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openbabel

Convert chemical file formats and generate 3D coordinates from SMILES.

124|25|Updated Feb 20, 2026
Search Tags:#rendering#workflows#molecule#smiles#format-conversion#openbabel#3d-coordinates
One-click install
npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel-jinzhezenggroup
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: openbabel
Source: https://github.com/jinzhezenggroup/computational-chemistry-agent-skills/tree/main/data-processing/openbabel
Command: npx skills add https://github.com/jinzhezenggroup/computational-chemistry-agent-skills --skill openbabel-jinzhezenggroup

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

A versatile CLI tool for converting molecular file formats, generating 3D coordinates from SMILES, rendering 2D chemical structure images, and preparing or extracting structures for computational workflows.

USE WHEN you need to convert between chemical file formats (e.g., xyz, pdb, mol, smi, gjf), generate 3D structures from SMILES using --gen3d, render molecule images (PNG/SVG), or extract geometries from simulation logs to build new inputs.

Core Features & Use Cases

  • Format interconversion among common file types (xyz, pdb, mol, smi, gjf) for integration into computational pipelines.
  • Generate 3D structures from SMILES using --gen3d to seed models or simulations.
  • Render molecule images in PNG or SVG for visualization and reporting, and extract geometries from simulation logs to build new inputs.

Quick Start

Convert a SMILES string to a 3D structure and render its 2D image.

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?▼

To convert SMILES to a 3D molecular structure, you can use the openbabel tool with the --gen3d flag to generate 3D coordinates from the SMILES string. This produces geometry files like xyz, pdb, or mol for computational workflows.

What is the best way to convert between chemical file formats like xyz, pdb, and mol?▼

The best way to convert between chemical file formats like xyz, pdb, and mol is using a format interconversion tool. It processes input files and outputs the desired format, integrating seamlessly into computational pipelines.

Can I render 2D chemical structure images from a SMILES string?▼

Yes, you can render 2D chemical structure images from a SMILES string. The tool generates visualization files in PNG or SVG formats, which are useful for reporting and analyzing molecular structures.

Do I need internet access to generate 3D coordinates from SMILES?▼

Yes, you need internet access to generate 3D coordinates from SMILES. The tool operates through the openbabel-wheel obabel interface and requires both the uvx integration and an active internet connection to function.

How do I extract geometries from simulation logs to build new input files?▼

To extract geometries from simulation logs to build new input files, use the format conversion tool to parse the log and output the structure in a required format like xyz or gjf. This prepares structures for subsequent simulation workflows.

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