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XDrawChem Changelog

All notable changes to XDrawChem are documented here. Entries are derived from the Debian changelog and commit history.

2.1.0 — 2026-05-25

New Features

  • 3D structure generation restored — Tools → "Build 3D model of molecule" now produces a 3D MDL molfile locally using OpenBabel's OBBuilder for initial coordinate generation followed by 250 steps of MMFF94 (or UFF fallback) conjugate-gradients minimization. The original BUILD3D code called a Fortran-based CGI service on SourceForge that no longer exists; the feature had been disabled with a placeholder dialog. No network call required now.
  • MDL MOL/SDF file I/O — chemdata_mdl.cpp now reads and writes standard MDL MOL and SDF files via OpenBabel, replacing the previous no-op stubs.
  • SDF multi-record browser — When opening an .sdf file via File → Open, a browser dialog lists all records with molecule names and lets the user navigate with Previous/Next, import individual records, or import all at once.
  • CIP R/S and E/Z stereochemistry labels — Tools → "Show CIP labels" toggles display of Cahn-Ingold-Prelog descriptors computed by OpenBabel.
    • R/S (tetrahedral): shown in bold blue text next to chiral centers (e.g. asymmetric carbon atoms with wedge/hash bonds).
    • E/Z (cis/trans): shown at the midpoint of stereogenic double bonds.
    • Labels are cached and only recomputed when the molecule structure changes.

Bug Fixes

  • Memory leaks in application_ob.cpp — OBNewLoad() and OBNewSave() now properly delete temporary OBMol objects.
  • Memory leak in molecule_obmol.cpp — convertToOBMol() no longer leaks the returned OBMol* on error paths.

Qt / C++ Modernisation

  • Remaining SIGNAL()/SLOT() string macros converted to pointer-to-member syntax across application.cpp, render2d_event.cpp, and main.cpp. Zero string-based connect() calls remain in active code.
  • qDebug() runtime noise gated behind QLoggingCategory — all qDebug() / qInfo() / qWarning() calls in the chemistry and I/O layers now use category macros so they can be silenced with QT_LOGGING_RULES=xdc=false.

Code Cleanup

  • netaccess.cpp — removed large commented-out QHttp-based dead code and unreachable slotFinished / slotData / rf slots.
  • Repository cleanup — legacy Qt3/Qt4 source trees removed from master; source directory renamed from xdrawchem-qt5/ to xdrawchem/.
  • Flatpak — cleaned up bare-name desktop/metainfo/icon copies inside the sandbox so appstreamcli compose does not see duplicate <id> entries and reject the build.

Documentation

  • README: updated screenshot to reflect current UI.
  • backlog.md: refreshed to reflect completed v2.1 items.

2.0.1 — 2026-04-23

Security / correctness

  • Fix three instances of malloc/strcpy buffer overflow + use-after-free on QByteArray temporary in OpenBabel format resolution (application_ob.cpp, tool_2d3d.cpp)
  • Fix potential buffer overflow in char type[5] strcpy on user-defined atom labels (molecule_obmol.cpp, ioiface.cpp)
  • Replace system() shell invocation for Ghemical/KryoMol send with QProcess::startDetached to eliminate shell injection risk
  • Remove dead http.cpp/http.h module and dead XDC_SERVER / getenv code paths
  • Fix -Wreorder warning in CMLParser constructor

UI fixes

  • Ring menu: wire Amino Acids, Nucleic Acids, Sugars, and Useful Groups submenus to setRingAction (they were silent since the Qt6 port)
  • Ring menu: add setData() to Useful Groups (FMOC, BOC, DABCYL, DABSYL, DANSYL, EDANS, Biotin) so dispatch actually works
  • Custom ring submenu: restore dispatch via per-action lambda forwarding to FromRingMenu (silent since the Qt6 port; user-saved rings can be placed again)
  • Custom ring save: fix signal-11 crash on save caused by uninitialised ringmenu member pointer in application.h
  • Custom ring menu refresh: swap only the User-defined submenu in place rather than rebuilding the whole ring menu (avoids a paint-device warning and stale defaultAction pointers in drawRingButton)
  • Property panel: refresh on ring placement, name-to-structure, selection change, clipboard operations, undo, text/label edits, delete (previously only refreshed for raw drawing actions)
  • Property panel: track currently-selected molecule rather than always showing the first molecule
  • Amino Acids menu: remove non-natural amino acids (nitrophenylalanine, statine) that can still be retrieved via PubChem lookup

Packaging

  • Debian: bump Standards-Version to 4.7.2
  • Flatpak: app-id renamed to io.github.bryanherger.xdrawchem (Flathub requirement)
  • Flatpak: desktop and metainfo files now install with reverse-DNS filenames
  • Flatpak: OpenBabel build uses cmake-ninja + builddir:true for sandbox correctness
  • DEB and RPM: include the reverse-DNS desktop / metainfo / icon copies in debian/xdrawchem.install and %files (CMake installs both bare and reverse-DNS names; both packaging systems are strict about unpackaged files)
  • RPM %files: use literal io.github.bryanherger.* glob patterns so future reverse-DNS additions (e.g. MIME icons) don't need spec changes
  • Added index.html for GitHub Pages redirect to repo

