mirror of
https://github.com/rdk/p2rank.git
synced 2026-06-04 12:44:24 +08:00
Add post-2.5.1 audit punch-list to misc/dev
Captures findings from a 10-agent audit of all changes between tag 2.5.1 and develop. Grouped by severity: high-priority bugs, inconsistencies, doc/config drift, stale comments, test-isolation gaps, perf nits. No items are fixed here -- this is a triage backlog to work through as the surrounding code is touched.
This commit is contained in:
rdk
382
misc/dev/audit-post-2.5.1.md
Normal file
382
misc/dev/audit-post-2.5.1.md
Normal file
@@ -0,0 +1,382 @@
|
||||
# Post-2.5.1 Audit Findings
|
||||
|
||||
Punch-list captured from a 10-agent audit of all changes between tag `2.5.1`
|
||||
and `develop` (branch `develop`, ~218 commits, ~523 files). Each item is
|
||||
grouped by severity. File paths are repo-relative; line numbers reflect
|
||||
state at audit time and may drift.
|
||||
|
||||
This is a tech-debt / triage backlog — items here have not been fixed.
|
||||
Resolve items individually as the surrounding code is touched, or schedule
|
||||
focused cleanups.
|
||||
|
||||
---
|
||||
|
||||
## Highest-priority bugs (real or near-real)
|
||||
|
||||
- **`VoxelHashAssigner` cell-prune lower bound is too aggressive.**
|
||||
`src/main/groovy/cz/siret/prank/program/routines/predict/output/grid/assign/VoxelHashAssigner.java:58`
|
||||
uses `(di²+dj²+dk²)·spacing²` as a lower bound that ignores the sub-cell offset
|
||||
of `q`. Concrete miss with shipping defaults: `q=(0.59,0,0)`, `spacing=1.2`,
|
||||
`cutoff=2.5` skips a cell whose true distance is ~2.17 Å. Silently breaks the
|
||||
"both assigners agree" invariant documented on `PocketAssigner.java:23-26`.
|
||||
Existing test (`PocketGridBuilderTest.groovy:158`) misses it because its
|
||||
single SAS point lands exactly on a lattice center. Fix: correct the lower
|
||||
bound (`max(0, |di|*spacing − spacing/2)` per axis), or drop the prune.
|
||||
|
||||
- **Lazy-init race on singleton energy features.**
|
||||
`MethylEnergyFeature.groovy:28-40`, `MethylEnergyCloud{,X,XFull,X2,X2Full}SF.groovy:67-80`,
|
||||
`AbstractProbeEnergyFeature.groovy:47-59,66`.
|
||||
`calculator`/`config` are non-volatile fields on registry singletons; multiple
|
||||
worker threads can construct (and observe partially constructed) calculators.
|
||||
`ConcurrencyTest.groovy:27-28` constructs the calculator on the main thread
|
||||
before spawning threads, so the test does NOT cover the race it was meant to
|
||||
validate. Fix: `volatile` + DCL, or do one-shot init under a synchronized guard
|
||||
in `preProcessProtein`; update the concurrency test to construct under contention.
|
||||
|
||||
- **PyMOL pocket-grid renderer ignores rank gaps.**
|
||||
`src/main/groovy/cz/siret/prank/program/visualization/renderers/PocketGridPymolRenderer.groovy:167,201,242`
|
||||
loop `for (rank = 1; rank <= maxRank; rank++)`. If a pocket rank is missing
|
||||
(`{1,3}`), the script emits an empty `pocket_grid_2` and shifts palette indices.
|
||||
ChimeraX was fixed in commit `a3efd084`; PyMOL still has the latent bug.
|
||||
Comment at lines 131-132 even acknowledges it. Fix: iterate
|
||||
`grid.pocketToPointIndices.keySet()` like ChimeraX does.
|
||||
|
||||
- **Coulomb plumbing is dead code.**
|
||||
`EnergyCalculator.getAtomCharge` always returns 0
|
||||
(`src/main/groovy/cz/siret/prank/features/implementation/energy2/calc/EnergyCalculator.groovy:351-357`).
|
||||
`enableCoulomb`, `dielectricConstant`, `coulombConstant` are structurally
|
||||
inert. `testCationProbeIncludesBothLJAndCoulombTerms`
|
||||
(`EnergyCalculatorTest.groovy:194-209`) is a false positive against its own
|
||||
name. Either wire charges, or rip the Coulomb path out.
