Redesign Vina log panel + fix z-index overlay in docking viewer

DockingViewer: use correct pdbe-molstar viewerInstance API for representation switching

DockingViewer: full toolbar with representation/color switching, screenshot, camera controls

Fix Molstar drag: remove overflow-hidden, use direct container without absolute positioning

Fix loading overlay: detect Molstar via canvas element, add event listener, remove blocking z-index

Fix Molstar viewer: prevent double-init, fix container sizing, separate interaction updates

Fix DockingViewer: use pdbe-molstar web component instead of broken JS API

Docking viewer upgrade: Molstar GPU rendering, proper interaction geometry, 3D dashed-line rendering

Fix docking route mismatches: GET /status/{id}, frontend pdb URL prefix

fix: add missing /api prefix to audit fetch URLs so rewrite proxy reaches backend router at /api/audit/event

feat: add interaction fingerprinting and 3Dmol.js viewer to molecular docking page

feat: add query coverage, organism, and query accession to BLAST results

fix: stabilize useAuditTrail return reference with useMemo, remove setLoading(true) from effect re-fetches

fix: remove opacity:0 flicker from all pages

fix: prevent opacity flicker on job results page, add pathway_enrichment migration

fix: handle NCBI UNKNOWN status and add pathway_enrichment to frontend status order

feat: add DNA sequence output across BLAST, UniProt, sequencing, primers, and SequenceRetrieval

fix: resolve Vercel build errors (handleFind, SAMPLE_DNA, Set iteration)

feat: add Translate CDS tool to /analyze/tools page

feat: implement 8 tool bridges (F1-F8) + audit child components

fix: prevent page scroll when zooming phylo tree (non-passive wheel listener)

feat: interactive phylo tree — pan/zoom, hover highlight, collapse/expand, node selection

feat: improve phylo tree viz — branch length labels, bigger nodes, hub labels, tooltips, ML recommendation

feat: instrument 7 tool pages with usage audit trail

feat: 4-layer audit/observability system

Fix pipeline stuck issue: synthetic FASTQ fallback and demo mode

Fix sequencing dropdown: hardcoded defaults so dropdown works before backend deploys

Phase 3: Sequencing pipeline (FASTQ -> QC -> alignment -> variant calling -> report)

fix: replace iframe structure viewer with PDBe Molstar web component

fix: replace broken PDBe embed URL with Mol* viewer (molstar.org)

feat: molecular docking (AutoDock Vina) + docs site + Sentry + cache stats + Phase 2 docs update

fix: replace dead embed.rcsb.org iframe with PDBe Mol* viewer

feat: complete Phase 2 — API keys, share links, export, pipeline steps, guest upgrade

refactor: enhance dashboard with quick tools, jobs with filter tabs, settings with profile identity

fix: default import PhyloTreeViewer in alignment, report, and PipelineResults

feat: dedicated phylo router (NJ/UPGMA/ML), local PhyML binary, standalone phylo page, PhyloTreeViewer redesign

fix: accurate phylogenetic tree visualization — proportional branch lengths, scale bar, bootstrap labels, circular layout mode

feat: in-memory pipeline v2 with MSA, phylo tree, domains; PipelineResults component; standalone phylo page; report page; wizard step checkboxes

fix: convert AlignmentView.tsx light-theme classes to dark void theme tokens

fix: use embed.rcsb.org instead of www.rcsb.org for clean 3D viewer iframe

feat: add PNG/TSV/JSON/CSV/FASTA export to all 8 tool components

fix: use STRING-DB image API for accurate PPI diagram, add PNG/TSV/copy export buttons

fix: primer error handling, interactions scores, structure comparison API

fix: forward backend error detail in 4 components

fix: handle non-200 responses in domains, interactions, ramachandran, SS components

feat: domains, interactions, primers, structure analysis, wizard, phylo tree, conservation

Fix invisible fonts in Reactome DiagramJs: isolate widget from dark-theme CSS overrides

Add Reactome diagrams, KEGG search, pathway enrichment (pipeline + standalone)

Security, crash fixes, demo prep, dead code removal

Fix structure viewer iframe: embed.rcsb.org is dead → use www.rcsb.org/3d-view/{pdbId}