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openbabel-conversion

Convert chemical file formats and generate 3D structures and conformers.

33|6|Updated Mar 17, 2026
Search Tags:#cheminformatics#rdkit#conformer-generation#openbabel#3d-coordinates#chemical-formats#reaction-smarts
One-click install
npx skills add https://github.com/xjtulyc/awesome-rosetta-skills --skill openbabel-conversion
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: openbabel-conversion
Source: https://github.com/xjtulyc/awesome-rosetta-skills/tree/main/skills/02-chemistry/openbabel-conversion
Command: npx skills add https://github.com/xjtulyc/awesome-rosetta-skills --skill openbabel-conversion

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

This Skill solves the problem of turning chemical representations into the format your downstream tools require, including producing valid 3D coordinates and conformers from 2D inputs.

Core Features & Use Cases

  • Chemical File Format Interconversion: Convert between SDF, SMILES, MOL2, PDB, XYZ, and related formats to standardize inputs for different pipelines.
  • 3D Coordinate Generation: Generate 3D structures from 2D SMILES using OpenBabel building and/or RDKit embedding workflows.
  • Conformer Enumeration: Create multiple candidate conformers (e.g., via RDKit ETKDG) and select low-energy structures for docking/MD or screening.
  • Reaction SMARTS Application: Transform reactants using reaction SMARTS and return product SMILES after sanitization.

Quick Start

Convert a list of SMILES strings into PDB structures with generated 3D coordinates and standardized atom mapping.

Frequently Asked Questions about openbabel-conversion

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

FAQPage Schema
How do I convert SMILES to PDB and generate 3D coordinates for docking?▼

To convert SMILES to PDB and generate 3D coordinates, you can use OpenBabel for format interconversion and RDKit ETKDG workflows to build valid 3D structures from 2D inputs for downstream docking preparation.

What is the best way to generate low-energy conformers from a 2D SMILES string?▼

Generating low-energy conformers from 2D SMILES involves creating multiple candidate conformers via RDKit ETKDG embedding, allowing you to select optimized 3D structures for molecular dynamics or virtual screening workflows.

Can I use reaction SMARTS to transform reactants and return sanitized product SMILES?▼

Yes, you can apply reaction SMARTS to transform reactants and return sanitized product SMILES by utilizing RDKit functionalities to execute the reaction pattern and sanitize the resulting chemical structures.

How do I standardize SDF files into canonical SMILES for cheminformatics pipelines?▼

Standardizing SDF files into canonical SMILES is achieved through chemical file format interconversion using OpenBabel, which normalizes inputs across SDF, MOL2, PDB, and XYZ formats for different cheminformatics pipelines.

Do I need both OpenBabel and RDKit to prepare a ligand library with 3D structures?▼

You need OpenBabel for chemical file format interconversion and optional force-field 3D building, while RDKit is required for ETKDG conformer generation and SMARTS application during comprehensive ligand library preparation.

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