fix: pin python:3.11-slim-bookworm — trixie's gcc14 errors on fpocket's legacy C (incompatible-pointer-types); gcc12 builds clean

fix: fpocket clone tag 4.2.3 — tags carry no v prefix; wrong tag broke HF Space build (503s)

feat: techspec additions — de novo tier-6 branch, structure export, page capture + final synthesis

feat: optimize CASTp SASA with KDTree, add sequence input to CASTp + Structure Prep, ESMFold integration for unknown genes

fix: remove fpocket from Dockerfiles to unblock HF Spaces build

fix: fpocket build — correct tag 4.2.3, add libnetcdf-dev dependency

feat: structure preparation pipeline — broken chains → SWISS-MODEL repair → PyMOL cleanup → fpocket + CASTp

fix: PDBParser.get_pdb -> get_structure in castp.py

feat: add CASTp pockets, SWISS-MODEL, ESMFold + fix Dockerfiles

fix: NGS fallback to Python aligner when native tools missing; add missing re import in sequence_utils

fix: add --no-same-owner to worker Dockerfile tar command

fix: add --no-same-owner to backend Dockerfile tar commands

refactor: require native samtools/minimap2, delete hand-rolled BAM/BAI code

fix: correct BGZF virtual offsets in BAI, fix duplicate-read bug, install minimap2 everywhere

fix(ngs): dynamic locus + SAM-first igv.js for reliable genome browser

fix: repair BAI index generation and BAM record format for igv.js compatibility

fix(ngs): correct BAM record format and BAI index for igv.js

feat(ngs): pure-Python SAM to BAM converter with BGZF + BAI index for igv.js

chore: remove NGS rate limits

chore: increase daily rate limits for testing (50 global, 20 NGS)

fix: igv.js white screen — CIGAR ops, qual strings, locus format

feat: add igv.js genome browser + proper 6-step NGS pipeline

fix: NGS pipeline stuck in queued - worker fallback + migration fix

feat: add full 6-step NGS pipeline + fix sequencing WinError 193

feat(pipeline): multi-database UniProt identifier resolution

fix(pipeline): stop abandoning slow NCBI BLAST jobs + EBI fallback

feat(results): in-app share dialog + self-normalized dotplot scoring

feat(admet): ProTox 3.0 ML toxicity prediction — backend client + endpoint, frontend ProTox tab, restored sidebar chevron

feat(seq-tools): motif categories & structure overlay, dot-plot scoring & features, cross-tool links

feat(seq-tools): add sequence utilities, motif scanner and dot plot tools with frontend pages

feat(primers): add NCBI gene search + sequence retrieval, oligo QC and in-silico PCR verification with recharts graphs

fix(function-predict): add BP term, real AA composition, JSON export, UniProt distinction, and /learn topic

fix(pathways): read enrichment results from projection response, add p-value and gene ratio

Docking: flatten multi-chain obabel receptor output to a single model

Fix docking on Windows: resolve obabel from venv, use Windows Vina binary

Fix pipeline MSA/AI stall, add SwissADME-parity ADMET panel, PubChem search, docking ligand data

Add MSA pairwise refinement, new UI components (SmoothLoader, Reveal, CursorGlow, Parallax), rate-limit handling in AIInterpretation

Fix AI model fallback chain and enrich share message with result details

Fix share links, persist wizard jobs, add AI interpretation fallback, animate landing

Add global/local BLAST modes, full-length pairwise alignment view, standalone pairwise tool

feat(docking): Vina full-detail — parse 1.2.7 log (RMSD l.b./u.b., version, seed), RMSD table + run-config UI (3e)

feat(uniprot,domains): reviewed/organism filters + debounce/fast-path, PROSITE raw-sequence scan UI (3c,3d)

feat(alignment): multi-method MSA (clustalo/muscle/kalign/mafft/tcoffee) with method selector (3b)

feat(alignment): pairwise global/local alignment via BLAST hit 'Align pair' (3a)

feat(md): verified force field/solvent menu (ff14SB/ff15ipq/ff19SB/amberfb15/CHARMM36 x OBC1/OBC2/GBN2) with alanine-dipeptide createSystem startup probe; explicit errors for invalid combos; dynamic frontend menu

fix(blast): honor program/db/max_hits params, accept DNA queries, poll cap 65 min

fix(md): raise production budget to 25 min so runs aren't clamped to ~3 ps

fix(md): don't abandon long jobs after 5 min + trim workload

feat(md): clay simulation-parameter controls (force field, solvent, run length)

fix(md): reflect OXT across C-CA axis so GBSA stops NaNing on Linux CPU