Bumps faster-molecular-surface 1.0 -> 1.1, vendored in
lib/local-mvn-repo/. The 1.1 release adds a VdW radius fallback for
elements whose CDK Elements enum entry is null (Co, Ni, Cu, Rh, Os, Ir,
plus radioactive/synthetic). Without the fix, cobalamin-bearing
structures crashed surface computation under -cofactors.
PatchedCdkNumericalSurface wraps the default CDK NumericalSurface (used
when -use_optimized_surface 0) with the same fallback, via a Krypton
proxy for null-VdW atoms. Surface.groovy switched over to it. Unit tests
mirror the FMS-side regressions.
AnalyzeRoutine.cmdCofactors: replace Struct.getHetGroups with
Struct.getLigandGroups (2 call sites) so GDP/GTP/ATP and other groups
that BioJava classifies as NUCLEOTIDE/AMINOACID don't get falsely
reported as "name not in structure" in cofactor_matches.csv or omitted
from het_groups.csv. Mirrors the M1 fix applied earlier to
CofactorHandler.extractCofactorAtoms.
testsets.sh: new cofactors_full() function exercising the cofactor
demo + full datasets in p2rank-datasets2/other/cofactors/ (predict,
analyze cofactors, -aa_mapping composition, visualizations,
export-points). Uses -fail_fast 1 so per-structure errors surface as
test failures rather than silent skips.
- Add NativePanamaForest/NativePanamaForestAvx2 availability checks in ModelConverter
- Refactor flattening logic to separate trainable forest preparation from conversion
- Track all eval times and compute average excluding first run (caching warmup)
- Rename TIME_M to TIME_TRAINEVAL_AVG_M, add TIME_EVAL_AVG_M stat
Replace flat jar with local Maven repo dependency at correct path
(groupId/artifactId/version/). Fix GString-to-String type errors in
AnalyzeRoutine that broke compilation with @CompileStatic.
