openbabel-conversion

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.