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 compound representation. sourceID requires the numeric sourceID field.

  • 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 the complete current UniChem source catalog and verify returned length against totalSources….

UniChem_list_sources tool specification

Tool Information:

  • Name: UniChem_list_sources

  • Type: UniChemTool

  • Description: List the complete current UniChem source catalog and verify returned length against totalSources. The live catalog currently reports 25 active sources, not a fixed 40+ count. Use the returned source IDs rather than assuming historical mappings. Current major examples include ChEMBL=1, DrugBank=2, RCSB PDB=3, PDBe=5, ChEBI=7, HMDB=18, and PubChem=22.

Parameters:

No parameters required.

Example Usage:

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

UniChem_search_compound (Type: UniChemTool)#

Search UniChem by InChI, InChIKey, source compound ID, or UCI. Every returned compound is preserv…

UniChem_search_compound tool specification

Tool Information:

  • Name: UniChem_search_compound

  • Type: UniChemTool

  • Description: Search UniChem by InChI, InChIKey, source compound ID, or UCI. Every returned compound is preserved (important because source IDs can map one-to-many), totalCompounds is normalized and verified, and every source record retains its numeric source ID. Per compound, source_record_count, unique_source_count, and duplicate_source_records distinguish database coverage from multiple IDs in the same database. Live aspirin data includes many duplicate records within sources such as ClinicalTrials and BRENDA, so source record count must not be interpreted as unique database count.

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 compound representation. sourceID means a source compound ID and requires the numeric sourceID field.

  • 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)