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
  • Default Settings
  • Verbose default Settings
  • Maximum verbose default Settings
• path
  • Default Settings
  • Arguments
    • path
• input_cores & input_ligands
  • Default Settings
  • Optional arguments
    • .guess_bonds
    • .column
    • .row
    • .indices
    • input_cores
    • input_ligands
• Optional
  • Index
  • Default Settings
  • Arguments
    • Database
      • optional.database
        • optional.database.dirname
        • optional.database.read
        • optional.database.write
        • optional.database.overwrite
        • optional.database.thread_safe
        • optional.database.mol_format
        • optional.database.mongodb
    • Core
      • optional.core
        • optional.core.dirname
        • optional.core.anchor
        • optional.core.allignment
        • optional.core.subset
          • optional.core.subset.f
          • optional.core.subset.mode
          • optional.core.subset.follow_edge
          • optional.core.subset.cluster_size
          • optional.core.subset.weight
          • optional.core.subset.randomness
    • Ligand
      • optional.ligand
        • optional.ligand.dirname
        • optional.ligand.optimize
        • optional.ligand.anchor
          • optional.ligand.anchor.group
          • optional.ligand.anchor.group_idx
          • optional.ligand.anchor.group_format
          • optional.ligand.anchor.remove
          • optional.ligand.anchor.kind
          • optional.ligand.anchor.angle_offset
          • optional.ligand.anchor.dihedral
          • optional.ligand.anchor.multi_anchor_filter
        • optional.ligand.split
        • optional.ligand.cdft
        • optional.ligand.cone_angle
          • optional.ligand.cone_angle.distance
        • optional.ligand.branch_distance
    • QD
      • optional.qd
        • optional.qd.dirname
        • optional.qd.construct_qd
        • optional.qd.optimize
        • optional.qd.multi_ligand
        • optional.qd.bulkiness
          • optional.qd.bulkiness.h_lim
          • optional.qd.bulkiness.d
        • optional.qd.activation_strain
        • optional.qd.dissociate
• Bond Dissociation Energy
  • Default Settings
  • Arguments
    • optional.qd.dissociate.core_atom
    • optional.qd.dissociate.lig_count
    • optional.qd.dissociate.core_index
    • optional.qd.dissociate.core_core_dist
    • optional.qd.dissociate.lig_core_dist
    • optional.qd.dissociate.lig_pairs
    • optional.qd.dissociate.topology
    • optional.qd.dissociate.qd_opt
  • 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
  • Aliases
• The Database Class
  • Index
  • API
    • Database
      • Database.dirname
      • Database.csv_lig
      • Database.csv_qd
      • Database.hdf5
      • Database.mongodb
      • Database.update_mongodb()
      • Database.update_csv()
      • Database.update_hdf5()
      • Database.from_csv()
      • Database.from_hdf5()
      • Database.hdf5_availability()
    • DFProxy
      • DFProxy.ndframe
    • OpenLig
      • OpenLig.filename
      • OpenLig.write
    • OpenQD
      • OpenQD.filename
      • OpenQD.write
• The PDBContainer Class
  • Index
  • API
    • PDBContainer
      • PDBContainer.atoms
      • PDBContainer.bonds
      • PDBContainer.atom_count
      • PDBContainer.bond_count
      • PDBContainer.scale
      • PDBContainer.__init__()
  • API: Miscellaneous Methods
    • PDBContainer.__getitem__()
    • PDBContainer.__len__()
    • PDBContainer.keys()
    • PDBContainer.values()
    • PDBContainer.items()
    • PDBContainer.concatenate()
  • API: Object Interconversion
    • PDBContainer.from_molecules()
    • PDBContainer.to_molecules()
    • PDBContainer.to_rdkit()
    • PDBContainer.create_hdf5_group()
    • PDBContainer.validate_hdf5()
    • PDBContainer.from_hdf5()
    • PDBContainer.to_hdf5()
  • API: Set Operations
    • PDBContainer.intersection()
    • PDBContainer.difference()
    • PDBContainer.symmetric_difference()
    • PDBContainer.union()
• Data Types
  • Index
  • API
    • ATOMS_DTYPE
    • BONDS_DTYPE
    • ATOM_COUNT_DTYPE
    • BOND_COUNT_DTYPE
    • LIG_IDX_DTYPE
    • QD_IDX_DTYPE
    • BACKUP_IDX_DTYPE
    • DT_DTYPE
    • VERSION_DTYPE
    • INDEX_DTYPE
    • MSG_DTYPE
    • FORMULA_DTYPE
    • LIG_COUNT_DTYPE
• HDF5 Access Logging
  • Index
  • API
    • create_hdf5_log()
    • update_hdf5_log()
    • reset_hdf5_log()
    • log_to_dataframe()
• HDF5 Property Storage
  • Index
  • API
    • create_prop_group()
    • create_prop_dset()
    • update_prop_dset()
    • validate_prop_group()
    • index_to_pandas()
    • prop_to_dataframe()
• Context Managers
  • Index
  • API
    • AsArray
      • AsArray.mol
      • AsArray._xyz
    • SplitMol
      • SplitMol.mol
      • SplitMol.bonds
      • SplitMol.cap_type
      • SplitMol._at_pairs
      • SplitMol._vars_backup
      • SplitMol._tmp_mol_list
    • RemoveAtoms
      • RemoveAtoms.mol
      • RemoveAtoms.atoms
      • RemoveAtoms._bonds
• 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
  • nanoCAT.recipes.mark_surface
    • Index
    • API
      • replace_surface()
  • nanoCAT.recipes.bulk
    • Index
    • API
      • bulk_workflow()
      • fast_bulk_workflow()
  • nanoCAT.recipes.surface_dissociation
    • Index
    • API
      • dissociate_surface()
      • dissociate_bulk()
      • row_accumulator()
  • nanoCAT.recipes.charges
    • Index
    • API
      • get_lig_charge()
  • nanoCAT.recipes.coordination_number
    • Index
    • API
      • get_coordination_number()
      • coordination_outer()
  • Index
  • API
    • add_ligands()
    • export_dyes()
    • sa_scores()
  • nanoCAT.recipes.multi_ligand_job
  • nanoCAT.recipes.mol_filter
    • Index
    • API
      • get_mol_length()
      • filter_mol()
      • filter_data()
  • nanoCAT.recipes.cdft_utils
    • Index
    • API
      • run_jobs()
      • get_global_descriptors()
      • cdft
  • nanoCAT.recipes.entropy
    • Index
    • API
      • get_entropy()
  • nanoCAT.recipes.fast_sigma
    • Index
    • API
      • run_fast_sigma()
      • get_compkf()
      • read_csv()
      • sanitize_smiles_df()
• Multi-ligand attachment
  • optional.qd.multi_ligand.ligands
  • optional.qd.multi_ligand.anchor
• Subset Generation
  • Index
  • API
    • uniform_idx()
    • distribute_idx()