Unichem Tools

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

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

Available Tools

UniChem_connectivity_search (Type: UniChemTool)

Connectivity (cross-source) search in UniChem: find all compounds across the 40+ source databases…

UniChem_connectivity_search tool specification

Tool Information:

  • Name: UniChem_connectivity_search

  • Type: UniChemTool

  • Description: Connectivity (cross-source) search in UniChem: find all compounds across the 40+ source databases that share the same connectivity layer as the query - i.e. salts, stereoisomers, tautomers, and charge/protonation/isotope variants of the input structure. Each returned match carries a per-match ‘comparison’ object of boolean flags (charge, connectivity, formula, isotope, protonation, stereoDbond, stereoSp3, HAtoms, …) showing exactly how that match differs from the query. Use this (rather than UniChem_search_compound, which does exact-structure matching) to discover related forms of a molecule across databases. Example: aspirin InChIKey ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’ returns response ‘Success’ with totalCompounds 15 across 1044 source entries.

Parameters:

  • compound (string) (required) The compound identifier to search. Typically a (full or connectivity-layer) InChIKey, e.g. ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’ (aspirin). Can also be a source compound ID when type=’sourceID’.

  • type (string) (required) Type of the compound identifier. One of: ‘inchikey’, ‘sourceID’, ‘uci’. Default: ‘inchikey’.

  • sourceID ([‘integer’, ‘null’]) (optional) Required when type=’sourceID’. The source database ID (e.g., 1=ChEMBL, 2=DrugBank, 7=ChEBI, 22=PubChem).

Example Usage:

query = {
    "name": "UniChem_connectivity_search",
    "arguments": {
        "compound": "example_value",
        "type": "example_value"
    }
}
result = tu.run(query)

UniChem_list_sources (Type: UniChemTool)

List all chemical database sources registered in UniChem. Returns the complete catalog of 40+ dat…

UniChem_list_sources tool specification

Tool Information:

  • Name: UniChem_list_sources

  • Type: UniChemTool

  • Description: List all chemical database sources registered in UniChem. Returns the complete catalog of 40+ databases with their source IDs, names, descriptions, compound counts, and URLs. Use this to discover which databases are available for cross-referencing and to find source IDs for the UniChem_search_compound tool. Major sources include ChEMBL (id=1), DrugBank (id=2), PDBe (id=3), PubChem (id=22), KEGG (id=6), ChEBI (id=7), HMDB (id=18).

Parameters:

No parameters required.

Example Usage:

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

UniChem_search_compound (Type: UniChemTool)

Search UniChem for a chemical compound by InChIKey, source compound ID, or UCI (UniChem Compound …

UniChem_search_compound tool specification

Tool Information:

  • Name: UniChem_search_compound

  • Type: UniChemTool

  • Description: Search UniChem for a chemical compound by InChIKey, source compound ID, or UCI (UniChem Compound Identifier). Returns cross-references to the compound across 40+ chemical databases including ChEMBL, DrugBank, PDBe, PubChem, KEGG, ChEBI, HMDB, and more. UniChem is EBI’s unified chemical cross-referencing service. Example: searching InChIKey ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’ (aspirin) returns mappings to CHEMBL25, DB00945, C01405, etc.

Parameters:

  • compound (string) (required) The compound identifier to search. Can be an InChIKey (e.g., ‘BSYNRYMUTXBXSQ-UHFFFAOYSA-N’), source compound ID (e.g., ‘CHEMBL25’), or UCI number.

  • type (string) (required) Type of the compound identifier. One of: ‘inchikey’, ‘sourceID’, ‘uci’. Default: ‘inchikey’.

  • sourceID ([‘integer’, ‘null’]) (optional) Required when type=’sourceID’. The source database ID (e.g., 1=ChEMBL, 2=DrugBank, 7=ChEBI, 22=PubChem). Use UniChem_list_sources to see all IDs.

Example Usage:

query = {
    "name": "UniChem_search_compound",
    "arguments": {
        "compound": "example_value",
        "type": "example_value"
    }
}
result = tu.run(query)