chem-similarity-search
OfficialFind close chemical analogs via PubChem
Education & Research#drug discovery#data export#pubchem#smiles#pug-rest#lead optimization#chemical similarity
Authorlearningmatter-mit
Version1.0.0
Installs0
System Documentation
What problem does it solve?
This Skill helps you discover structurally similar chemical compounds for a given target molecule so you can identify analogs, alternative precursors, and candidate replacements.
Core Features & Use Cases
- PubChem 2D fast similarity search: Queries PubChem’s fastsimilarity_2d endpoint to rank related compounds by 2D molecular fingerprint similarity.
- SMILES- or CID-based querying: Accepts either a SMILES string or an exact PubChem CID to reduce input friction and parsing ambiguity.
- Structured results export: Saves matched compounds with CID, canonical/absolute SMILES, IUPAC name, formula, molecular weight, and PubChem URLs for downstream selection.
Quick Start
Ask the skill to search PubChem for compounds similar to aspirin using CID 2244 with a similarity threshold of 95 and save the top 5 matches to your chosen output folder.
Dependency Matrix
Required Modules
urllibjsonpathlibtimeargparse
Components
scripts
đź’» Claude Code Installation
Recommended: Let Claude install automatically. Simply copy and paste the text below to Claude Code.
Please help me install this Skill: Name: chem-similarity-search Download link: https://github.com/learningmatter-mit/AtomisticSkills/archive/main.zip#chem-similarity-search Please download this .zip file, extract it, and install it in the .claude/skills/ directory.
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