|
||||
|
||||
- **PUResNet `surfaceAtoms` come from a separate `Structure`.**
|
||||
`src/main/groovy/cz/siret/prank/domain/loaders/pockets/PUResNetLoader.groovy:50,55`.
|
||||
The Concavity fix (`c143e0fa`) only re-routed the `Prediction` binding;
|
||||
PUResNet has the same identity-mismatch class still uncaught (atoms are from
|
||||
a sub-PDB, not from `queryProtein`). ConcavityLoader's own `cutoutShell` still
|
||||
runs against the residue subset rather than `queryProtein.exposedAtoms`. Fix:
|
||||
re-link atoms by PDB serial against `queryProtein.allAtoms.getByID`, mirroring
|
||||
`FPocketLoader.groovy:137`.
|
||||
|
||||
- **`AhojUbsSiteParser` will crash on "older full" CSVs.**
|
||||
`src/main/groovy/cz/siret/prank/domain/loaders/AhojUbsSiteParser.groovy:46`
|
||||
uses `pocket_class` as the sole marker but then unconditionally reads
|
||||
`rg`/`n_unp_pockets`/`n_unp_pockets_multichain` in `AhojSiteInfo.fromCsvRecord`.
|
||||
Commons CSV throws `IllegalArgumentException` for unmapped header names.
|
||||
Fix: add `record.isMapped(name)` guards, or pick a marker column guaranteed
|
||||
present in every variant.
|
||||
|
||||
- **`Ligands.loadLigandsFromSeparateFiles` doesn't filter cofactors.**
|
||||
`src/main/groovy/cz/siret/prank/domain/Ligands.groovy:140-198`.
|
||||
When `load_ligands_from_separate_files=true`, the cofactor branch in
|
||||
`Protein.loadStructure` (`Protein.groovy:574-592`) adds cofactor atoms to
|
||||
`proteinAtoms`, but the loader has no `.findAll { !loaderParams.isCofactor(it) }`
|
||||
guard. The cofactor becomes an *ignored Ligand* with contact distance ≈ 0.
|
||||
Self-acknowledged as cosmetic in `documentation/cofactors.md:421-429` and
|
||||
dev doc Known Limitation #1, but no test exercises it.
|
||||
|
||||
- **Aromatic-probe energy cap is applied before the cosine switch.**
|
||||
`EnergyCalculator.groovy:248-250` clips pre-switch, then multiplies by
|
||||
`neighbor.switchValue` at line 291. May be intended, but contradicts inline doc
|
||||
and `testAromaticRingEnergyCap` (`EnergyCalculatorTest.groovy:132-146`) doesn't
|
||||
exercise the divergence (single atom inside RON window). Decide per-atom vs
|
||||
per-point capping and align doc + test.
|
||||
|
||||
- **Centroid-source divergence across pocket loaders.**
|
||||
Pocketeer uses the server-supplied JSON `centroid`; FPocket uses voronoi
|
||||
centerOfMass; Concavity/PUResNet use geometric centroid post-fix;
|
||||
Seq2Pocket/SwinSite use `gridPoints.centroid`/`surfaceAtoms.centroid`. No
|
||||
documented contract for what "centroid" means across loaders. Either document
|
||||
the policy or normalize to geometric.
|
||||
|
||||
- **`RescorePocketsRoutine.checkDataset` has an empty truthy branch.**
|
||||
`src/main/groovy/cz/siret/prank/program/routines/predict/RescorePocketsRoutine.groovy:48-56`
|
||||
has `if (runFpocketAdHoc) { /* comment */ }` — the check appears inverted.
|
||||
Re-verify intended semantics.
|
||||
|
||||
---
|
||||
|
||||
## Inconsistencies (renames / strategy lookups / cross-format / code vs docs)
|
||||
|
||||
- **`NewPymolRenderer` class name is stale** — `NewPymolRenderer.groovy:28`.
|
||||
Two distinct active classes (`NewPymolRenderer` vs `PymolRenderer`). The
|
||||
"New" prefix predates a refactor. The cofactor block depends on a static
|
||||
method on the misnamed class (`PymolRenderer.groovy:147`). Rename.
|
||||
|
||||
- **Assigner vs filler lookup styles disagree.** Assigners go through
|
||||
`PocketAssignerRegistry`; fillers use a hand-written switch
|
||||
(`PocketGridBuilder.java:118-127`) plus a hard-coded `['morph_closing','none']`
|
||||
list (`Main.groovy:223`). Two places to keep in sync per new filler.
