Installation¶
Dependencies¶
pygen-structures depends upon the RDKit for molecule representations and numpy for representations of the adjacency matrix. Running the full set of tests requires pytest and OpenMM.
Installation Steps¶
There are other ways to install the required dependencies, but the easiest way by far is to use conda. Instructions, including the installation of test dependencies, are outlined below. Alternatively, OpenMM and the RDKit can be compiled from source; pytest and numpy can be installed using pip.
Install the conda package manager. Make sure the
conda
executable is in your PATH.Set up a conda environment with the relevant dependencies (or install them in your base distribution). This can be done with the following command:
conda create -n pygen-structures -c rdkit -c omnia 'python>=3.6' 'rdkit>=2018.3' numpy 'openmm>=7.4' pytest
Activate the conda environment:
conda activate pygen-structures
Use
pip
to install pygen-structures in this environment:pip install pygen-structures
Installation complete! You will have to activate this environment using
conda activate pygen-structures
each time you want to use it.Test the installation:
pytest --pyargs pygen_structures
To install only the runtime dependencies, use the following command in step 2:
conda create -n pygen-structures -c rdkit 'python>=3.6' 'rdkit>=2018.3' numpy