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Documentation Index

Fetch the complete documentation index at: https://mintlify.com/pranavkrishnasuresh/chemAgent/llms.txt

Use this file to discover all available pages before exploring further.

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Overview

The pubchem_fetcher.py module handles all interactions with the PubChem REST API, fetching chemical compound information using multiple search strategies (CID, formula, and name-based lookups).

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Constants

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PUBCHEM_API_BASE

PUBCHEM_API_BASE = "https://pubchem.ncbi.nlm.nih.gov/rest/pug"
Base URL for the PubChem PUG REST API.

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Functions

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fetch_pubchem_data

Retrieves chemical compound descriptions from PubChem using multiple API endpoints.
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terms
list[str]
required
List of chemistry terms extracted from the user query
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context
str
Formatted string containing all retrieved PubChem descriptions, or empty string if no data found

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Search Strategy

For each term, the function attempts three different PubChem endpoints:
  1. CID (Compound ID): /compound/cid/{term}/description/JSON
  2. Formula: /compound/formula/{term}/description/JSON
  3. Name: /compound/name/{term}/description/JSON
This multi-endpoint approach maximizes the chances of finding relevant data regardless of how the user phrases their query.

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Error Handling

  • requests.exceptions.RequestException: Silently skips failed requests
  • ValueError: Handles JSON parsing errors gracefully
  • Timeouts set to 10 seconds per request

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extract_pubchem_descriptions

Parses PubChem API responses to extract description text.
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data
dict
required
JSON response from PubChem API
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descriptions
str | None
Concatenated description strings, or None if no descriptions found

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Example Usage

from plan_execute_agent.pubchem_rag.pubchem_fetcher import fetch_pubchem_data

# Fetch data for multiple chemistry terms
terms = ["aspirin", "C9H8O4", "acetylsalicylic acid"]
context = fetch_pubchem_data(terms)
print(context)

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Response Format

The function returns formatted text blocks for each successful query: 
**Term**: aspirin
**Endpoint**: /compound/name/aspirin/description/JSON
Aspirin is a salicylate drug that inhibits cyclooxygenase...

**Term**: C9H8O4
**Endpoint**: /compound/formula/C9H8O4/description/JSON
Acetylsalicylic acid is an organic compound...

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PubChem API Structure

The function expects responses in this format: 
{
  "InformationList": {
    "Information": [
      {
        "Description": "Chemical description text..."
      }
    ]
  }
}

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Integration Notes

  • Called by query_chemistry_related() in the RAG pipeline
  • Provides the context that feeds into the LLM response generator
  • Designed to be fault-tolerant, continuing even if some requests fail
  • No API key required (uses public PubChem endpoints)

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Source Location

  • fetch_pubchem_data: plan_execute_agent/pubchem_rag/pubchem_fetcher.py:6
  • extract_pubchem_descriptions: plan_execute_agent/pubchem_rag/pubchem_fetcher.py:40

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