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iupac-name-identification-biot5

Identify IUPAC names from SMILES strings or common names using BioT5, MolT5, and RDKit.

1.1k|132|Updated Apr 13, 2023
Search Tags:#qa#nomenclature#molecule#rdkit#iupac#biot5#molt5
One-click install
npx skills add https://github.com/PharMolix/OpenBioMed --skill iupac-name-identification-biot5
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: iupac-name-identification-biot5
Source: https://github.com/PharMolix/OpenBioMed/tree/main/skills/iupac-name-identification-biot5
Command: npx skills add https://github.com/PharMolix/OpenBioMed --skill iupac-name-identification-biot5

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This skill identifies the IUPAC name of a molecule from either a SMILES string or a common molecule name, enabling precise systematic nomenclature for chemical data workflows.

Core Features & Use Cases

  • Identify IUPAC names from SMILES or common names.
  • Use BioT5 as the default QA model with MolT5 as an alternative and a fallback to RDKit MolToIUPACName if QA fails.
  • Real-world use: annotate large molecule libraries with IUPAC nomenclature for downstream analyses or publications.

Quick Start

Provide a SMILES string or a common molecule name to obtain its IUPAC name.

Frequently Asked Questions about iupac-name-identification-biot5

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

FAQPage Schema
How do I get an IUPAC name from a SMILES string?▼

To get an IUPAC name from a SMILES string, you can use a QA model like BioT5 to identify the systematic nomenclature, automatically falling back to RDKit if the initial model fails.

Can I identify a molecule's IUPAC name using a common name instead of SMILES?▼

Yes, you can identify the IUPAC name using a common name instead of SMILES. The system accepts a common molecule name as input and translates it into standard IUPAC nomenclature.

What happens if BioT5 fails to generate the correct IUPAC name?▼

If BioT5 fails to generate the correct IUPAC name, the system uses MolT5 as an alternative QA model, and ultimately falls back to RDKit MolToIUPACName to ensure a valid name is returned.

What is the best way to annotate large molecule libraries with systematic nomenclature?▼

The best way to annotate large molecule libraries with systematic nomenclature is processing SMILES strings or common names through a QA model, yielding plain text IUPAC names for downstream analyses.

Does the IUPAC name identification tool require external dependencies?▼

No, the IUPAC name identification tool requires no external dependencies to function. It internally handles the QA models and RDKit fallback logic to output the chemical nomenclature seamlessly.

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