drug-db-pubchem
OfficialFetch PubChem compound data in bulk.
Education & Research#drug discovery#data retrieval#cheminformatics#pubchem#pug-rest#compound properties#sdf download
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill removes manual lookups by automating PubChem Compound queries to retrieve standardized identifiers, computed properties, and optional structure files for downstream drug-discovery or cheminformatics workflows.
Core Features & Use Cases
- Multi-modal compound search: Find PubChem CIDs by name, SMILES, InChI, InChIKey, CID, or molecular formula.
- Property retrieval for automation: Pull key computed properties (e.g., molecular weight, XLogP, TPSA, HBD/HBA, rotatable bonds, canonical/isomeric SMILES, InChI/InChIKey, IUPAC name) in a reproducible JSON output.
- Optional enrichment: Retrieve a limited set of synonyms and optionally download 2D/3D SDF structures with 3D-to-2D fallback when available.
- Rate-limited, retry-aware querying: Uses adaptive rate limiting and exponential backoff to handle PubChem throttling (503) safely for batch/agent use.
Quick Start
Query PubChem for aspirin by name (exact match) and write the results to a JSON file: python .agents/skills/drug-db-pubchem/scripts/query_pubchem.py --name "aspirin" --name_type complete --max_results 5 --outdir research/pubchem/aspirin --output aspirin.json
Dependency Matrix
Required Modules
None requiredComponents
scripts
💻 Claude Code Installation
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Please help me install this Skill: Name: drug-db-pubchem Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#drug-db-pubchem Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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