Installing ClustTraj

Installing clusttraj is simple and can be achieved using pip:

pip install clusttraj

This will automatically install the package and its dependencies.

We recommend performing the installation in an empty virtual environment.

Dependencies

clustttraj dependencies should be installed automatically by pip.

Currently, the following dependencies are installed:

• NumPy

• OpenBabel

• RMSD

• QML

• SciPy

• scikit-learn

• matplotlib

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"