sketch

A desktop chemical structure editor (Qt 6 / QML) for drawing, editing, and analyzing molecules — 2D structure drawing, reactions, biopolymer sequences, and a growing IUPAC name generator, backed by the Indigo cheminformatics toolkit.

Features

• 2D molecule drawing and editing (atoms, bonds, rings, templates, R-groups)
• Reaction drawing and biopolymer sequence support
• Structure cleanup/layout, aromatization, InChI/SMILES conversion, and CIP stereodescriptors via Indigo
• Chemical-structure-image recognition (OCR) via Imago for the Insert Image feature
• A from-scratch IUPAC name generator (src/app/IupacNamer.cpp) built incrementally against the official Blue Book text — see IUPAC Blue Book Coverage.md for current section-by-section coverage

Tech stack

• UI: Qt 6 Quick / QML (Sketch.App QML module), Fluent Windows 11 style
• Backend: C++20 (src/app/), a pure in-process document model (DocumentState, EditableMolecule) with no scripting layer — exposed to QML via Q_INVOKABLE
• Chemistry: Indigo toolkit (indigo.dll), Imago (imago.dll)
• Build: CMake 3.24+, qt_add_executable / qt_add_qml_module
• Platform: Windows only (the build links .dll/.lib files directly; no Linux/macOS path exists in CMakeLists.txt today)

An earlier version of this app ran its chemistry logic through an embedded QuickJS-ng script engine (chem-core.js, src/worker/*.js). That engine has been fully retired — every document now runs on the C++ DocumentState model exclusively — and its files were relocated (not deleted) to archive/js-engine/ for reference.

Installation

This project only builds on Windows today, with the MinGW toolchain (not MSVC — the vendored Indigo/Imago DLLs are MinGW-built and their exports are not directly linkable by link.exe).

1. Prerequisites

Install these first, in any order:

• Qt 6.6 or newer (developed against 6.11.1) with the MinGW 64-bit kit, via the Qt online installer or the aqtinstall command-line tool. You need at minimum the Core, Gui, Qml, Quick, QuickControls2, and Concurrent modules — these are included in a standard Qt Quick installation.
• The MinGW toolchain that ships with Qt's MinGW kit (e.g. C:\Qt\Tools\mingw1310_64, or a standalone C:\mingw64 install using the same GCC major version as your Qt kit). This must be a real, separate MinGW install on disk — do not rely on a different MinGW/MSYS2 copy (e.g. one bundled with Git Bash, Conda, or MSYS2) being first on PATH, since a mismatched libstdc++/libgcc ABI causes runtime crashes (STATUS_ENTRYPOINT_NOT_FOUND) that look unrelated to any code change.
• CMake 3.24 or newer — https://cmake.org/download/ (or winget install Kitware.CMake).

2. Vendor Indigo and Imago

Indigo and Imago are not committed to this repository (they're large binary SDKs — see .gitignore and THIRD-PARTY-NOTICES.md) and must be placed on disk yourself, at the repo root, before configuring the build:

indigo/
    LICENSE
    api/c/indigo/            (indigo.h and friends)
    api/c/indigo-inchi/
    api/c/indigo-renderer/
    lib/
        indigo.dll
        indigo-inchi.dll
        indigo-renderer.dll

imago/
    LICENSE
    include/
        imago_c.h
    lib/
        imago.dll

Both are Apache-2.0 (EPAM Systems). Build them yourself from source with your MinGW toolchain — https://github.com/epam/indigo and https://github.com/epam/Imago — matching the directory layout above, or obtain a prebuilt MinGW-compatible distribution from elsewhere and copy the headers/DLLs into the same layout. CMakeLists.txt expects these exact paths (indigo/api/c/..., indigo/lib/*.dll, imago/include/imago_c.h, imago/lib/imago.dll); nothing else about their internal build process matters to this project.

3. Configure

From the repo root, in PowerShell (not Git Bash's own shell — it may resolve a different mingw32-make/compiler than the one Qt's CMake integration expects):

cmake -B build -G "MinGW Makefiles" `
    -DCMAKE_PREFIX_PATH="C:\Qt\6.11.1\mingw_64" `
    -DCMAKE_C_COMPILER="C:\mingw64\bin\gcc.exe" `
    -DCMAKE_CXX_COMPILER="C:\mingw64\bin\g++.exe"

Adjust CMAKE_PREFIX_PATH to your actual Qt kit path and the compiler paths to your actual MinGW install. Without an explicit -G "MinGW Makefiles", CMake may default to a Visual Studio generator it finds on the machine and then fail to locate Qt6 at all (Qt6Config.cmake not found) — the generator and the Qt kit must be the same toolchain family.

