Installing on Windows

How to build MolForma from source on Windows with Microsoft Visual C++ (MSVC) and install it into a folder. The libraries for the build (RDKit and VTK among them) come from vcpkg and from source; NWChem for calculations goes into Ubuntu on WSL (Windows Subsystem for Linux).

The steps are for Windows 11 (x64) and MolForma 1.0.0. They were checked on 2026-10-28 on Windows 11 Home with Visual Studio Community 2026 (Verified configuration).

There is no installer or binary download of MolForma for Windows. You build it from the source on GitHub, and cmake --install makes a MolForma folder that holds the Qt and Open Babel files it needs. NWChem has no official Windows build, so the Ubuntu package in WSL is used, started through two batch files that come with MolForma (nwchem.cmd and mpirun.cmd).

Required software

• Open Babelit is not in vcpkg, so it is built from source with MSVC (3. Build Open Babel).
• RDKit and VTKboth are optional and are enabled only when CMake finds them at build time (4. Build RDKit and VTK (optional)). Without VTK, QPainter (CPU) draws the 3D view (3D rendering).
• Pythonused neither for building nor at run time.

Run the commands below in “x64 Native Tools Command Prompt for VS” from the Start menu (a command prompt set up for MSVC). The working folder is C:\dev.

1. Install Visual Studio, Git and Qt

1. Install Visual Studio (Community is fine) with the workload “Desktop development with C++”. It brings MSVC, the Windows SDK and “C++ CMake tools for Windows” (CMake and Ninja).
2. Install Git for Windows. Its Perl (C:\Program Files\Git\usr\bin\perl.exe) is used to build Open Babel.
3. Install Qt with the Qt Online Installer, choosing “MSVC 2022 64-bit” under a Qt 6 version (a Qt account is needed). Below it is in C:\Qt\6.11.2\msvc2022_64. Qt for MSVC 2022 also works with the MSVC of Visual Studio 2026.

2. Install the libraries with vcpkg

Get vcpkg and install Eigen, zlib and libxml2.

cd /d C:\dev
git clone https://github.com/microsoft/vcpkg.git
vcpkg\bootstrap-vcpkg.bat -disableMetrics
vcpkg\vcpkg install --triplet x64-windows eigen3 zlib libxml2[core]

The headers, libraries and DLLs go into C:\dev\vcpkg\installed\x64-windows.

3. Build Open Babel

Get the source of Open Babel 3.2.1, build it and install it into C:\dev\openbabel-install.

cd /d C:\dev
git clone -c core.autocrlf=false -c core.eol=lf --depth 1 --branch openbabel-3-2-1 https://github.com/openbabel/openbabel.git
cd openbabel
cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=C:/dev/openbabel-install ^
  -DCMAKE_PREFIX_PATH=C:/dev/vcpkg/installed/x64-windows -DOB_USE_PREBUILT_BINARIES=OFF ^
  -DWITH_INCHI=OFF -DWITH_MAEPARSER=OFF -DWITH_COORDGEN=OFF -DBUILD_GUI=OFF -DENABLE_TESTS=OFF ^
  "-DPERL_EXECUTABLE=C:/Program Files/Git/usr/bin/perl.exe"
cmake --build build -j 4
cmake --install build

• -c core.autocrlf=false -c core.eol=lf: keeps the LF line endings of the data files. By default Git for Windows converts them to CRLF, and with that data 3D structures of ring molecules (cyclohexane, for example) cannot be generated.
• -DWITH_INCHI=OFF: the InChI library in Open Babel 3.2.1 does not link with MSVC. MolForma does not use InChI.
• -DOB_USE_PREBUILT_BINARIES=OFF and the others: leave out parts that are not in the Open Babel source or are downloaded while configuring (the GUI, the Maestro format, Coordgen).

C:\dev\openbabel-install\bin gets openbabel-3.dll and the format plugins (*.obf), and bin\data the force-field and other data. Open Babel’s CMake package (lib\cmake\openbabel3) is installed there too, and MolForma finds Open Babel through it (the MSVC build makes no pkg-config file).

4. Build RDKit and VTK (optional)

RDKit (strict stereo perception, residue recognition) and VTK (OpenGL drawing of the 3D view) are optional. RDKit is not in vcpkg, and vcpkg’s VTK uses vcpkg’s own Qt, so both are built from source. To leave them out, skip this section and remove C:/dev/rdkit-install and C:/dev/vtk-install from CMAKE_PREFIX_PATH in 5. Build MolForma. On a 4-core PC, Boost and RDKit took about 40 minutes and VTK about 45 minutes (partly run at the same time).

