pubchem-database
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
npx skills add LeonChaoX/qinyan-academic-skills --skill pubchem-database --agent claude-code
Same command for any agent — swap --agent for codex, cursor, copilot.
Weekly change comes from our own snapshots, not the repository page — it measures attention, not adoption.
# 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.Compo
- Overview
- When to Use This Skill
- Core Capabilities
- 1. Chemical Structure Search
- 2. Property Retrieval
- 3. Similarity Search
- 4. Substructure Search
- 5. Format Conversion
- 6. Structure Visualization
- 7. Synonym Retrieval
- 8. Bioactivity Data Access
- 9. Comprehensive Compound Annotations
- Installation Requirements
- Helper Scripts
uv pip install pubchempy uv pip install requests uv pip install pandas
What does the pubchem-database skill do?
Query PubChem via PUG-REST API/PubChemPy (110M+ compounds). Search by name/CID/SMILES, retrieve properties, similarity/substructure searches, bioactivity, for cheminformatics.
How do I install it?
Run `npx skills add LeonChaoX/qinyan-academic-skills --skill pubchem-database --agent claude-code` — it drops the skill into your project so the agent can pick it up. Swap the --agent value for codex, cursor or copilot if you use one of those.
Where does this skill come from?
From LeonChaoX/qinyan-academic-skills, a repository with 759 stars. We read it straight from the repository tree rather than a submitted listing, so what you see here is what is actually published.
Is a popular skill a good skill?
Not necessarily. Stars measure attention, not adoption — a repository can trend for a week and be abandoned. That is why we show the weekly change from our own snapshots next to the total, instead of a single flattering number.