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c78519c98e
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.
here are 3rd party libraries that are not easily accessible from online repositories FastRandomForest is a Random Forests implementation by Fran Supek https://code.google.com/archive/p/fast-random-forest/ https://github.com/rdk/FasterForest local-mvn-repo is here to temporary hold jars and poms of modified libraries.