Installing on Ubuntu

How to build MolForma from source on Ubuntu, make a deb package and install it with apt. The development packages for the build and NWChem for calculations come from Ubuntu’s official repositories.

These steps are for Ubuntu 26.04 LTS (amd64) and MolForma 1.0.0. They were checked on 2026-10-28 in Docker’s ubuntu:26.04 (26.04.1 LTS) (see Verified configuration).

MolForma has no package in Ubuntu’s official repositories or in a PPA (as of 2026-10-28). You build it from the source on GitHub and make a deb package (molforma_1.0.0_amd64.deb) with CPack, which comes with CMake. As apt manages the installed package, apt remove removes it.

Required packages

The build needs these packages (see 1. Install the packages).

apt installs the packages used at run time automatically when it installs the deb package you make: the Qt 6 libraries and qt6-qpa-plugins, libopenbabel7 (with the format plugins and force-field data) and, when built with RDKit and VTK, librdkit1t64, libvtk9.5 and libvtk9.5-qt. The recommended packages qt6-translations-l10n (with the Japanese interface, Japanese for Qt’s standard dialogs such as file selection too) and fonts-noto-cjk (Japanese fonts) come in as well with apt’s default settings.

For calculations, install NWChem from the official repositories (universe) as nwchem (see 2. Install NWChem).

• RDKit and VTKBoth are optional. They are enabled only when CMake finds them at build time, and the deb package’s dependencies follow. Drawing with VTK also needs a GPU driver that provides OpenGL 3.2 or later.
• NWChemBuilding and saving input (“Save as job”) works without NWChem.

1. Install the packages

Update the package lists and install the required packages.

sudo apt update
sudo apt install build-essential cmake ninja-build git pkgconf file qt6-base-dev libeigen3-dev libopenbabel-dev

For RDKit and VTK, install these as well. VTK’s development package has many dependencies (the Java version of VTK and more): from a bare system, about 780 packages with the ones above, and about 1 GB to download.

sudo apt install librdkit-dev libboost-iostreams-dev libboost-serialization-dev libvtk9-dev libvtk9-qt-dev

2. Install NWChem

sudo apt install nwchem

This also brings in the Open MPI build of NWChem (nwchem-openmpi) and the MPI run time (openmpi-bin). NWChem goes to /usr/bin/nwchem and its basis set library to /usr/share/nwchem/. The basis set library works as installed, so you need neither ~/.nwchemrc nor NWCHEM_BASIS_LIBRARY. MolForma’s “3 Run settings” defaults (executable nwchem, launch with MPI, MPI launcher mpirun, 2 processes) launch this NWChem as they are.

3. Get the source and build

Get the source and build a Release build. Keep the folder you got and its build; updating uses them.

git clone https://github.com/hnakada123/MolForma.git
cd MolForma
cmake -S . -B build -G Ninja -DCMAKE_BUILD_TYPE=Release
cmake --build build -j 4

Running the third line, cmake -S . -B build … (the configuration: CMake looks for the libraries it needs and prepares the build), prints a line beginning with -- MolForma rendering: in the terminal. This line shows how the 3D view will be drawn. Near the end, the output looks like this, for example:

--   Found openbabel-3, version 3.1.1
-- MolForma rendering: VTK 9.5.2 (Qt6), with QPainter fallback
-- Configuring done (2.2s)
-- Generating done (0.2s)
-- Build files have been written to: …/MolForma/build

If it scrolled past, running the configuration command again prints the same line. The MolForma rendering: line means:

After installing the missing packages, start again from the configuration command. -j 4 is the number of compile jobs run at once; lower it if memory runs short.

To run the tests (optional), use the command below. They use neither NWChem nor the network. If you do not need the tests, adding -DBUILD_TESTING=OFF to the configuration command shortens the build.

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

4. Make and install the package

Make the deb package in build and install it with apt. With ./, apt takes it as a file rather than a package name and installs the missing dependencies with it.

cd build
cpack -G DEB
sudo apt install ./molforma_1.0.0_amd64.deb

cpack works out the dependencies from the shared libraries the executable uses (dpkg-shlibdeps) and writes them into the package. The package places these files (dpkg -L molforma lists them). The file type and menu information is updated automatically when it is installed.

5. Start and check

Run molforma in a terminal or choose “MolForma” in the list of applications. The interface language follows the system 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, it reads “3D rendering: QPainter (CPU)”.
2. Open “3 Run settings” and check that below the “NWChem executable” and “MPI launcher” fields appear /usr/bin/nwchem and /usr/bin/mpirun, where PATH found them.
3. Try a calculation on a small molecule. The steps are in recipe 1 Building from atoms and bonds.

Updating and removing

Updating

Update the source, rebuild, make the package again and install it. While the version number stays the same, apt does not install it again unless you add --reinstall.

cd MolForma
git pull --ff-only
cmake --build build -j 4
cd build
cpack -G DEB
sudo apt install --reinstall ./molforma_1.0.0_amd64.deb

Upgrading Ubuntu to a new release changes the versions of libraries such as Qt, Open Babel, RDKit and VTK; MolForma may then stop starting, or be removed because its dependencies cannot be met. In that case, delete build, start again from the configuration in 3. Get the source and build, make the package again and install it.

Removing

sudo apt remove molforma

The application settings (~/.config/MolForma/), autosaves (~/.local/share/MolForma/) and calculation jobs (by default ~/MolForma/jobs) remain; delete them by hand if you no longer need them. The development packages installed in 1. Install the packages remain too; if you no longer need them, remove them by name with sudo apt remove, and what came in with them with sudo apt autoremove. sudo apt remove nwchem followed by sudo apt autoremove removes NWChem.

Troubleshooting

Verified configuration

On 2026-10-28, in Docker’s ubuntu:26.04 (Ubuntu 26.04.1 LTS, amd64), the following was checked.

• In a container with the packages above, the source configured and built (with both RDKit and VTK), and all 14 CTest tests passed (both serially and in parallel). Under Xvfb with Mesa’s software OpenGL, the optional test of the VTK rendering path (3D rendering) passed too.
• cpack -G DEB made the deb package, and in another, bare container apt install ./molforma_1.0.0_amd64.deb and apt install nwchem installed with their dependencies. As a normal user, molforma started and reported version 1.0.0, and the file types were registered.
• Without a ~/.nwchemrc, mpirun -np 2 nwchem completed an HF/6-31G* calculation of the hydrogen molecule. MolForma’s run settings test that uses a real NWChem (optional) completed an HF/STO-3G calculation of water with 2 MPI processes, with an SCF energy of −74.945628203255 Hartree.

A real desktop (VTK rendering on a GPU, GNOME’s list of applications) and other versions such as Ubuntu 24.04 LTS were not checked.

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