PLAN.md and SPEC.md were pre-implementation design docs for the pocket-grid
feature. The feature has shipped, so they're frozen artifacts in the active
todo/ namespace. Delete them and strip the three "see SPEC.md" comments that
pointed at SPEC.md from Main.groovy and the predict/rescore routines.
Also reassess the PyMOL rank-gap entry in the audit: P2Rank ranks pockets
contiguously throughout the predict path and all in-tree loaders (except
SiteHoundLoader), so the previously-listed "renderer ignores rank gaps" is
cosmetic-only (empty objects in the Models panel for small pockets whose
filled BitSet ended up empty). Downgrade to a parity nit under
Inconsistencies; promote the PUResNet surfaceAtoms re-linking to the Top-5.
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.
The -cofactors flag and dataset cofactors column accept LigandDefinition
specifiers ("FAD", "FAD[atom_id:N]", "FAD[contact_res_ids:A_T259,A_D246]").
Matched HET groups merge into the protein surface (proteinAtoms) and are
excluded from ligand listings; per-item resolution lets a dataset column
override the global Params.cofactors.
New: analyze cofactors subcommand (HETATM survey + specifier dry-run),
PyMOL teal-stick visualization (vis_highlight_cofactors), distant-cofactor
and chain-excluded WARN diagnostics, aa_mapping collision WARN (R19),
drop-in safety benchmark with byte-equality on a never-present specifier.
Documentation in documentation/cofactors.md (user-facing) and
documentation/dev/cofactors.md (engineering record with R1-R24 design choices
and post-merge audit fixes). Tests in CofactorHandlerTest,
CofactorIntegrationTest, CofactorPipelineTest, CofactorAnalyzeTest,
DataTableCsvTest plus a Log4jCapture test helper.
