Pubchem Tools

Configuration File: pubchem_tools.json Tool Type: Local Tools Count: 9

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

Available Tools

PubChem_get_CID_by_SMILES (Type: PubChemRESTTool)

Retrieve corresponding CID list by SMILES string.

PubChem_get_CID_by_SMILES tool specification

Tool Information:

  • Name: PubChem_get_CID_by_SMILES

  • Type: PubChemRESTTool

  • Description: Retrieve corresponding CID list by SMILES string.

Parameters:

  • smiles (string) (required) SMILES expression (e.g., “CC(=O)OC1=CC=CC=C1C(=O)O” corresponds to aspirin).

Example Usage:

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

PubChem_get_CID_by_compound_name (Type: PubChemRESTTool)

Retrieve corresponding CID list (IdentifierList) by chemical name.

PubChem_get_CID_by_compound_name tool specification

Tool Information:

  • Name: PubChem_get_CID_by_compound_name

  • Type: PubChemRESTTool

  • Description: Retrieve corresponding CID list (IdentifierList) by chemical name.

Parameters:

  • name (string) (required) Chemical name (e.g., “Aspirin” or IUPAC name).

Example Usage:

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

PubChem_get_associated_patents_by_CID (Type: PubChemRESTTool)

Get a list of patents associated with a specific compound CID.

PubChem_get_associated_patents_by_CID tool specification

Tool Information:

  • Name: PubChem_get_associated_patents_by_CID

  • Type: PubChemRESTTool

  • Description: Get a list of patents associated with a specific compound CID.

Parameters:

  • cid (integer) (required) PubChem compound ID to query, e.g., 2244 (Aspirin).

Example Usage:

query = {
    "name": "PubChem_get_associated_patents_by_CID",
    "arguments": {
        "cid": 10
    }
}
result = tu.run(query)

PubChem_get_compound_2D_image_by_CID (Type: PubChemRESTTool)

Get 2D structure image (PNG format) of compound by CID.

PubChem_get_compound_2D_image_by_CID tool specification

Tool Information:

  • Name: PubChem_get_compound_2D_image_by_CID

  • Type: PubChemRESTTool

  • Description: Get 2D structure image (PNG format) of compound by CID.

Parameters:

  • cid (integer) (required) Compound ID to get image for, e.g., 2244.

  • image_size (string) (optional) Optional parameter, image size, like “200x200” (default).

Example Usage:

query = {
    "name": "PubChem_get_compound_2D_image_by_CID",
    "arguments": {
        "cid": 10
    }
}
result = tu.run(query)

PubChem_get_compound_properties_by_CID (Type: PubChemRESTTool)

Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, …

PubChem_get_compound_properties_by_CID tool specification

Tool Information:

  • Name: PubChem_get_compound_properties_by_CID

  • Type: PubChemRESTTool

  • Description: Get a set of specified molecular properties through CID (Compound ID), such as molecular weight, IUPAC name, Canonical SMILES.

Parameters:

  • cid (integer) (required) PubChem compound ID to query, e.g., 2244 (Aspirin).

Example Usage:

query = {
    "name": "PubChem_get_compound_properties_by_CID",
    "arguments": {
        "cid": 10
    }
}
result = tu.run(query)

PubChem_get_compound_synonyms_by_CID (Type: PubChemRESTTool)

Get complete list of synonyms for compound by CID.

PubChem_get_compound_synonyms_by_CID tool specification

Tool Information:

  • Name: PubChem_get_compound_synonyms_by_CID

  • Type: PubChemRESTTool

  • Description: Get complete list of synonyms for compound by CID.

Parameters:

  • cid (integer) (required) Compound ID to query synonyms for, e.g., 2244.

Example Usage:

query = {
    "name": "PubChem_get_compound_synonyms_by_CID",
    "arguments": {
        "cid": 10
    }
}
result = tu.run(query)

PubChem_get_compound_xrefs_by_CID (Type: PubChemRESTTool)

Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.

PubChem_get_compound_xrefs_by_CID tool specification

Tool Information:

  • Name: PubChem_get_compound_xrefs_by_CID

  • Type: PubChemRESTTool

  • Description: Get external references (XRefs) for compound by CID, including links to ChEBI, DrugBank, KEGG, etc.

Parameters:

  • cid (integer) (required) Compound ID to query external references for, e.g., 2244.

  • xref_types (array) (required) List of external database types to query, e.g., [“RegistryID”, “RN”, “PubMedID”].

Example Usage:

query = {
    "name": "PubChem_get_compound_xrefs_by_CID",
    "arguments": {
        "cid": 10,
        "xref_types": ["item1", "item2"]
    }
}
result = tu.run(query)

PubChem_search_compounds_by_similarity (Type: PubChemRESTTool)

Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above …

PubChem_search_compounds_by_similarity tool specification

Tool Information:

  • Name: PubChem_search_compounds_by_similarity

  • Type: PubChemRESTTool

  • Description: Search by similarity (Tanimoto coefficient), returns CID list of compounds with similarity above threshold to given SMILES molecule, returns no more than 10 CIDs (MaxRecords=10)

Parameters:

  • smiles (string) (required) SMILES expression of target molecule.

  • threshold (number) (optional) Similarity threshold (between 0 and 1), e.g., 0.9 means 90% similarity.

Example Usage:

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

PubChem_search_compounds_by_substructure (Type: PubChemRESTTool)

Search for all CIDs in PubChem that contain the given substructure (SMILES).

PubChem_search_compounds_by_substructure tool specification

Tool Information:

  • Name: PubChem_search_compounds_by_substructure

  • Type: PubChemRESTTool

  • Description: Search for all CIDs in PubChem that contain the given substructure (SMILES).

Parameters:

  • smiles (string) (required) SMILES of substructure (e.g., “c1ccccc1” corresponds to benzene ring).

Example Usage:

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