Pdbe Ligands Tools#

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

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

Available Tools#

PDBe_get_residue_listing (Type: PDBeLigandsTool)#

Get per-residue information for a PDB structure, optionally filtered by chain. Molecules, chains …

PDBe_get_residue_listing tool specification

Tool Information:

  • Name: PDBe_get_residue_listing

  • Type: PDBeLigandsTool

  • Description: Get per-residue information for a PDB structure, optionally filtered by chain. Molecules, chains within each molecule, and residues within each chain are independently paginated. Inspect total/returned/truncated/next-offset fields at every level to avoid silently missing residues.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘4hhb’, ‘3ert’, ‘1tup’, ‘6lu7’. Case-insensitive.

  • chain_id ([‘string’, ‘null’]) (optional) Optional chain ID to filter (e.g., ‘A’, ‘B’). If not provided, all chains are returned.

  • molecule_offset (integer) (optional) Zero-based molecule offset.

  • molecule_limit (integer) (optional) Molecules returned per page (default 10, maximum 500).

  • chain_offset (integer) (optional) Zero-based chain offset applied within every returned molecule.

  • chain_limit (integer) (optional) Chains returned per molecule (default 5, maximum 500).

  • residue_offset (integer) (optional) Zero-based residue offset applied within every returned chain.

  • residue_limit (integer) (optional) Residues returned per chain (default 30, maximum 5000).

Example Usage:

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

PDBe_get_structure_ligands (Type: PDBeLigandsTool)#

Get ligands (drug-like molecules, cofactors, ions) bound in a PDB structure. Ligands and annotati…

PDBe_get_structure_ligands tool specification

Tool Information:

  • Name: PDBe_get_structure_ligands

  • Type: PDBeLigandsTool

  • Description: Get ligands (drug-like molecules, cofactors, ions) bound in a PDB structure. Ligands and annotations within each ligand are independently paginated. Inspect total/returned/truncated/next-offset fields at both levels; large structures can contain hundreds or thousands of ligand instances.

Parameters:

  • pdb_id (string) (required) PDB entry ID (4-character code). Examples: ‘4hhb’ (hemoglobin), ‘3ert’ (estrogen receptor + tamoxifen), ‘1m17’ (EGFR + erlotinib), ‘6lu7’ (SARS-CoV-2 main protease + inhibitor). Case-insensitive.

  • ligand_offset (integer) (optional) Zero-based ligand offset.

  • ligand_limit (integer) (optional) Ligands returned per page (default 50, maximum 500).

  • annotation_offset (integer) (optional) Zero-based annotation offset applied within every returned ligand.

  • annotation_limit (integer) (optional) Annotations returned per ligand (default 5, maximum 500).

Example Usage:

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