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.

  1. Install the conda package manager. Make sure the conda executable is in your PATH.

  2. 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
    
  3. Activate the conda environment:

    conda activate pygen-structures
    
  4. Use pip to install pygen-structures in this environment:

    pip install pygen-structures
    
  5. Installation complete! You will have to activate this environment using conda activate pygen-structures each time you want to use it.

  6. 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