Pdbe Compound Tools#

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

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

Available Tools#

PDBe_get_compound_structures (Type: PDBECompoundTool)#

Get every PDB structure containing a chemical compound through explicit limit/offset pages from P…

PDBe_get_compound_structures tool specification

Tool Information:

  • Name: PDBe_get_compound_structures

  • Type: PDBECompoundTool

  • Description: Get every PDB structure containing a chemical compound through explicit limit/offset pages from PDBe’s official compound/in_pdb endpoint. Returns exact total, next_offset, PDB IDs, and occurrence qualifiers (ligand type, total copies, distinct copies). Follow next_offset while has_more is true; ATP and NAG occur in thousands of structures.

Parameters:

  • comp_id (string) (required) PDB chemical component ID (3-letter code). Examples: ‘ATP’, ‘HEM’, ‘NAG’, ‘FAD’, ‘NAD’, ‘ZN’, ‘GOL’. Case-insensitive.

  • limit (integer) (optional) Maximum structure-occurrence records to return

  • offset (integer) (optional) Zero-based structure offset; continue with next_offset

Example Usage:

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

PDBe_get_compound_summary (Type: PDBECompoundTool)#

Get detailed chemical compound information from PDBe by PDB chemical component ID. Returns comple…

PDBe_get_compound_summary tool specification

Tool Information:

  • Name: PDBe_get_compound_summary

  • Type: PDBECompoundTool

  • Description: Get detailed chemical compound information from PDBe by PDB chemical component ID. Returns complete SMILES, systematic names, and all cross-references without the former 15-reference cutoff, with explicit counts, plus formula, weight, charge, type, InChI, and first observation. Useful for protein-ligand and chemical-evidence analysis.

Parameters:

  • comp_id (string) (required) PDB chemical component ID (3-letter code). Examples: ‘ATP’, ‘HEM’ (heme), ‘NAG’ (N-acetylglucosamine), ‘CFF’ (caffeine), ‘GOL’ (glycerol), ‘ZN’ (zinc ion), ‘FAD’, ‘NAD’. Case-insensitive.

Example Usage:

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