skills.rest
jackspace
jackspaceCOMMUNITY
Explore all skills by this author →
GitHub

pubchem-database

Query PubChem compound records and retrieve molecular properties via PubChemPy or PUG-REST.

16|7|Updated Nov 20, 2025
Search Tags:#similarity#pubchem#pubchempy#smiles#substructure#CID
One-click install
npx skills add https://github.com/jackspace/ClaudeSkillz --skill pubchem-database-jackspace
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-db-pubchem-database
Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill pubchem-database-jackspace

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires pubchempy, requests, pandas, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill enables programmatic access to PubChem via PubChemPy and PUG-REST for compound lookup, property retrieval, similarity/substructure searches, and bioactivity data.

Core Features & Use Cases

  • Structure search by name, CID, SMILES, InChI
  • Retrieve molecular properties (MW, XLogP, TPSA, etc.)
  • Similarity and substructure searches
  • Access bioactivity data and compound annotations

Quick Start

Install PubChemPy, fetch a compound by name (aspirin), and read key properties (MW, SMILES).

Frequently Asked Questions about pubchem-database

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I query PubChem by compound name, CID, or SMILES?▼

Query PubChem using PubChemPy or PUG-REST API by providing a compound name, CID identifier, or SMILES string. The Skill automates lookups across multiple identifier types and returns matching compound records with full property data.

What molecular properties can I retrieve from PubChem?▼

Retrieved properties include MolecularFormula, MolecularWeight, CanonicalSMILES, IsomericSMILES, InChI, InChIKey, XLogP, TPSA, HBondDonorCount, HBondAcceptorCount, RotatableBondCount, Complexity, and Charge, along with bioactivity annotations.

Can I perform similarity and substructure searches in PubChem?▼

Yes, similarity and substructure searches are supported through the Skill's integration with PubChemPy and PUG-REST. Provide a SMILES or InChI string to find related compounds or matching substructures with ranked results.

How do I batch process multiple compounds from PubChem?▼

Batch processing multiple identifier inputs is supported; the Skill handles format conversions and property retrieval across large compound sets, with pandas integration for structured output and downstream analysis.

What's the difference between using PubChemPy versus PUG-REST for compound lookups?▼

Both PubChemPy and PUG-REST are supported. PubChemPy offers a direct Python interface; PUG-REST provides programmatic HTTP access. The Skill abstracts both, selecting based on query type and returning consistent property formats.

Can I access bioactivity data and compound annotations from PubChem?▼

Yes, the Skill retrieves bioactivity data and compound annotations alongside core molecular properties, enabling integration of biological activity information into cheminformatics workflows.

Related Skills

Explore More Data & Analytics Skills→
learningmatter-mitlearningmatter-mit
144

drug-db-pubchem

Retrieve PubChem compound identifiers and metadata via PUG-REST queries.

Official
Intermediate
Lord1EgyptLord1Egypt
2

deepchem

Train graph neural networks for molecular property prediction on chemical datasets.

Community
Advanced
yf8578yf8578
1

rdkit

Calculate molecular descriptors and generate fingerprints from SMILES strings using RDKit.

Community
Advanced
InternScienceInternScience
28

molclaw-compound-retrieve

Retrieve canonical SMILES strings from PubChem for batch compound names.

Official
Basic