pubchem-database

PubChem Database

Prerequisites

1. `uv`: Read the uv skill and follow its Setup instructions to ensure

uv is installed and on PATH.

1. User Notification: If .licenses/pubchemdatabaseLICENSE.txt does not

already exist in the workspace root directory then (1) prominently notify the user to check the terms at https://pubchem.ncbi.nlm.nih.gov/docs/citation-guidelines and https://pubchem.ncbi.nlm.nih.gov/docs/pug-rest, then (2) create the file recording the notification text and timestamp.

Quick Start

PubChem queries are executed via a robust Python wrapper script to respect terms-of-service and handle complex JSON parsing. This script allows safe multi-agent use of APIs.

Example: Resolve a chemical name to its Compound ID (CID)

uv run scripts/pubchem_api.py resolve --name "aspirin" --output result.json

Core Rules

• Use the Wrapper: ALWAYS execute the provided helper scripts to query the

database rather than accessing the database directly. The scripts automatically enforce the required rate limit gracefully.

• Read the generated JSON output file, and process it with jq or code.
• Verify Facts: ALWAYS verify information retrieved from memory with a

database query if the user asks for a specific fact that can be checked in PubChem. Do not rely solely on internal knowledge.

• Notification: If this skill is used, ensure this is mentioned in the

output.

Core Capabilities

1. Compound Resolution (Name or InChI to Identifiers) Convert chemical/trade names or InChI strings into PubChem CIDs, SMILES, and InChIKeys.

uv run scripts/pubchem_api.py resolve --name "ibuprofen" --output result.json
# OR
uv run scripts/pubchem_api.py resolve --inchi "InChI=1S/C3/c1-3-2/i1+1" --output result.json

2. Physical & Chemical Property Retrieval Fetch computed properties (e.g., MolecularWeight, XLogP, TPSA).

uv run scripts/pubchem_api.py properties --cid 2244 --output result.json

3. Synonyms and Trade Names Find alternative names and brand names.

uv run scripts/pubchem_api.py synonyms --cid 2244 --output result.json

Advanced Context

4. Safety and Hazard Information (GHS) Retrieve Global Harmonized System hazard statements and handling precautions (uses PUG-View).

uv run scripts/pubchem_api.py safety --cid 2244 --output result.json

5. Drug and Medication Information Fetch FDA pharmacology data, mechanism of action, and therapeutic uses (uses PUG-View).

uv run scripts/pubchem_api.py pharmacology --cid 2244 --output result.json

6. Custom Heading (PUG-View) Retrieve any specific heading from the PUG-View system (e.g., 'Geometry', 'Crystal Structures').

uv run scripts/pubchem_api.py view --cid 3939 --heading "Crystal Structures" --output result.json

7. Image Generation Retrieve 2D chemical structure images. The script returns a Markdown-formatted image link.

uv run scripts/pubchem_api.py image --cid 2244 --output result.json

Complex Search & Biology

8. Structure-Based Searching (Similarity & Substructure) Find molecules similar to a SMILES string or containing a specific substructure.

uv run scripts/pubchem_api.py similarity --smiles "CC(=O)OC1=CC=CC=C1C(=O)O" --output result.json

and

uv run scripts/pubchem_api.py substructure --smiles "C1=CC=CC=C1" --output result.json

9. BioAssay & Target Interactions Identify genes or proteins a chemical interacts with.

uv run scripts/pubchem_api.py assays --cid 2244 --output result.json

Advanced Usage & Workflows

10. Cross-references (Xrefs) Fetch identifiers cross-referenced with a CID (e.g., PatentID, PubMedID).

uv run scripts/pubchem_api.py xrefs --cid 2244 --type "PatentID" --output result.json

11. Property Range Search Find CIDs within a specific property range. Supported features include: molecular_weight, heavy_atom_count, xlogp, tpsa, h_bond_donor_count, h_bond_acceptor_count, rotatable_bond_count, exact_mass, monoisotopic_mass, and complexity.

uv run scripts/pubchem_api.py range --feature molecular_weight --min 400.0 --max 400.05 --output result.json

12. Custom PUG-REST Query Execute a raw path against the PUG-REST API.

uv run scripts/pubchem_api.py query --path "compound/cid/2244/xrefs/PatentID/JSON" --output result.json

Fallback Search Strategies

If direct resolution by name or formula fails (e.g., for complex compounds or specific ions):

• Search for parent/neutral molecule: If searching for an ion or salt, try

searching for the neutral parent compound.

• Deconstruct complex formulas: If a complex formula returns no results,

try searching for major components or ligands.

• Use substructure or similarity search: If you have a SMILES string or

can generate one for a component, use it to find related compounds.

Complex Queries and Multi-Step Tasks

• Custom/Complex Queries: For more details, read

references/endpoints.md to construct raw PUG-REST URLs.

• Multi-Step Tasks: For complex tasks like drug discovery pipelines,

follow the checklists in references/workflows.md.