RDKit

Install the Boost libraries that RDKit uses with vcpkg.

cd /d C:\dev
vcpkg\vcpkg install --triplet x64-windows boost-algorithm boost-any boost-assign boost-container boost-crc boost-dynamic-bitset ^
  boost-flyweight boost-format boost-functional boost-graph boost-integer boost-iostreams[core] boost-json ^
  boost-lexical-cast boost-multi-array boost-multiprecision boost-numeric-conversion boost-optional ^
  boost-parameter boost-predef boost-property-map boost-property-tree boost-random boost-range ^
  boost-rational boost-smart-ptr boost-tokenizer boost-unordered boost-variant2

Get the source of RDKit Release_2026_09_1, build only its C++ libraries and install them into C:\dev\rdkit-install. While configuring, RDKit’s CMake downloads Catch2, better-enums and RingDecomposerLib from GitHub.

cd /d C:\dev
git clone -c core.autocrlf=false -c core.eol=lf --depth 1 --branch Release_2026_09_1 https://github.com/rdkit/rdkit.git
cd rdkit
cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=C:/dev/rdkit-install ^
  -DCMAKE_PREFIX_PATH=C:/dev/vcpkg/installed/x64-windows -DRDK_INSTALL_INTREE=OFF ^
  -DRDK_BUILD_PYTHON_WRAPPERS=OFF -DRDK_BUILD_CPP_TESTS=OFF -DRDK_TEST_MMFF_COMPLIANCE=OFF ^
  -DRDK_USE_BOOST_SERIALIZATION=OFF -DRDK_USE_BOOST_IOSTREAMS=OFF -DRDK_USE_BOOST_STACKTRACE=OFF ^
  -DRDK_BUILD_COORDGEN_SUPPORT=OFF -DRDK_BUILD_MAEPARSER_SUPPORT=OFF -DRDK_BUILD_CHEMDRAW_SUPPORT=OFF ^
  -DRDK_BUILD_PUBCHEMSHAPE_SUPPORT=OFF -DRDK_BUILD_DESCRIPTORS3D=OFF -DRDK_BUILD_FREETYPE_SUPPORT=OFF
cmake --build build -j 4
cmake --install build

• With MSVC, RDKit makes static libraries (*.lib). They are built into the MolForma executable, so the installed folder gets no RDKit DLLs.
• The Python wrappers, fonts for drawing pictures (FreeType), Coordgen, the Maestro and ChemDraw formats, PubChem shape alignment and the 3D descriptors are not built, as MolForma does not use them.

VTK

Get the source of VTK 9.7.1 and build only the modules MolForma uses, for your Qt (the same configuration as the AppImage). Check that the SHA-256 that certutil prints is cae04fd355004cb916a409db79d53a208f1221e975aeacc7540ee67b148ee91a before unpacking.

cd /d C:\dev
curl -L -o VTK-9.7.1.tar.gz https://vtk.org/files/release/9.7/VTK-9.7.1.tar.gz
certutil -hashfile VTK-9.7.1.tar.gz SHA256
tar -xzf VTK-9.7.1.tar.gz
cd VTK-9.7.1
cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=C:/dev/vtk-install ^
  -DCMAKE_PREFIX_PATH=C:/Qt/6.11.2/msvc2022_64 -DBUILD_SHARED_LIBS=ON -DVTK_QT_VERSION=6 ^
  -DVTK_BUILD_TESTING=OFF -DVTK_BUILD_EXAMPLES=OFF -DVTK_WRAP_PYTHON=OFF -DVTK_WRAP_JAVA=OFF -DVTK_USE_MPI=OFF ^
  -DVTK_GROUP_ENABLE_Imaging=DONT_WANT -DVTK_GROUP_ENABLE_MPI=DONT_WANT -DVTK_GROUP_ENABLE_Qt=DONT_WANT ^
  -DVTK_GROUP_ENABLE_Rendering=DONT_WANT -DVTK_GROUP_ENABLE_StandAlone=DONT_WANT ^
  -DVTK_GROUP_ENABLE_Views=DONT_WANT -DVTK_GROUP_ENABLE_Web=DONT_WANT ^
  -DVTK_MODULE_ENABLE_VTK_CommonCore=YES -DVTK_MODULE_ENABLE_VTK_CommonDataModel=YES ^
  -DVTK_MODULE_ENABLE_VTK_FiltersSources=YES -DVTK_MODULE_ENABLE_VTK_RenderingCore=YES ^
  -DVTK_MODULE_ENABLE_VTK_RenderingOpenGL2=YES -DVTK_MODULE_ENABLE_VTK_GUISupportQt=YES ^
  -DVTK_MODULE_ENABLE_VTK_InteractionStyle=YES
cmake --build build -j 4
cmake --install build

