Installing ClustTraj

Installing clusttraj is simple and can be achieved using pip:

pip install clusttraj

This will automatically install clusttraj and its Python dependencies, except for Open Babel.

We recommend performing the installation in an empty virtual environment.

Dependencies

Most clusttraj dependencies are installed automatically by pip. Open Babel is a runtime dependency, but it is not installed by default.

Currently, the following dependencies are used:

• NumPy

• OpenBabel

• RMSD

• SciPy

• scikit-learn

• matplotlib

If you use Conda, install Open Babel from conda-forge before installing clusttraj:

conda install -c conda-forge openbabel
pip install clusttraj

For pip-only environments, clusttraj provides an optional dependency that installs the openbabel-wheel package:

pip install "clusttraj[openbabel]"

Avoid mixing Conda Open Babel and openbabel-wheel in the same environment. If you see Open Babel import or linker errors, remove one provider and reinstall Open Babel from the package manager used by that environment.

qmllib is an optional dependency for one of the reordering algorithms and can be installed with:

pip install "clusttraj[qml]"

Since the qml project development has been slow, we provide a fork repository in which we updated the package to be installable in modern enviroments with newer versions of Python and libraries. This modified version can be downloaded and installed from this link.

Installation Problems

If you have problems installing clusttraj because installing qml fails, try installing qml yourself first. For Python 3.11, you might have to either disable setuptools distutils setting the environment variable SETUPTOOLS_USE_DISTUTILS=stdlib before installing, or downgrading setuptools to a version prior than 60.0. For example, you could install qml with:

pip install "setuptools<60"
pip install "qml @ git+https://github.com/hmcezar/qml@develop"