Setting up a molecule

To set up a new molecule all you need is a file containing the structure for the molecule, supported file types include xyz, mol, mol2, and sdf files.

  1. Create a new directory for your molecule:
    > mkdir molecule_name
    > mv molecule.xyz molecule_name/
    > cd molecule_name
    
  2. Initialise the molecule in autoenrich (remember to activate your conda environment !!)
    > autoenrich molcule_name init --init_file molecule.xyz
    

    If you did not already have a preferences file in your folder (usually named ENRICH.json), then the program will create one for you, and prompt you to run the init command again once you are happy with the settings.

  3. Run the command again after editting the ENRICH.json preferences file.
    > vim ENRICH.json # make some changes
    > autoenrich molcule_name init --init_file molecule.xyz
    

    This creates a .pkl file to store the molecule progress and other data, and checks the preferences file for issues. Your autoenrich folder should look like this: ```

    • my_autoenrich_folder/
    • molecule_name/
      • molecule.xyz
    • molecule.pkl
    • ENRICH.json ```

Next step: Conformational search