# Pubchem Database

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds).

- Repository: https://github.com/benchflow-ai/skillsbench (1888 stars)
- Category: Engineering
- License: Unknown
- Last updated: 2026-10-24
- Runs scripts: yes, review before use

## Install

Claude Code: `npx skills add benchflow-ai/skillsbench --skill pubchem-database -g -a claude-code -y`
Codex: `npx skills add benchflow-ai/skillsbench --skill pubchem-database -g -a codex -y`
Cursor: `npx skills add benchflow-ai/skillsbench --skill pubchem-database -g -a cursor -y`
Gemini CLI: `npx skills add benchflow-ai/skillsbench --skill pubchem-database -g -a gemini-cli -y`

## Description

Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

# PubChem Database

## Overview

PubChem is the world's largest freely available chemical database with 110M+ compounds and 270M+ bioactivities. Query chemical structures by name, CID, or SMILES, retrieve molecular properties, perform similarity and substructure searches, access bioactivity data using PUG-REST API and PubChemPy.

## When to Use This Skill

This skill should be used when:
- Searching for chemical compounds by name, structure (SMILES/InChI), or molecular formula
- Retrieving molecular properties (MW, LogP, TPSA, hydrogen bonding descriptors)
- Performing similarity searches to find structurally related compounds
- Conducting substructure searches for specific chemical motifs
- Accessing bioactivity data from screening assays
- Converting between chemical identifier formats (CID, SMILES, InChI)
- Batch processing multiple compounds for drug-likeness screening or property analysis

## Core Capabilities

### 1. Chemical Structure Search

Search for compounds using multiple identifier types:

**By Chemical Name**:
```python
import pubchempy as pcp
compounds = pcp.get_compounds('aspirin', 'name')
compound = compounds[0]
```

**By CID (Compound ID)**:
```python
compound = pcp.Compound.from_cid(2244)  # Aspirin
```

**By SMILES**:
```python
compound = pcp.get_compounds('CC(=O)OC1=CC=CC=C1C(=O)O', 'smiles')[0]
```

**By InChI**:
```python
compound = pcp.get_compounds('InChI=1S/C9H8O4/...', 'inchi')[0]
```

**By Molecular Formula**:
```python
compounds = pcp.get_compounds('C9H8O4', 'formula')
# Returns all compounds matching this formula
```

### 2. Property Retrieval

Retrieve molecular properties for compounds using either high-level or low-level approaches:

**Using PubChemPy (Recommended)**:
```python
import pubchempy as pcp

# Get compound object with all properties
compound = pcp.get_compounds('caffeine', 'name')[0]

The rest: https://github.com/benchflow-ai/skillsbench/blob/HEAD/tasks-extra/find-topk-similiar-chemicals/environment/skills/pubchem-database/SKILL.md