Cath Tools

Configuration File: cath_tools.json Tool Type: Local Tools Count: 2

This page contains all tools defined in the cath_tools.json configuration file.

Available Tools

CATH_get_domain_summary (Type: CATHTool)

Get CATH structural classification for a specific protein domain from PDB. Domains are identified…

CATH_get_domain_summary tool specification

Tool Information:

  • Name: CATH_get_domain_summary

  • Type: CATHTool

  • Description: Get CATH structural classification for a specific protein domain from PDB. Domains are identified by PDB code + chain + domain number (e.g., 1cukA01). Returns the full CATH hierarchy (Class, Architecture, Topology, Homologous superfamily) and residue count. Example: ‘1cukA01’ returns CATH ID 2.40.50.140.116.1.1.1.1 (Mainly Beta class, Nucleic acid-binding proteins superfamily) with 212 residues.

Parameters:

  • domain_id (string) (required) CATH domain ID: PDB code (4 chars) + chain (1 char) + domain number (2 digits). Examples: ‘1cukA01’ (ubiquitin conjugating enzyme), ‘1x54A01’ (DNA-binding domain), ‘4hhbA00’ (hemoglobin alpha). Use lowercase PDB code.

Example Usage:

query = {
    "name": "CATH_get_domain_summary",
    "arguments": {
        "domain_id": "example_value"
    }
}
result = tu.run(query)

CATH_get_superfamily (Type: CATHTool)

Get CATH protein structure superfamily information by CATH ID. CATH classifies protein domain str…

CATH_get_superfamily tool specification

Tool Information:

  • Name: CATH_get_superfamily

  • Type: CATHTool

  • Description: Get CATH protein structure superfamily information by CATH ID. CATH classifies protein domain structures into a four-level hierarchy: Class, Architecture, Topology, Homologous superfamily. Superfamilies group evolutionarily related domains. Returns classification name, number of families, and domain counts. Example: 2.40.50.140 returns ‘Nucleic acid-binding proteins’ with 227 S35 families and 2,879 total domains.

Parameters:

  • superfamily_id (string) (required) CATH superfamily ID in C.A.T.H format. Examples: ‘2.40.50.140’ (Nucleic acid-binding proteins), ‘3.40.50.300’ (P-loop NTPases), ‘1.10.510.10’ (Globin-like), ‘2.60.40.10’ (Immunoglobulin-like).

Example Usage:

query = {
    "name": "CATH_get_superfamily",
    "arguments": {
        "superfamily_id": "example_value"
    }
}
result = tu.run(query)