General Overview & Getting Started

A basic recipe for running CAT:

1. Create two directories named ‘core’ and ‘ligand’. The ‘core’ directory should contain the input cores & the ‘ligand’ should contain the input ligands. The quantum dots will be exported to the ‘QD’ directory.

2. Customize the job settings to your liking, see CAT/examples/input_settings.yaml for an example. Note: everything under the optional section does not have to be included in the input settings. As is implied by the name, everything in optional is completely optional.

3. Run CAT with the following command: init_cat input_settings.yaml

4. Congratulations, you just ran CAT!

The default CAT settings, at various levels of verbosity, are provided below.

Default Settings

path: None

input_cores:
    - Cd68Se55.xyz:
        guess_bonds: False

input_ligands:
    - OC(C)=O
    - OC(CC)=O

Verbose default Settings

path: None

input_cores:
    - Cd68Se55.xyz:
        guess_bonds: False

input_ligands:
    - OC(C)=O
    - OC(CC)=O

optional:
    database:
        dirname: database
        read: True
        write: True
        overwrite: False
        mol_format: [pdb, xyz]
        mongodb: False

    core:
        dirname: core
        dummy: Cl

    ligand:
        dirname: ligand
        optimize: True
        split: True
        cosmo-rs: False

    qd:
        dirname: QD
        optimize: False
        activation_strain: False
        dissociate: False

Maximum verbose default Settings

path: None

input_cores:
    - Cd68Se55.xyz:
        guess_bonds: False

input_ligands:
    - OC(C)=O
    - OC(CC)=O

optional:
    database:
        dirname: database
        read: True
        write: True
        overwrite: False
        mol_format: [pdb, xyz]
        mongodb: False

    core:
        dirname: core
        dummy: Cl

    ligand:
        dirname: ligand
        optimize: True
        split: True
        cosmo-rs: False

    qd:
        dirname: QD
        optimize: False
        activation_strain: False
        dissociate:
            core_atom: Cd
            lig_count: 2
            core_core_dist: 5.0
            lig_core_dist: 5.0
            topology:
                6: vertice
                7: edge
                9: face

            job1: False
            s1: False
            job2: False
            s2: False