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
thread_safe: False
mol_format: (pdb, xyz)
mongodb: False
core:
dirname: core
anchor: Cl
subset: null
ligand:
dirname: ligand
optimize: True
split: True
anchor: null
cosmo-rs: False
qd:
dirname: qd
construct_qd: True
optimize: False
bulkiness: 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: (core, ligand, qd)
write: (core, ligand, qd)
overwrite: False
thread_safe: False
mol_format: (pdb, xyz)
mongodb: False
core:
dirname: core
anchor: Cl
subset: null
ligand:
dirname: ligand
split: True
anchor: null
cosmo-rs: False
optimize:
use_ff: False
job1: null
s1: null
job2: null
s2: null
qd:
dirname: qd
construct_qd: True
optimize: False
bulkiness: False
activation_strain: False
dissociate:
core_atom: Cd
lig_count: 2
keep_files: True
core_core_dist: 5.0
lig_core_dist: 5.0
topology: {}
job1: False
s1: False
job2: False
s2: False