Cath Tools

Configuration File: cath_tools.json Tool Type: Local Tools Count: 4

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_funfam (Type: CATHTool)

Get details for a specific functional family (FunFam) within a CATH superfamily. Returns FunFam n…

CATH_get_funfam tool specification

Tool Information:

  • Name: CATH_get_funfam

  • Type: CATHTool

  • Description: Get details for a specific functional family (FunFam) within a CATH superfamily. Returns FunFam name, description, member count, seed alignment size, DOPS quality score, and representative domain ID. FunFams represent groups of domains predicted to share the same biological function. Use CATH_list_funfams to browse FunFams within a superfamily, or CATH_get_domain_summary to find which FunFam a specific domain belongs to.

Parameters:

  • superfamily_id (string) (required) CATH superfamily ID (e.g., ‘1.10.510.10’).

  • funfam_number (string) (required) FunFam number within the superfamily (e.g., ‘1’, ‘83’). Get from CATH_list_funfams or CATH_get_domain_summary.

Example Usage:

query = {
    "name": "CATH_get_funfam",
    "arguments": {
        "superfamily_id": "example_value",
        "funfam_number": "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)

CATH_list_funfams (Type: CATHTool)

List functional families (FunFams) within a CATH superfamily. FunFams group protein domains that …

CATH_list_funfams tool specification

Tool Information:

  • Name: CATH_list_funfams

  • Type: CATHTool

  • Description: List functional families (FunFams) within a CATH superfamily. FunFams group protein domains that share the same function, identified by conserved specificity-determining residues. Returns FunFam numbers, names, member counts, and representative domain IDs. Example: superfamily 1.10.510.10 (Globin-like) has 4,524 FunFams including CaM kinase (2,698 members) and Myosin light chain kinase (1,234 members). Use CATH_get_superfamily to find superfamily IDs first.

Parameters:

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

  • max_results (integer) (optional) Maximum number of FunFams to return (default: 25).

Example Usage:

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