Compound Attachment Tool 0.9.11

CAT is a collection of tools designed for the construction of various chemical compounds. Further information is provided in the documentation.


  • Download miniconda for python3: miniconda (also you can install the complete anaconda version).
  • Install according to: installConda.
  • Create a new virtual environment, for python 3.7, using the following commands:
    • conda create --name CAT python
  • The virtual environment can be enabled and disabled by, respectively, typing:
    • Enable: conda activate CAT
    • Disable: conda deactivate

Dependencies installation

Using the conda environment the following packages should be installed:

  • rdkit : conda install -y --name CAT --channel conda-forge rdkit

Package installation

Finally, install CAT using pip:

  • CAT: pip install git+ --upgrade

Now you are ready to use CAT.

Input files

Running CAT and can be done with the following command: init_cat my_settings.yaml. The user merely has to provide a yaml file with the job settings, settings which can be tweaked and altered to suit ones purposes (see example1). Alternatively, CAT can be run like a regular python script, bypassing the command-line interface (i.e. python, see example2).

An extensive description of the various available settings is available in the documentation.