Pdb Inventory Tools#

Configuration File: pdb_inventory_tools.json Tool Type: Local Tools Count: 1

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

Available Tools#

PDB_inspect_structure (Type: PDBInventoryTool)#

Inspect local legacy PDB or public ID (1UBQ). Reports selected-model coordinates, chains, SEQRES …

PDB_inspect_structure tool specification

Tool Information:

  • Name: PDB_inspect_structure

  • Type: PDBInventoryTool

  • Description: Inspect local legacy PDB or public ID (1UBQ). Reports selected-model coordinates, chains, SEQRES declarations, missing sequence metadata, glycan-name counts and coincident atoms. Inventory only; no reconstruction, chemistry or binding validation.

Parameters:

  • pdb_path ([‘string’, ‘null’]) (optional) Local legacy PDB path; stays local. Exactly one input source.

  • pdb_content ([‘string’, ‘null’]) (optional) Inline legacy PDB coordinates; stays local. Exactly one input source.

  • pdb_id ([‘string’, ‘null’]) (optional) Four-character public RCSB identifier, e.g. 1UBQ; downloads only this public PDB.

  • model_index ([‘integer’, ‘null’]) (optional) Model by file order, default 1. Models are never pooled.

  • expected_chain_lengths ([‘object’, ‘null’]) (optional) Expected exact protein-chain length mapping, e.g. {“A”:76}. Coordinate counts and protein SEQRES declarations are compared separately; neither check verifies biological sequence identity.

  • glycan_residue_names ([‘array’, ‘null’]) (optional) Additional caller-declared glycan residue names, including GLYCAM labels. Counts ATOM and HETATM; names do not validate chemistry.

  • protein_residue_aliases ([‘object’, ‘null’]) (optional) Caller declarations mapping nonstandard protein names to canonical 3-letter amino acids; e.g. NLN to ASN for a known GLYCAM input.

  • max_residue_details ([‘integer’, ‘null’]) (optional) Bound residue detail lists, default 100. Counts and coordinate sequences stay complete; truncation is reported.

Example Usage:

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