skills.rest
InternScience
InternScienceOFFICIAL
Explore all skills by this author →
GitHub

molclaw-compound-retrieve

Retrieve canonical SMILES strings from PubChem for batch compound names.

28|2|Updated Mar 31, 2026
Search Tags:#cheminformatics#batch-processing#pubchem#smiles#compound-retrieval#molecular-data
One-click install
npx skills add https://github.com/InternScience/MolClaw --skill molclaw-compound-retrieve
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: molclaw-compound-retrieve
Source: https://github.com/InternScience/MolClaw/tree/main/skills/L1_tools/molclaw-compound-retrieve
Command: npx skills add https://github.com/InternScience/MolClaw --skill molclaw-compound-retrieve

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Rapidly obtain canonical SMILES strings for chemical compounds given human-readable names, eliminating manual searches and accelerating dataset curation or downstream cheminformatics tasks.

Core Features & Use Cases

  • Batch name-to-SMILES retrieval: Accepts lists of compound names and returns corresponding SMILES mappings.
  • Status-aware responses: Returns success/partial_success/error statuses and messages to surface missing or ambiguous results.
  • Use Case: Populate a compound dataset for virtual screening by converting supplier or literature compound names into machine-readable SMILES for property calculation and model input.

Quick Start

Ask the skill to retrieve SMILES for a list of compound names, for example, retrieve SMILES for aspirin and caffeine.

Frequently Asked Questions about molclaw-compound-retrieve

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

FAQPage Schema
How do I retrieve SMILES strings from PubChem using compound names?▼

Retrieve canonical SMILES from PubChem by submitting a batch list of compound names. The tool returns a mapping of compound names to SMILES strings while indicating missing or unresolved entries.

Can I fetch SMILES for multiple compounds in batch?▼

Fetch SMILES for multiple compounds by supplying a batch list of names. The response provides a success, partial_success, or error status alongside the compound-to-SMILES mapping, flagging missing entries.

What happens if PubChem cannot resolve a compound name to a SMILES string?▼

Unresolved compound names return a partial_success or error status. The response includes a compound_name to smiles mapping that explicitly flags missing or ambiguous entries so you can identify gaps in your dataset.

Does this SMILES retrieval tool handle missing or ambiguous PubChem entries?▼

The tool handles missing or ambiguous PubChem entries by returning status-aware responses. It outputs success, partial_success, or error statuses alongside the compound-to-SMILES mapping to clearly flag unresolved results.

Why convert compound names to canonical SMILES for cheminformatics workflows?▼

Converting compound names to canonical SMILES provides machine-readable molecular structures required for cheminformatics workflows. This accelerates dataset curation, virtual screening, and property calculation pipelines by eliminating manual searches.

Related Skills

Explore More Education & Research Skills→
swaruplabswaruplab
94

metabolomics-workbench-database

Retrieve Metabolomics Workbench studies, compounds, and RefMet data via REST API.

Community
Intermediate
InternScienceInternScience
28

molclaw-mol-structure-metrics

Compute molecular structure complexity metrics for SMILES lists.

Official
Intermediate
Yezez9Yezez9

datamol

Parse, standardize, and analyze molecular structures with RDKit via Python.

Community
Intermediate
yf8578yf8578
1

pubchem-database

Query PubChem via PubChemPy and PUG-REST for compound properties and bioactivity data.

Community
Intermediate