The VTK DLLs go into C:\dev\vtk-install\bin. Drawing with VTK also needs a GPU driver with OpenGL 3.2 or later.

5. Build MolForma

Get the source and build it in Release mode. Keep the source folder and build for updates.

cd /d C:\dev
git clone https://github.com/hnakada123/MolForma.git
cd MolForma
cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release ^
  "-DCMAKE_PREFIX_PATH=C:/Qt/6.11.2/msvc2022_64;C:/dev/openbabel-install;C:/dev/rdkit-install;C:/dev/vtk-install;C:/dev/vcpkg/installed/x64-windows"
cmake --build build -j 4

Near the end of the output of cmake -S . -B build … (configuring), the Open Babel found and the 3D rendering method appear. Without VTK it reads MolForma rendering: QPainter (Qt6-enabled VTK development package not found). RDKit was found if rdkit_DIR in the CMake cache (build\CMakeCache.txt) is C:/dev/rdkit-install/lib/cmake/rdkit.

-- Found OpenBabel3, version 3.2.1, in C:/dev/openbabel-install/bin
-- MolForma rendering: VTK 9.7.1 (Qt6), with QPainter fallback

Building copies beside each executable in build the DLLs it uses (those of Qt, Open Babel, VTK and vcpkg), Open Babel’s plugins and a qt.conf naming the Qt folder, so build\molforma.exe starts without setting PATH.

To run the tests (optional); they use neither NWChem nor the network:

ctest --test-dir build --output-on-failure

6. Install

Install from build. Here it goes to the per-user place for apps (%LOCALAPPDATA%\Programs\MolForma), which needs no administrator rights.

cmake --install build --prefix "%LOCALAPPDATA%\Programs\MolForma"

windeployqt gathers the DLLs, plugins and translations of Qt, and CMake the DLLs needed from Open Babel, VTK and vcpkg, so that MolForma starts from this folder alone (about 190 MB with RDKit and VTK, about 110 MB without them).

To start MolForma from the Start menu, make a shortcut (optional) by running this in PowerShell:

$s = (New-Object -ComObject WScript.Shell).CreateShortcut("$env:APPDATA\Microsoft\Windows\Start Menu\Programs\MolForma.lnk")
$s.TargetPath = "$env:LOCALAPPDATA\Programs\MolForma\bin\molforma.exe"
$s.Save()

The MSVC runtime (MSVCP140.dll and others) is not in the folder; a PC with Visual Studio has it. To use the folder on another PC, install the “Microsoft Visual C++ Redistributable” (x64) there.

7. Install NWChem (WSL)

Install NWChem into Ubuntu on WSL. If you do not use WSL yet, run wsl --install in PowerShell as administrator, restart, and set up the Ubuntu user name and password. Then run in the command prompt:

wsl sudo apt update
wsl sudo apt install nwchem

On Ubuntu 24.04 this installs NWChem 7.2.2 with the Open MPI build (nwchem-openmpi) and the MPI runtime (openmpi-bin). The basis set library works as installed, so ~/.nwchemrc is not needed.

MolForma uses the two batch files in nwchem-wsl of the installed folder. Both run NWChem in the default WSL distribution, working in the job folder (which WSL sees under /mnt/c/…).

In MolForma, open “Edit → Preferences…” and save these defaults of the run settings. Keep the launch mode “MPI” and 2 MPI processes. <user> is your Windows user name (%LOCALAPPDATA% cannot be used there; enter the expanded path).

The defaults are used for new projects and when opening structure files. Change projects you already made the same way in “3 Run settings”. If you add the nwchem-wsl folder to the Windows PATH, the names nwchem and mpirun (the defaults of the run settings) work as they are.