|
||||
|
||||
- **`NoOpFiller` returns input BitSet without cloning, `MorphologicalCloser`
|
||||
clones.** Mixed ownership semantics; `PocketShapeFiller.java:30` contract is
|
||||
silent. Risk of silent corruption if a future caller mutates the per-pocket
|
||||
BitSet under `fill=none`.
|
||||
|
||||
- **`SphericityDescriptor` degenerate convention diverges** —
|
||||
`SphericityDescriptor.java:32,48`. Empty pocket → 0.0, single-point pocket → 1.0.
|
||||
Volume / RadiusOfGyration / PrincipalMoments / NumGridPoints return 0 for both.
|
||||
Joining columns: one says "perfectly spherical", others say "empty".
|
||||
|
||||
- **`PocketGridPdbSidecar.write` called by both renderers** —
|
||||
`PocketGridPymolRenderer.groovy:121` + `PocketGridChimeraXRenderer.groovy:157`.
|
||||
When both are enabled, same sidecar PDB is written twice (identical content).
|
||||
|
||||
- **CSV `NaN`/`INF` handling is unspecified.** `Formatter` emits `NaN`/`∞`;
|
||||
INT columns silently coerce NaN to 0 (`TableExporter.groovy:142`). Document
|
||||
in `documentation/export-pocket-descriptors.md` and `export-points.md`, or
|
||||
pick a canonical sentinel.
|
||||
|
||||
- **Sort-direction comment in `PrincipalMomentsDescriptor.java:96-101`** says
|
||||
"Sort descending." while `Arrays.sort` is ascending. Downstream indexing
|
||||
compensates; comment is misleading.
|
||||
|
||||
- **Cofactor case-sensitivity mismatch.** `CofactorHandler.parseOne`
|
||||
(`CofactorHandler.groovy:325-335`) uppercases; `Dataset.LigandDefinition.parse`
|
||||
(`Dataset.groovy:761-805`) does not. `Params.groovy:536-537` doc claims
|
||||
case-sensitive while cofactors are normalized.
|
||||
|
||||
- **`distro/prank.bat` misses JVM flags.** Lines 11-13 set only the three
|
||||
`--add-opens`. Missing `--enable-native-access=ALL-UNNAMED` and the
|
||||
Java-23+ `--sun-misc-unsafe-memory-access=allow` block that `distro/prank`
|
||||
and `prank.sh` apply. zstd-jni native warnings + future-Java compatibility
|
||||
gap on Windows.
|
||||
|
||||
- **`atomRoleCache`/`atomChargeCache` keyed by BioJava `Atom` identity.**
|
||||
`EnergyCalculator.groovy:131-132`. Atoms across proteins are distinct
|
||||
identities; cache never hits across proteins and grows monotonically — slow
|
||||
leak for long-running calculators.
|
||||
|
||||
- **`computeEnergyForPoint` returns `List<Double>` (boxed).**
|
||||
`EnergyCalculator.groovy:146-179`. Boxing per neighbor per probe in the hot
|
||||
loop. Legacy `LJEnergyCalculator.computeEnergyForPoint` returns `double`.
|
||||
|
||||
- **`Evaluation.closestPocket()` ignores `site_eval_sas_pts_as_atoms`.**
|
||||
`Evaluation.groovy:81` doc says "considering DCA measure" but uses
|
||||
`site.atoms.dist(p.centroid)` unconditionally. Diverges from DCA semantics
|
||||
when the param is enabled.
|
||||
|
||||
- **`Evaluation.getStats()` returns `LinkedHashMap`** (comment claims "keep
|
||||
insertion order"), but the immediate caller `EvalResults.getStats()` puts
|
||||
everything into a `TreeMap` (`EvalResults.groovy:189`) — insertion order is
|
||||
lost. Either drop the misleading comment or use `LinkedHashMap` downstream.
|
||||
|
||||
- **PyMOL grid `solvent_radius=0` vs ChimeraX non-zero probe.**
|
||||
`PocketGridPymolRenderer.groovy:189-190` vs `PocketGridChimeraXRenderer.groovy:264`.
|
||||
`vis_pocket_grid_volume_radius` means different things to the two renderers.
|
||||
Documented in code; not in the param help.
|
||||
|
||||
- **`pocket=0` (unassigned) points never reach the PDB sidecar.**
|
||||
`PocketGridPdbSidecar.java:56-60` iterates `grid.getPocketToPointIndices()`
|
||||
only. When `-pocket_grid_include_unassigned 1`, CSV/Parquet has the rows
|
||||
but visualization silently drops them. Document or extend.
