openbabel

What problem does it solve?

This Skill addresses the challenge of interoperability between the myriad of chemical file formats, enabling seamless data conversion and manipulation for computational chemistry tasks.

Core Features & Use Cases

• Format Conversion: Convert between over 110 chemical file formats (SMILES, SDF, PDB, CIF, Gaussian, etc.).
• 3D Structure Generation: Create 3D coordinates from 2D structures or SMILES strings.
• Substructure Searching: Identify specific molecular patterns using SMARTS.
• Force Field Calculations: Perform basic molecular mechanics optimizations.
• Use Case: Convert a large library of molecules from SDF format to PDB format, adding hydrogens and generating initial 3D coordinates for each.

Quick Start

Use the openbabel skill to convert the file 'molecule.sdf' to 'molecule.pdb'.