openbabel

Convert molecular formats and generate 3D coordinates with Open Babel.

181|20|Updated Apr 29, 2026

Search Tags:#format-conversion #openbabel #3d-coordinates #molecular-formats #hydrogen-addition #chemistry-tools

Ready to run

npx skills add https://github.com/Hello-QM/catgo-LRG --skill openbabel-hello-qm

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: openbabel
Source: https://github.com/Hello-QM/catgo-LRG/tree/main/server/catgo/workflow/skills/data/openbabel
Command: npx skills add https://github.com/Hello-QM/catgo-LRG --skill openbabel-hello-qm

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Convert molecular formats and generate 3D coordinates for molecular structures, enabling seamless interconversion and structure generation in computational chemistry workflows.

Core Features & Use Cases

Format interconversion: Convert SMILES, SDF/MOL, PDB, MOL2, XYZ, CIF, and more between formats.
3D coordinate generation: Generate 3D coordinates for 2D representations or initial structures.
Hydrogen handling: Add or adjust hydrogens as needed during conversion.
Use Case: Prepare input geometries for docking, quantum chemistry calculations, or HPC workflows using Open Babel.

Quick Start

Convert a SMILES string to a 3D geometry using Open Babel.

Frequently Asked Questions about openbabel

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

FAQPage Schema

How do I convert SMILES to a 3D molecular structure for computational chemistry workflows?▼

Open Babel generates 3D coordinates from 2D representations like SMILES to create input geometries for docking or quantum chemistry calculations. It handles interconversion between common molecular formats seamlessly.

Can I convert PDB files to SDF or MOL2 format for molecular dynamics simulations?▼

Open Babel supports interconversion among SMILES, SDF/MOL, PDB, MOL2, XYZ, and CIF formats for cheminformatics workflows. You can convert PDB files to SDF or MOL2 to prepare structures for molecular dynamics.

What is the best way to add hydrogens to a molecular structure during format conversion?▼

Open Babel provides hydrogen handling features to add or adjust hydrogens as needed during format conversion. This ensures correct protonation states when preparing molecular structures for downstream analysis.

Do I need to install Open Babel separately to generate 3D coordinates for CIF files?▼

You must have Open Babel installed via apt or conda to generate 3D coordinates for CIF files. Optional Python bindings are also available if you need to script the coordinate generation process.

Does Open Babel support XYZ format conversion for HPC computational workflows?▼

Open Babel supports XYZ format conversion for HPC computational workflows. It enables seamless interconversion of XYZ files with other common formats to prepare input geometries for large-scale calculations.