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XDrawChem — Consolidated Backlog

Compiled from all session history, GitHub issues, Debian tracker, and competitive analysis As of v2.0.1 — April 2026

[BryanH - I will work on some or all of these eventually, but if anything here should be a priority, copy the item and create an issue]

Status at v2.0.1

Completed in v2.1 cycle:

  • 3D structure generation restored using local OpenBabel (OBBuilder + MMFF94/UFF minimization)
  • MDL Mol/SDF I/O fully implemented via OpenBabel (was previously stubbed out)
  • SDF multi-record browser UI for browsing and importing individual records
  • CIP R/S and E/Z stereochemistry labels computed via OpenBabel stereo API
    • Tetrahedral R/S labels shown next to chiral centers
    • Cis/trans E/Z labels shown at double-bond midpoints
    • Toggle via Tools → Show CIP labels
  • Memory leaks in OBNewLoad, OBNewSave, convertToOBMol() fixed
  • All SIGNAL()/SLOT() macros converted to pointer-to-member syntax
  • qDebug() calls gated behind QLoggingCategory (xdc_logging.h/cpp)
  • Legacy Qt3/Qt4 source trees removed from master
  • Source directory renamed from xdrawchem-qt5/ to xdrawchem/
  • Flatpak appstream duplicate-component issue fixed
  • debian/watch file added for Debian tracker compatibility
  • Release build: zero compiler warnings

Completed in v2.0.1 cycle (post-v2.0):

  • Security: buffer-overflow UB in OpenBabel format resolution + atom-label strcpy fixed
  • Security: shell injection risk in Ghemical/KryoMol launch eliminated (QProcess::startDetached)
  • Ring menu: AA / NA / Sugars / Useful Groups / Custom rings dispatch restored
  • Property panel updates on every data-mutation path (draw, ring, NTS, paste, undo, delete, selection)
  • Flatpak: full Flathub-ready manifest with reverse-DNS app-id
  • DEB / RPM: reverse-DNS file copies included alongside bare names
  • Debian Standards-Version bumped to 4.7.2

Completed in rc3→rc4 cycle:

  • Replaced dead woodsidelabs.com endpoints with PubChem REST API (2.2, 2.3)
    • "Find on PubChem…" (Ctrl+F) searches by name, CAS, or formula
    • Molecule Information dialog (Ctrl+I) populates CAS, IUPAC name, synonyms
  • Dative bond toolbar icon now shows a distinct half-arrow XPM (2.4)
  • Dative bond rubber-band preview fixed during drag
  • Arrow tool: button-click now activates last-chosen arrow type
  • Arrow tool: bracket_type initialised so first use draws correct arrow
  • Live property panel (4.5): docked widget showing MW and formula, hidden by default; enable via Tools → Properties
  • CHANGELOG.md created from debian/changelog and session history (2.5)
  • Ubuntu 22.04 (Jammy) DEB added to CI matrix (3.1)
  • Fedora 41 RPM added to CI matrix (3.2)
  • Flathub manifest io.github.bryanherger.xdrawchem.yml + CI workflow (3.5)
  • AppStream metainfo.xml: fixed name tags, added rc3/rc4 releases, screenshot URL updated
  • Lone pairs / orbitals / charges: confirmed already implemented via SYM_* symbol system (SYM_2E, SYM_PLUS, SYM_MINUS, p_orbital, etc.) — no further work needed (5.3)

Completed previously (rc1–rc3):

  • Qt6 + CMake port, all deprecation warnings cleared on all platforms
  • 13 test suites, 274 tests, 100% passing
  • Bugs fixed: #9–#19 (geometry, arrows, SMILES, OpenBabel 3, translations)
  • Features added: IUPAC/PubChem naming, valence checking, PDF/SVG/PNG export, ACS style, dative bond, canonical SMILES, name-to-structure, InChI input
  • CI/CD: Windows (MSVC + NSIS), macOS (DMG), DEB (Ubuntu 24.04), RPM (Rocky 9), Release workflow
  • Single VERSION file at repo root; About/Support dialogs updated with GitHub links

SECTION 1 — Open GitHub Issues

Check https://github.com/bryanherger/xdrawchem/issues for any new ones.

SECTION 2 — Code Quality / Technical Debt

2.5 CHANGELOG.md — Created. Keep updated going forward; debian/changelog is the source of truth.

2.6 Help window HTML docs — The doc/ folder contains aging HTML that references Qt3-era UI. Could be modernised in place or linked to a GitHub Wiki.

