Rcsb Data Tools

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

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

Available Tools

RCSBData_get_assembly (Type: RCSBDataTool)

Get biological assembly details for a PDB structure from the RCSB Data API. Returns oligomeric st…

RCSBData_get_assembly tool specification

Tool Information:

  • Name: RCSBData_get_assembly

  • Type: RCSBDataTool

  • Description: Get biological assembly details for a PDB structure from the RCSB Data API. Returns oligomeric state (monomeric, dimeric, tetrameric, etc.), stoichiometry, polymer/nonpolymer entity counts in the assembly, symmetry operations, and evidence for the biological relevance of the assembly. Example: ‘4HHB’ assembly 1 returns ‘tetrameric’ with 2 polymer entities (alpha and beta hemoglobin).

Parameters:

  • pdb_id (string) (required) PDB entry ID (4 characters). Examples: ‘4HHB’ (hemoglobin tetramer), ‘1TUP’ (p53 dimer), ‘3PQR’ (insulin hexamer).

  • assembly_id (string) (optional) Assembly identifier (default ‘1’ for the first/preferred assembly). Most structures have assembly 1 as the biologically relevant form.

Example Usage:

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

RCSBData_get_entry (Type: RCSBDataTool)

Get comprehensive structure metadata for a PDB entry from the RCSB Data API. Returns experimental…

RCSBData_get_entry tool specification

Tool Information:

  • Name: RCSBData_get_entry

  • Type: RCSBDataTool

  • Description: Get comprehensive structure metadata for a PDB entry from the RCSB Data API. Returns experimental method, resolution, deposition/release dates, polymer/nonpolymer entity counts, molecular weight, assembly count, space group, and unit cell dimensions. This is the direct REST endpoint for PDB entry details, complementing GraphQL-based tools. Example: ‘4HHB’ returns hemoglobin at 1.74A by X-ray diffraction, deposited 1984-03-07, 2 polymer entities.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4 characters). Examples: ‘4HHB’ (hemoglobin), ‘1TUP’ (p53-DNA complex), ‘1M17’ (EGFR kinase), ‘6LU7’ (SARS-CoV-2 main protease).

Example Usage:

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

RCSBData_get_nonpolymer_entity (Type: RCSBDataTool)

Get non-polymer entity (ligand/small molecule) details from a PDB structure via the RCSB Data API…

RCSBData_get_nonpolymer_entity tool specification

Tool Information:

  • Name: RCSBData_get_nonpolymer_entity

  • Type: RCSBDataTool

  • Description: Get non-polymer entity (ligand/small molecule) details from a PDB structure via the RCSB Data API. Returns the chemical name, component ID, formula weight, chain assignments, and any DrugBank or other database annotations. Useful for identifying what ligands, cofactors, or ions are bound in a structure. Example: ‘4HHB’ entity 3 returns ‘PROTOPORPHYRIN IX CONTAINING FE’ (HEM), the heme group bound to hemoglobin.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4 characters). Examples: ‘4HHB’ (hemoglobin + heme), ‘3ERT’ (estrogen receptor + tamoxifen), ‘6LU7’ (SARS-CoV-2 + inhibitor).

  • entity_id (string) (required) Entity ID within the PDB entry. Non-polymer entities typically start after the polymer entities. Use pdbe_get_entry_molecules or RCSBGraphQL_get_structure_summary to discover entity IDs.

Example Usage:

query = {
    "name": "RCSBData_get_nonpolymer_entity",
    "arguments": {
        "pdb_id": "example_value",
        "entity_id": "example_value"
    }
}
result = tu.run(query)