2.0 — 2026-04-09

Infrastructure / CI

  • Flatpak: fix RapidJSON 1.1.0 const-member build error on GCC 14 (-fpermissive)
  • Flatpak: pre-install RapidJSON as a module; add --disable-rofiles-fuse
  • Release: fix DEB filename collision when noble and jammy extracted together
  • Windows: replace Chocolatey/SourceForge NSIS fallback with winget install NSIS.NSIS

(All rc4 changes below)

2.0rc4 — 2026-04

Bug fixes (UAT)

  • Dative bond toolbar button now shows a distinct half-arrow icon (was blank)
  • Dative bond rubber-band preview now draws correctly while dragging
  • Arrow tool: clicking the button face now activates the last-chosen arrow type
  • Arrow tool: bracket_type properly initialised so first use draws the correct arrow

Infrastructure

  • Dead woodsidelabs.com endpoints replaced with PubChem REST API
    • "Find on PubChem…" (Ctrl+F) now searches PubChem by name, CAS, or formula
    • Molecule Information dialog (Ctrl+I) now populates CAS, IUPAC name, synonyms
  • netaccess.cpp rewritten: NetAccess is now a plain QObject (not a QDialog)
  • "Build 3D model" menu item shows informative dialog (server was defunct)
  • CMake: generated/defs.h output directory avoids name collision with executable
  • All deprecation warnings cleared on Linux (GCC 13), macOS (Xcode 16), Windows (MSVC)

2.0rc3 — 2026-03-31

New features

  • Name-to-structure: Tools → "Name to structure…" accepts IUPAC, common, and CAS names via PubChem REST API (backlog 5.7)
  • InChI input: SMILES dialog detects InChI= prefix and routes through OpenBabel (5.8)

Infrastructure

  • Single VERSION file at repository root; all four platform builds read from it
  • defs.h.in template with @APP_VERSION@ placeholder; CMake stamps it at build time
  • About/Support dialogs: replaced SourceForge URLs with GitHub repo and issues links
  • All 13 translation files updated to match new C++ source strings
  • RPM spec: %{xdcver} macro; -DAPP_VERSION passed through Docker via environment
  • RPM %files: added xdrawchem.metainfo.xml
  • macOS: ob_compat.h force-included for Xcode 16 / libc++19 (removes std::binary_function)
  • Windows: NSIS makensis.exe found dynamically; ilammy/msvc-dev-cmd replaced with inline vcvarsall.bat x64

2.0rc2 — 2026-03-30

New features

  • Dative (coordinate covalent) bond type (bond order 9, half-arrowhead rendering)
  • ACS publication style preset
  • Improved SVG export via Qt6 QSvgGenerator
  • Copy as SVG or 300 dpi PNG to clipboard
  • Canonical SMILES output via OpenBabel
  • IUPAC name lookup via PubChem REST API
  • PubChem structure browser integration
  • Valence checking
  • PDF export
  • Georgian translation (contributed by EkaterinePapava)

Bug fixes

  • Qt 6.2 compatibility: QMenu::addAction argument order fixed in application.cpp and helpwindow.cpp (keysequence must be last argument)

Testing

  • 13 test suites, 274 tests, all passing

2.0rc1 — 2026-03-26

Port to Qt6 + CMake

  • Zero build warnings or errors against Qt 6.2+
  • CMakeLists.txt replaces legacy qmake .pro files
  • QXmlSimpleReader → QXmlStreamReader (removed in Qt6)
  • QHttp usage removed (removed in Qt5)
  • 266 Qt3-era foreach → C++11 range-for loops
  • Old-style SIGNAL/SLOT macros → pointer-to-member syntax throughout

Bug fixes

  • Fix #9: double bond inner-line geometry at non-linear angles
  • Fix #10: "Clean up molecule" preserves molecule orientation (Procrustes alignment)
  • Fix #13: curved arrow tips aligned using arc tangent direction
  • Fix #14: Bézier arrow drawing (was entirely non-functional)
  • Fix #15: SMILES output no longer produces ** (MDL Molfile column fix)
  • Fix #18: OpenBabel 3 builds without manual .pro file editing

Infrastructure

  • GitHub Actions CI for DEB (Ubuntu 24.04), RPM (Rocky 9), Windows (MSVC), macOS
  • AppStream xdrawchem.metainfo.xml for GNOME Software / KDE Discover
  • .desktop file and application icon for desktop integration

Testing

  • 261-test unit suite (10 suites), executed during every build

1.10.2 — 2016-12-11

  • Initial Debian packaging