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pubchem-database

Query PubChem via PUG-REST and PubChemPy to retrieve chemical compound data.

52|6|Updated Nov 24, 2025
Search Tags:#SMILES#similarity#substructure#CID#PUG-REST#PubChem
One-click install
npx skills add https://github.com/ovachiever/droid-tings --skill pubchem-database-ovachiever
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pubchem-database
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/pubchem-database
Command: npx skills add https://github.com/ovachiever/droid-tings --skill pubchem-database-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

Access PubChem programmatically to search, map, and retrieve chemical data with PUG-REST and PubChemPy.

Core Features & Use Cases

  • Search by name, CID, SMILES and fetch properties
  • Similarity and substructure searches to discover related compounds
  • ID mapping between databases via PubChem
  • Bioactivity data retrieval via PUG-REST

Quick Start

Example: search for aspirin by name and fetch molecular weight: pubchem: pubchempy usage example includes code.

Frequently Asked Questions about pubchem-database

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

FAQPage Schema
How do I search PubChem for chemical compounds by name or SMILES?▼

PubChem search retrieves compound data using PUG-REST or PubChemPy by querying compound names, CIDs, SMILES strings, or InChI identifiers. The Skill returns molecular properties, structures, and bioactivity records matching your search criteria.

Can I perform similarity and substructure searches on PubChem?▼

Yes, PubChem similarity and substructure searches identify related compounds and structural matches. The Skill leverages PUG-REST endpoints to find compounds with similar scaffolds or exact substructure matches, useful for drug discovery and chemical screening.

What molecular properties can I retrieve from PubChem?▼

PubChem retrieval includes MolecularFormula, MolecularWeight, CanonicalSMILES, IsomericSMILES, InChI, InChIKey, XLogP, TPSA, HBondDonorCount, and HBondAcceptorCount. These properties support molecular profiling, ADMET prediction, and compound characterization.

How do I map chemical identifiers between PubChem and other databases?▼

PubChem ID mapping converts between CIDs, SMILES, InChI, and external identifiers across databases. The Skill uses PUG-REST endpoints to cross-reference compounds and standardize identifier formats for data integration workflows.

Can I batch process multiple compounds or run large-scale screening?▼

Yes, the Skill supports batch queries and asynchronous operations for processing multiple compounds efficiently. This enables high-throughput screening, bulk property retrieval, and large-scale chemical library analysis without API rate-limit delays.

What dependencies do I need to access PubChem programmatically?▼

PubChem access requires pubchempy and requests libraries. PubChemPy wraps the REST API; requests handles HTTP communication. Both dependencies enable compound queries, property downloads, and format conversions in Python workflows.

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