4. Build

$env:PATH = "C:\mingw64\bin;$env:PATH"
C:\mingw64\bin\mingw32-make.exe -C build -j4

This builds the sketch executable plus 10 standalone test executables (see Testing below). A post-build step copies indigo.dll/indigo-inchi.dll/indigo-renderer.dll/ imago.dll from step 2 next to sketch.exe, and copies assets/monomer_library.ket into indigo/data/molecules/basic/ — both automatic, no manual copying needed.

5. Run

.\run_sketch.bat

run_sketch.bat (not committed to git — create it yourself if missing) puts Qt's mingw_64\bin and indigo\lib on PATH before launching, since Windows resolves DLLs from PATH when they aren't next to the .exe:

@echo off
set PATH=C:\Qt\6.11.1\mingw_64\bin;%~dp0indigo\lib;%PATH%
start "" "%~dp0build\sketch.exe"

Or run build\sketch.exe directly, provided the same two directories are already on PATH in that shell.

Reconfiguring after moving/removing vendored files

If you ever delete or move build/ and reconfigure, or if CMake reports it can't find a subdirectory that used to exist, delete the stale cache first — CMake refuses to switch generators or toolchains in place:

Remove-Item build\CMakeCache.txt, build\CMakeFiles -Recurse -Force

Then repeat step 3.

Testing

Ten standalone C++/Qt test executables are registered with CTest — built automatically by the same mingw32-make -j4 from step 4 above:

cd build
ctest --output-on-failure

Expected: 100% tests passed, 0 tests failed out of 10.

Test	Covers
iupac_namer_test	The IUPAC namer's own growing regression suite
fused_ring_orientation_test	Geometric ring-orientation module, used by the IUPAC namer's degree-3+ branching-fusion mechanism (IupacNamer.cpp's computePreferredOrientation call)
fused_ring_direction_detector_test	Geometric ring-direction module, used by the same branching-fusion mechanism (IupacNamer.cpp's detectFusedRingDirections call)
editable_molecule_test	Core molecule-editing operations
document_state_test	Document-level state (undo/redo, selection, commands)
render_primitives_test	Geometry → render-primitive conversion
sdf_batch_test	SDF/RDF batch import
clipboard_preview_test	Clipboard paste-preview geometry
biopolymer_sequence_view_test	Biopolymer sequence view snapshot model
render_primitives_to_variant_test	Render-primitive → QML-variant conversion

Project layout

src/app/          C++ backend: DocumentState (document model), EditableMolecule,
                   IndigoService, ImagoService, IupacNamer, AppController
src/v8_process.*  QML-facing command surface (name is historical — no JS engine
                   behind it anymore; every command runs on DocumentState directly)
*.qml             UI: MainWindow, ChemCanvas, panels, dialogs, toolbars
js/               Small live QML-side JS utility modules (Selection, ToolLabels,
                   ThumbnailPainter) — unrelated to the retired scripting engine below
tests/            C++ test suites (see Testing above)
archive/js-engine/  The retired QuickJS-ng-based chemistry engine (chem-core.js,
                   the old worker/*.js command scripts, qjs_engine.*, the vendored
                   quickjs-ng source) — kept for reference, not built
indigo/, imago/   Vendored Indigo/Imago headers and DLLs (not committed — see
                   Installation above)
docs/             Design/analysis notes

Documentation

• IUPAC Blue Book Coverage.md — IUPAC namer coverage tracked against the Blue Book
• THIRD-PARTY-NOTICES.md — third-party licenses (Ketcher, Indigo, Imago)
• Architecture Map.md / Features To Be Implemented.md — kept locally as working notes, not committed to this repository (see .gitignore)

License and third-party notices

This repository does not currently declare its own license. See THIRD-PARTY-NOTICES.md for the licenses of bundled third-party components (Ketcher, Indigo, Imago — all Apache License 2.0).