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