51ee Fix DCC criterion to use predefined site centroid for ResidueSites rdk 2026-03-04 04:00:18 +01:00
• 53500dd129 Fix SAS point classification stats for explicit-site datasets and improve cluster logging rdk 2026-03-04 03:55:17 +01:00
• c9ad8f71ff Add vis_site_centers param for rendering site/pocket centroids in PyMOL rdk 2026-03-04 02:47:43 +01:00
• d5715d9797 Fix PyMol renderer: bulk selections, CIF-to-PDB conversion, site-based labeling rdk 2026-03-04 01:13:48 +01:00
• 026be7eae5 Improve analyze binding-sites: visualizations, site radius, eager loading rdk 2026-03-03 21:58:55 +01:00
• 9e9a500836 Bump version to 2.6.0-dev.4 rdk 2026-03-03 15:00:46 +01:00
• c9fef83950 Use AtomKdTree interface in Atoms and minor cleanups rdk 2026-03-03 15:00:36 +01:00
• 997727e878 Add explicit sites loading and analyze binding-sites command rdk 2026-03-03 15:00:31 +01:00
• 8f5da9fdcd Add fused addWeighted and O(N²) single-linkage clusterer rdk 2026-03-03 05:13:05 +01:00
• 261dae09c9 Rename consolidate() to sparsify() and add surface_sparsify param rdk 2026-03-03 02:23:19 +01:00
• a66a973e1c Refactor KdTree into AtomKdTree interface with V1/V2 implementations rdk 2026-03-03 00:17:38 +01:00
• 6d47285116 Add kdtree_implementation param and fix quickselect duplicate-key hang rdk 2026-03-02 22:20:59 +01:00
• 24b9f5f709 Optimize KdTree3D build: bottom-up bounds, eliminate redundant traversals rdk 2026-03-02 21:15:41 +01:00
• 76026b9297 Refactor Dataset item cache clearing and fix processItem typo rdk 2026-03-02 20:52:07 +01:00
• 7f4d37b5c4 Add comparative benchmark test for v1 vs v2 KdTree rdk 2026-03-02 20:52:05 +01:00
• 6cce0eb016 Rewrite KdTree as immutable, hardcoded 3D implementation in v2 package rdk 2026-03-02 20:13:47 +01:00
• 5d9ec9eb58 Fix bugs and add error reporting to analyze subcommands rdk 2026-03-02 09:59:36 +01:00