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

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

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

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

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

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

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

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

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(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

fix(md): surface real OpenMM error message + traceback in fallback diagnostics

fix(md): add missing C-terminal OXT so unterminated termini (1TIM HIS 248) build in OpenMM

fix(md): BioPython fallback crash on Atom.element.name ('str' object has no attribute 'name')

feat(md): temperature/KE, Rg and SASA traces; fix OpenMM in deployed image

feat(md): real OpenMM production runs with accurate Ca RMSD

fix: harden BLAST pipeline against NCBI timeouts and server overload

feat: expanded Domain & Motif Analysis with all features and cross-project links

test: comprehensive validation & fuzz testing with bug fixes

fix: case-insensitive accession lookup - normalize to uppercase at entry points

fix: AlphaFold lookup for NCBI RefSeq accessions

fix: BLAST pipeline crash — accession misclassification + missing error handling

fix: num_aromatic_rings -> n_aromatic_rings in CYP panel

feat: ADMET 3a/3b split — mark RDKit descriptors as production, toxicity/ADMET as rule-based heuristic

fix: wrap all Fragments.fr_* calls in safe _fg() wrapper

fix: mol_volume fallback referenced labute_asa before definition

fix: MolVolume with triple fallback (CalcMolecularVolume -> Descriptors3D -> ASA estimate)