Pdb Link Audit Tools#
Configuration File: pdb_link_audit_tools.json
Tool Type: Local
Tools Count: 1
This page contains all tools defined in the pdb_link_audit_tools.json configuration file.
Available Tools#
PDB_compare_declared_links (Type: PDBLinkAuditTool)#
Compare explicit reference PDB LINK distances against a local PDB model. Resolves exact atoms wit…
PDB_compare_declared_links tool specification
Tool Information:
Name:
PDB_compare_declared_linksType:
PDBLinkAuditToolDescription: Compare explicit reference PDB LINK distances against a local PDB model. Resolves exact atoms with optional chain/residue remapping and reports missing/ambiguous endpoints. Local diagnostic only; no inferred bonds, chemistry or binding validation.
Parameters:
reference_pdb_path([‘string’, ‘null’]) (optional) Local reference legacy PDB path; exactly one path or content for this input. Never uploaded.reference_pdb_content([‘string’, ‘null’]) (optional) Local reference legacy PDB content; exactly one path or content for this input. Never uploaded.reference_model_index([‘integer’, ‘null’]) (optional) Select model by file order, default1; models never pooled.observed_pdb_path([‘string’, ‘null’]) (optional) Local observed legacy PDB path; exactly one path or content for this input. Never uploaded.observed_pdb_content([‘string’, ‘null’]) (optional) Local observed legacy PDB content; exactly one path or content for this input. Never uploaded.observed_model_index([‘integer’, ‘null’]) (optional) Select model by file order, default1; models never pooled.max_length_error_angstrom([‘number’, ‘null’]) (optional) Maximum absolute deviation from reference coordinate distance, default0.3 Angstrom; not an ideal bond-length rule.chain_map([‘object’, ‘null’]) (optional) Explicit reference-to-observed chain map, default identity. A blank PDB chain ID is one space.residue_map([‘array’, ‘null’]) (optional) Explicit residue-number/insertion remapping within the chain map. Unmapped residues retain IDs; no sequence alignment or residue reconstruction.
Example Usage:
query = {
"name": "PDB_compare_declared_links",
"arguments": {
}
}
result = tu.run(query)