|
||||
|
||||
---
|
||||
|
||||
## Doc / config drift
|
||||
|
||||
- **README badge stuck at 2.5.1.** `README.md:11` vs `build.gradle:25`
|
||||
(`2.6.0-dev.9`). Typo `./make-disro.sh` at `README.md:225`.
|
||||
|
||||
- **Removed flags/commands still referenced in docs:**
|
||||
- `documentation/random-examples.md:7,12,17,22` — singular `-conservation_dir`
|
||||
(removed in 2.2, renamed to `-conservation_dirs`).
|
||||
- `documentation/hidden-commands.md:65` — `fasta-mask` (actual: `fasta-masked`).
|
||||
- `documentation/hidden-commands.md:83` — `analyze reduce-to-chains`
|
||||
(actual: `transform reduce-to-chains`).
|
||||
- `documentation/training-score-transformers.md:4` — `*_pockets.csv` (actual:
|
||||
`*_predictions.csv`).
|
||||
|
||||
- **`src/main/resources/help.txt` is severely outdated.** Lists only 5 commands;
|
||||
`Main.groovy:621-645` registers 12+. Typos `dafault`, `comamnd`. Doesn't
|
||||
mention any 2.6 loader rescorers despite `documentation/rescoring.md`
|
||||
describing 10.
|
||||
|
||||
- **`distro/config/default.groovy:128-130`** comments `ignore_het_groups` as
|
||||
"considered cofactor". After `-cofactors` shipped in 2.6, this is actively
|
||||
misleading. Same comment in `distro/config/default_rescore.groovy:120-122`.
|
||||
|
||||
- **`distro/config/default.groovy` is missing new params:**
|
||||
`cofactors`, `cofactor_max_protein_dist`, `aa_mapping`, `vis_highlight_cofactors`.
|
||||
|
||||
- **`documentation/cofactors.md:190,389`** say "logs an INFO warning"; code
|
||||
logs `WARN` (`CofactorHandler.groovy:222,261`).
|
||||
`documentation/dev/cofactors.md:36,39` also describe R11/R14 as "INFO"
|
||||
while line 69 of the same file documents the promotion to WARN.
|
||||
|
||||
- **`Params.groovy:536-537`** doc on cofactor matching is stale (claims
|
||||
case-sensitive — actually normalized).
|
||||
|
||||
- **`feature-setup.md:8`** still says "P2Rank version: 2.4"; collapsibles
|
||||
hardcode `P2Rank 2.3-dev.1`. Line 120 says "providing custom tables is not
|
||||
implemented yet (as for P2Rank 2.4.2)" while the very next bullet describes
|
||||
the `csv` feature that does this.
|
||||
|
||||
- **`feature-setup.md:125`** typo `{peorein_file_name}`.
|
||||
|
||||
- **`documentation/aa-mapping.md:21`** typo `ommited`, extra space before comma.
|
||||
|
||||
- **`documentation/readme.md`** index misses `cofactors.md`, `conservation.md`,
|
||||
`export-pocket-grid.md`, `export-pocket-descriptors.md`.
|
||||
|
||||
- **`misc/todo/pocket_grid/{SPEC,PLAN}.md`** still mention
|
||||
`export_pocket_grid_pml` (renamed to `vis_pocket_grid`).
|
||||
|
||||
- **CI matrix is `17,21,25,26` only** (`.github/workflows/develop.yml:23`).
|
||||
README claims "Java 17 or later (tested up to Java 25)"; 18–20/22/23/24 not
|
||||
exercised; "tested up to Java 25" lags the now-present 26.
|
||||
|
||||
- **Distribution switched temurin → oracle** (`develop.yml:31`, commit
|
||||
`1997ab94`). No doc note explains the choice.
|
||||
|
||||
- **`PocketDescriptor.java:29-31` "fits in i32" contract** is unenforced;
|
||||
a descriptor producing `1e20` for an INT column silently emits
|
||||
`Integer.MAX_VALUE` or wraps. Add `Math.toIntExact` at the writer.
|
||||
|
||||
- **`PointExportData.create()` doc says "(for predict mode)"**
|
||||
(`PointExportData.groovy:141`) but it's also used by `rescore`
|
||||
(`ModelBasedRescorer.groovy:97,168`).