• The batch files pass the thread counts (OMP_NUM_THREADS, OPENBLAS_NUM_THREADS, OMP_STACKSIZE) on to WSL through WSLENV. “Additional environment variables” do not reach WSL; if you need them, add their names to the WSLENV line of the batch files.
• “Stop” ends cmd.exe, wsl.exe and mpirun and NWChem in WSL together after 2 seconds (“3 Run settings”).
• WSL sees the job folder (by default C:\Users\<user>\MolForma\jobs) much like a network drive, so calculations that write large scratch files are slower than when run on Linux directly.

8. Start and check

Start MolForma from “MolForma” in the Start menu or from %LOCALAPPDATA%\Programs\MolForma\bin\molforma.exe. The display language follows the Windows language (“Language (after restart)” in “Edit → Preferences…” switches it; it takes effect after a restart).

1. Open “Help → About MolForma” and check that it reads “MolForma 1.0.0” and, with RDKit and VTK installed, “Stereochemistry and residue recognition (RDKit): Enabled” and “3D rendering: VTK (OpenGL)”. Where OpenGL is unavailable (some remote desktops and virtual machines), it reads “3D rendering: QPainter (CPU)”.
2. Type CC1CCCCC1 (methylcyclohexane) into the search field of the parts palette and check that “Build 3D from SMILES “CC1CCCCC1”” makes a 3D candidate (this uses Open Babel and its data).
3. Open “3 Run settings” and check that the pre-run check finds the NWChem executable and the MPI launcher.
4. Try a calculation on a small molecule; the steps are in Recipe 1 Building from atoms and bonds.

The settings are kept in %APPDATA%\MolForma\MolForma.ini and the autosave copies of unsaved work in %LOCALAPPDATA%\MolForma\autosave (the Windows registry is not used).

Updating and removing

Updating

Update the source, rebuild it and install it again in the same place. As long as Open Babel, RDKit, VTK, Qt and the vcpkg libraries stay the same, you need not configure again as in 5. Build MolForma.

cd /d C:\dev\MolForma
git pull --ff-only
cmake --build build -j 4
cmake --install build --prefix "%LOCALAPPDATA%\Programs\MolForma"

After changing the Qt version, rebuild VTK with that Qt too, delete the build of MolForma and configure again with the new Qt folder in CMAKE_PREFIX_PATH. Delete the installed folder before installing again, so that no files of the old Qt remain.

Removing

Delete the installed folder %LOCALAPPDATA%\Programs\MolForma and, if you made it, the Start menu shortcut (%APPDATA%\Microsoft\Windows\Start Menu\Programs\MolForma.lnk). The settings (%APPDATA%\MolForma), autosave copies (%LOCALAPPDATA%\MolForma) and calculation jobs (by default %USERPROFILE%\MolForma\jobs) remain; delete them by hand if you no longer need them. The build folders under C:\dev (MolForma, Open Babel, RDKit, VTK, vcpkg and their *-install folders) can also be deleted. Remove NWChem with wsl sudo apt remove nwchem followed by wsl sudo apt autoremove.

Troubleshooting

Verified configuration

On 2026-10-28 the following was checked with this configuration:

• Configuring and building Open Babel, RDKit, VTK and MolForma with the steps above, with all 14 CTest tests passing (the RDKit checks run instead of being skipped); all 14 also pass in a configuration without RDKit and VTK.
• On a real desktop (GPU OpenGL), the optional test of the VTK rendering path (test_rendering with MOLFORMA_REQUIRE_VTK=1; see 3D rendering) passes.
• The folder made by cmake --install starts without the folders of Qt, Open Babel or vcpkg in PATH, and generates 3D structures from the SMILES of cyclohexane and methylcyclohexane.
• NWChem installed with apt into Ubuntu 24.04 on WSL starts through mpirun.cmd and nwchem.cmd; in MolForma’s run settings test (the optional test with real NWChem), an HF/STO-3G calculation of water with 2 MPI processes completes with an SCF energy of −74.945628203255 Hartree, and stopping a running calculation also ends mpirun and NWChem in WSL.

vcpkg was the vcpkg.exe that comes with Visual Studio, with the ports of the matching version (tag 2026.06.24). Windows 10 and Windows on ARM64 were not checked.

Related: Installation and required packages by OS, 3D rendering, “3 Run settings”