CAT Documentation
For a more detailed description of the CAT compound builder read the documentation. The documentation is divided into three parts: The basics, further details about the input cores & ligands and finally a more detailed look into the customization of the various jobs.
- General Overview & Getting Started
- path
- input_cores & input_ligands
- Optional
- Bond Dissociation Energy
- Default Settings
- Arguments
- Arguments - Job Customization
optional.qd.dissociate.keep_files
optional.qd.dissociate.xyn_pre_opt
optional.qd.dissociate.job1
optional.qd.dissociate.s1
optional.qd.dissociate.job2
optional.qd.dissociate.s2
- Index
- API
dissociate_ligand()
MolDissociater
MolDissociater.mol
MolDissociater.core_idx
MolDissociater.ligand_count
MolDissociater.max_dist
MolDissociater.topology
MolDissociater.remove_bulk()
MolDissociater.assign_topology()
MolDissociater.get_pairs_closest()
MolDissociater.get_pairs_distance()
MolDissociater.combinations()
MolDissociater.__call__()
- Type Aliases
- The Database Class
- The PDBContainer Class
- Data Types
- HDF5 Access Logging
- HDF5 Property Storage
- Context Managers
- Ensemble-Averaged Activation Strain Analysis
- Strain/Distortion
- Interaction
- Total Energy
- Examples
- activation_strain
optional.qd.activation_strain.use_ff
optional.qd.activation_strain.md
optional.qd.activation_strain.iter_start
optional.qd.activation_strain.dump_csv
optional.qd.activation_strain.el_scale14
optional.qd.activation_strain.lj_scale14
optional.qd.activation_strain.distance_upper_bound
optional.qd.activation_strain.k
optional.qd.activation_strain.shift_cutoff
optional.qd.activation_strain.job1
optional.qd.activation_strain.s1
- Recipes
- Multi-ligand attachment
- Subset Generation