|
||||
|
||||
---
|
||||
|
||||
## Stale comments / dead code
|
||||
|
||||
- **"Immutable calculator instance" comments in 6 energy feature files** after
|
||||
the lazy-init refactor: `MethylEnergyFeature.groovy:22`,
|
||||
`MethylEnergyCloud{,X,XFull,X2,X2Full}SF.groovy:27/30`.
|
||||
|
||||
- **`EnergyCalculatorConfig.roleRulesCSV` + `role-rules.csv` resource are
|
||||
wired but read nowhere.** `EnergyCalculatorConfig.groovy:28,40,143,162-164`.
|
||||
`AtomRole.classify` is hardcoded.
|
||||
|
||||
- **`PocketShapeFiller.java:24` and `Params.groovy:896-897`** use the term
|
||||
"surface atom"; actual inputs are SAS points (pre-SAS-revision wording).
|
||||
|
||||
- **`LoaderParams.groovy:60-66`** commented-out copy constructor;
|
||||
`:20-22` stale `TODO get rid of this global variable` on `ignoreLigandsSwitch`.
|
||||
|
||||
- **References to gitignored `local/PLAN_COFACTORS*.md`** in committed code:
|
||||
`CofactorPipelineTest.groovy:38`, `CofactorAnalyzeTest.groovy:17`,
|
||||
`documentation/dev/cofactors.md:6`.
|
||||
|
||||
- **`FPocketLoader.groovy:149`**: `pocket.centroid = pocket.voronoiCenters.centerOfMass`
|
||||
is dead because the `getCentroid` override at line 42 always recomputes.
|
||||
|
||||
- **`FPocketLoader.groovy:155`** `// probably not needed` (years old);
|
||||
`:142` fpocket3 TODO.
|
||||
|
||||
- **`ConcavityLoader.groovy:74`** `// TODO XXX` is meaningless;
|
||||
`:91` `///X correctsorting…` typo log marker; the class is not `@CompileStatic`.
|
||||
|
||||
- **`PUResNetLoader.groovy:55`** truncated comment mid-sentence (`// not all
|
||||
of them are necessarily on the surface but it s`).
|
||||
`:35` parameter named `liganatedProtein` but expects queryProtein.
|
||||
`:23-28` javadoc is a stub.
|
||||
|
||||
- **`PocketeerLoaderTest`** missing `predictionIsBoundToQueryProtein` and
|
||||
empty-input tests (every other new loader test has both).
|
||||
|
||||
- **`PocketGridBuilder.java:97-99`** "monomorphic dispatch, JIT-friendly"
|
||||
comment is wrong — bimorphic with two impls registered.
|
||||
|
||||
- **`PredictionPair.groovy:61,78,107,109`** still uses `criterium` after
|
||||
class rename (commit `2de315e9`).
|
||||
|
||||
- **`Evaluation.groovy:484`** rank-sentinel comment says 0; actual sentinel
|
||||
is `-1` (`PredictionPair.rankOfIdentifiedPocket`).
|
||||
|
||||
- **`Evaluation.groovy:132`** comment "Clear SAS points cache" — actually
|
||||
clears per-site lazy lookup, not the EvalContext cache.
|
||||
|
||||
- **`MethylEnergyFeature.groovy:67-70`** dangling try/catch skeleton;
|
||||
`:55` commented alternative path.
|
||||
|
||||
- **`prank.sh:13-15`** commented `-XX:+UseConcMarkSweepGC` (removed in JDK 14).
|
||||
|
||||
- **`misc/development-notes.md`** is down to a single 6-line note —
|
||||
merge into `misc/dev/technical-debt.md` or delete.
|
||||
|
||||
- **`distro/config/default_rescore.groovy:46`** `//== FAETURES` typo.
|
||||
|
||||
- **`distro/prank.bat:14`** last `set "JAVA_OPTS=%JAVA_OPTS%"` is a no-op.
|
||||
|
||||
- **`PocketGridChimeraXRenderer.groovy:81`** says PyMOL transparency is 0.7;
|
||||
actual `PROTEIN_TRANSPARENCY` in `PocketGridPymolRenderer.groovy:76` is 0.5.
|
||||
|
||||
- **`PocketGridBuilder.java:54-56`** meta-commentary about
|
||||
`Atoms.union`-vs-`Atoms.join` choice — reads as a leftover review note.
|
||||
|
||||
- **`VolsiteGridPointDescriptorTest.groovy:81`** comment claims testing the
|
||||
default `pocket_grid_volsite_radius=4.0`, but the test pins `RADIUS=4.0`
|
||||
via `@BeforeEach`.