SECTION 3 — Platform & Distribution

3.4 debian/watch file — ✅ Added. The Debian tracker can now track upstream releases automatically.

3.5 Flathub submission — Manifest created and CI workflow added. Actual submission requires a PR to github.com/flathub/flathub — do this after v2.1 ships.

3.8 Repository screenshot — Added (xdrawchem_screenshot_0.png). AppStream metainfo updated to reference it.

SECTION 4 — Feature Parity: Medium Priority

4.1 CIP R/S and E/Z stereochemistry labels — ✅ Implemented. OpenBabel's OBStereoFacade perceives tetrahedral (R/S) and cis/trans (E/Z) configurations. Labels are rendered in bold blue text next to chiral centers and at double-bond midpoints. Toggle via Tools → Show CIP labels. Encoding in CML/Molfile output remains for future work. Target: v2.1

4.2 Atom-to-atom reaction mapping — Numbers atoms across a reaction arrow. Needs new UI mode, DPoint field, and RXN format. High effort. Target: v2.1 or later

4.3 MDL SDF / RXN file support — ✅ Core I/O implemented in chemdata_mdl.cpp via OpenBabel. SDF browser UI added for multi-record navigation. RXN format support remains for future release. Target: v2.1

4.4 Formal charges and isotope labels on atoms — The bond-edit dialog has +/− radio buttons but they insert cosmetic text, not chemically meaningful Molfile charge fields. DPoint needs a formal_charge member and serialization in XDC/CML/MDL formats. Target: v2.1

4.5 Live property panel — Implemented (hidden by default). Update trigger coverage confirmed on all major paths. Could be promoted to enabled-by-default after wider testing. Polish in v2.1

4.6 Functional group / fragment template browser — Categorised palette for Boc, Fmoc, TBS, Bn, etc. Library curation + browseable UI. Target: v2.1 or later

4.7 S-Groups and polymer notation — SRU brackets, superatom abbreviations. Requires new data model. Target: v2.2

SECTION 5 — Feature Parity: Lower Priority

5.1 Structure-from-image OCR (OSRA) — Large integration project. Target: v2.2

5.2 Fischer, Haworth, and Newman projection tools — Medium effort for drawing; auto stereo assignment is harder. Target: v2.1 or later

5.4 Electron pushing arrows (mechanism tools) — Fishhook and two-electron arrows anchored to bonds/atoms. Existing curved arrow infrastructure is a starting point. Target: v2.1

5.5 Superscript/subscript in text labels — Qt QTextDocument rich text could handle this. Target: v2.1

5.6 SMARTS input — OB SMILES reader accepts most SMARTS already. True SMARTS output needs OB's writer. Low priority unless requested.

SECTION 6 — CI/CD & Infrastructure

6.1 GPG-signed packages — Neither RPM nor DEB are signed. Needed for proper apt/dnf repository hosting.

6.2 Apt/DNF repository hosting — Host on GitHub Pages so users can apt install xdrawchem.

6.3 Release workflow robustness — Current poller has a 20-minute timeout. workflow_run trigger would be more reliable once GitHub supports tags.

6.4 Ubuntu 22.04 DEB in release — Added to CI. Wire into release artifact download in release.yml once confirmed stable.

6.5 Code coverage reporting — gcov/lcov + Codecov upload.

6.6 Lintian clean — One lintian warning outstanding on the DEB.

SECTION 7 — Documentation

7.1 GitHub Wiki — Replace aging HTML help docs.

7.3 PACKAGING.md — Add Windows and macOS sections.

7.4 Keyboard shortcuts reference — One-page cheat sheet.

Priority Summary for v2.1 Planning

Priority Item Effort Notes
🔴 High 4.1 CIP R/S, E/Z labels Medium ✅ Labels rendered; CML/Molfile encoding remains
🔴 High 4.3 SDF / RXN file support Medium ✅ Core I/O + browser UI done. RXN remains
🟡 Medium 4.4 Formal charges + isotopes Medium Molfile chemical correctness
🟡 Medium 4.5 Property panel polish Low Could be enabled-by-default
🟡 Medium 3.5 Flathub PR submission Low Submit after v2.1 ships
🟡 Medium 5.4 Electron pushing arrows Medium Mechanism drawing
🟢 Lower 4.2 Reaction atom mapping High Important for reaction DBs
🟢 Lower 4.6 Fragment template browser Medium Organic chemistry workflows
🟢 Lower 6.1 GPG-signed packages Medium Security/trust
🟢 Lower 3.4 debian/watch file Low ✅ Done
🟢 Lower 5.1 OSRA image OCR High Very useful but large