Rcsb Graphql Tools

Configuration File: rcsb_graphql_tools.json Tool Type: Local Tools Count: 3

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

Available Tools

RCSBGraphQL_get_ligand_info (Type: RCSBGraphQLTool)

Get detailed chemical component (ligand) information from the PDB using the RCSB Data API. Return…

RCSBGraphQL_get_ligand_info tool specification

Tool Information:

  • Name: RCSBGraphQL_get_ligand_info

  • Type: RCSBGraphQLTool

  • Description: Get detailed chemical component (ligand) information from the PDB using the RCSB Data API. Returns the ligand name, molecular formula, molecular weight, SMILES, InChIKey, type (non-polymer, peptide-like, etc.), and known drug targets with their actions (inhibitor, substrate, cofactor, etc.) from DrugBank. Use this to look up small molecules, cofactors, or drugs found in PDB structures.

Parameters:

  • comp_id (string) (required) PDB chemical component identifier (3-letter code). Examples: ‘ATP’ (adenosine triphosphate), ‘HEM’ (heme), ‘NAG’ (N-acetylglucosamine), ‘STI’ (imatinib/Gleevec), ‘ZMA’ (zinc ion with methylamine), ‘FAD’ (flavin adenine dinucleotide), ‘NAD’ (nicotinamide adenine dinucleotide).

Example Usage:

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

RCSBGraphQL_get_polymer_entity (Type: RCSBGraphQLTool)

Get detailed polymer entity information from PDB structures including amino acid sequence, chain …

RCSBGraphQL_get_polymer_entity tool specification

Tool Information:

  • Name: RCSBGraphQL_get_polymer_entity

  • Type: RCSBGraphQLTool

  • Description: Get detailed polymer entity information from PDB structures including amino acid sequence, chain IDs, polymer type, source organism, and domain/family annotations (Pfam, GO terms). Each PDB entry can contain multiple polymer entities (chains). Use this to retrieve the protein sequence, identify chains, and find functional annotations for proteins in a PDB structure.

Parameters:

  • pdb_id ([‘string’, ‘null’]) (optional) PDB ID (will fetch entity 1 by default). Examples: ‘4HHB’ (hemoglobin), ‘1TUP’ (p53-DNA). Use entity_num to specify which entity.

  • entity_num ([‘integer’, ‘null’]) (optional) Entity number within the PDB entry (default: 1). PDB entries can have multiple polymer entities (1, 2, 3, …).

  • entity_ids ([‘string’, ‘null’]) (optional) Comma-separated list of entity IDs for batch query. Format: ‘PDB_ENTITY’ (e.g., ‘4HHB_1,4HHB_2’). Overrides pdb_id/entity_num.

Example Usage:

query = {
    "name": "RCSBGraphQL_get_polymer_entity",
    "arguments": {
    }
}
result = tu.run(query)

RCSBGraphQL_get_structure_summary (Type: RCSBGraphQLTool)

Get comprehensive structure summary for one or more PDB entries using the RCSB PDB Data API (Grap…

RCSBGraphQL_get_structure_summary tool specification

Tool Information:

  • Name: RCSBGraphQL_get_structure_summary

  • Type: RCSBGraphQLTool

  • Description: Get comprehensive structure summary for one or more PDB entries using the RCSB PDB Data API (GraphQL). Returns title, resolution, molecular weight, experimental method, deposition/release dates, primary citation (PubMed ID, journal, year), atom count, entity counts, and unit cell dimensions. Supports batch queries for multiple PDB IDs at once. Use this when you need detailed metadata about specific PDB structures beyond what basic PDB tools provide.

Parameters:

  • pdb_id ([‘string’, ‘null’]) (optional) Single PDB ID. Example: ‘4HHB’ (hemoglobin), ‘1TUP’ (p53-DNA complex), ‘6LU7’ (SARS-CoV-2 main protease).

  • pdb_ids ([‘string’, ‘null’]) (optional) Comma-separated list of PDB IDs for batch query. Example: ‘4HHB,1TUP,6LU7’. Maximum ~20 IDs per query.

Example Usage:

query = {
    "name": "RCSBGraphQL_get_structure_summary",
    "arguments": {
    }
}
result = tu.run(query)