|
||||
|
||||
- **`PocketDescriptorsTest.groovy:110-112`** arithmetic in the comment
|
||||
(`≈ sqrt(2)*5 ≈ 7.07`) doesn't match the geometry (centroid at (4.5,4.5,0),
|
||||
max dist ≈ 6.36). Asserted ratio still passes.
|
||||
|
||||
- **`AbstractScalarPocketDescriptor.java:21-23`** comment says "both shipped
|
||||
descriptors are multi-column" — accurate today, will silently lie when a
|
||||
scalar grid-point descriptor is added.
|
||||
|
||||
---
|
||||
|
||||
## Test-isolation gaps
|
||||
|
||||
- **`CofactorIntegrationTest.groovy:40-43`** mutates
|
||||
`LoaderParams.ignoreLigandsSwitch` in `@BeforeAll` without
|
||||
`@Isolated`/`@ResourceLock("Params")` and without saving/restoring. Compare
|
||||
`CofactorPipelineTest.groovy:55-65` and `CofactorAnalyzeTest.groovy:32-44`
|
||||
which do both correctly.
|
||||
|
||||
- **`LigandMatchingTest`** snapshots `Params.INSTANCE` but is not
|
||||
`@Isolated`/`@ResourceLock`-annotated.
|
||||
|
||||
- **`VolsiteGridPointDescriptorTest` / `VolsiteSmoothGridPointDescriptorTest`**
|
||||
mutate `Params.INSTANCE` in `@BeforeEach/@AfterEach` without the project's
|
||||
standard `@Isolated`/`@ResourceLock("Params")` annotations.
|
||||
|
||||
- **`PocketDescriptorRegistry` / `PocketGridPointDescriptorRegistry`** —
|
||||
`NamedRegistryHelper`-backed `LinkedHashMap` is not synchronized. The
|
||||
public `register/unregister` is exposed for tests but lacks a
|
||||
thread-safety note. If a future `register` happens during a feature
|
||||
extractor read, behavior is undefined.
|
||||
|
||||
---
|
||||
|
||||
## Performance nits
|
||||
|
||||
- **`computeEnergyForPoint` boxes doubles** (above).
|
||||
|
||||
- **`EnergyCalculator.groovy:170`** `config.probeParams[probe]` `EnumMap.get`
|
||||
per neighbor per probe; hoist to a pre-sized `ProbeParams[]` indexed by
|
||||
`probeIdx`.
|
||||
|
||||
- **`PocketGridBuilder.java:83`** `Map<Integer, BitSet> pocketToPointIndices`
|
||||
uses boxed `Integer` keys while the rest of the file goes to lengths to
|
||||
avoid boxing (`LongIntHashMap`, primitive `int[]`). Use `IntObjectHashMap`.
|
||||
|
||||
- **`MorphologicalCloser.fill` clones empty rawShell**
|
||||
(`MorphologicalCloser.java:30`); unnecessary, inconsistent with `NoOpFiller`.
|
||||
|
||||
- **`KdTreeAssigner.computeRawShell` dedup branch is dead**
|
||||
(`KdTreeAssigner.java:41`): every atom returned by the KD tree is in
|
||||
`latticeIndex` by construction.
|
||||
|
||||
---
|
||||
|
||||
## Top-5 if you only fix five things
|
||||
|
||||
1. **Fix `VoxelHashAssigner` cell-prune lower bound** (or drop it and rely on
|
||||
the post-fetch distance check). Restores the assigner-strategy equivalence
|
||||
the docs promise.
|
||||
2. **Apply the rank-gap fix to `PocketGridPymolRenderer`** — mirror what
|
||||
commit `a3efd084` did for ChimeraX.
|
||||
3. **Make energy-feature lazy-init actually thread-safe**
|
||||
(`MethylEnergyFeature`, `AbstractProbeEnergyFeature`); fix `ConcurrencyTest`
|
||||
to construct calculators under contention.
|
||||
4. **Guard `AhojSiteInfo.fromCsvRecord` with `record.isMapped(...)`** for the
|
||||
new `rg`/`n_unp_pockets[_multichain]` columns, so the parser doesn't crash
|
||||
on older "full" CSVs.
|
||||
5. **README/help.txt/`distro/prank.bat` trio**: bump the version badge, fix
|
||||
the `./make-disro.sh` typo, regenerate `help.txt` to list current commands,
|
||||
and bring Windows launcher JVM flags up to parity with the Bash launchers.
|
||||
Reference in New Issue
Block a user