Installation

Since conformer_rl can be run within a Conda environment, it should work on all platforms (Windows, MacOS, and Linux).

Prerequisites

  • We recommend installing in a new Conda environment.

  • Install dependencies

    • Install PyTorch . PyTorch version of 1.8.0 or greater is required for conformer_rl.

    • Install PyTorch Geometric .

      • Important Note: Please make sure to use the same package installer (i.e., Conda, Pip) for installing both PyTorch and PyTorch geometric.

    • Install RDKit:

      conda install -c conda-forge rdkit

  • Finally, install conformer_rl:

    pip install conformer-rl

Verify Installation

As a quick check to verify the installation has succeeded, navigate to the examples directory and run examples/test_example.py. The script should finish running in a few minutes or less. If no errors are encountered then most likely the installation has succeeded.

Additional Installation for Analysis/Visualization Tools

Some additional dependencies are required for visualizing molecules in Jupyter/IPython notebooks.

Firstly, install the dependencies required for visualizing molecules and figures in Jupyter (these should already be installed after installing conformer-rl):

pip install conformer-rl[visualization]

Install nodejs. This is only required for creating interactive molecule visualizations in Jupyter:

conda install nodejs

Install the jupyterlab_3dmol extension for visualizing molecules interactively in Jupyter:

jupyter labextension install jupyterlab_3dmol

You should now be able to use the analysis components of conformer-rl for generating figures and visualizing molecule in Jupyter. To test that the installation was succesful, try running the example Jupyter notebook:

jupyter-lab examples/example_analysis.ipynb

Additional Installation for Molecule Generation Tools

Additional dependencies are required for generating non-alkane molecules such as lignin. To install these dependencies run:

pip install conformer-rl[generate_molecules]

A full list of classes of molecules that conformer_rl can generate can be found in Molecule Generation.