skills.rest
InternScience
InternScienceOFFICIAL
Explore all skills by this author →
GitHub

chemical-file-converter

Convert chemical file formats with RDKit or Open Babel.

52|11|Updated Mar 10, 2026
Search Tags:#cheminformatics#rdkit#format-conversion#file-converter#openbabel#chemical
One-click install
npx skills add https://github.com/InternScience/ChemClaw --skill chemical-file-converter
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: chemical-file-converter
Source: https://github.com/InternScience/ChemClaw/tree/main/skills/chemical-file-converter
Command: npx skills add https://github.com/InternScience/ChemClaw --skill chemical-file-converter

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rdkit, openbabel, ase, and includes scripts (resource) components.

What problem does it solve?

Manual conversion between multiple chemical file formats is tedious and error-prone, slowing data curation and analysis workflows.

Core Features & Use Cases

  • Supports interconversion between XYZ, Gaussian input (.gjf/.com), MDL Molfile (.mol), Structure Data (.sdf/.sd), PDB, Tripos Mol2 (.mol2), SMILES (.smi/.smiles), CML and MOPAC formats.
  • Batch and single-file conversions via command-line, with optional Gaussian parameter customization and built-in fallback to Open Babel or RDKit.
  • Real-world use: normalize chemical datasets for QSAR modeling or molecular docking pipelines by converting all files to a common format.

Quick Start

Convert a single file such as molecule.xyz to molecule.gjf using the default Gaussian settings.

Frequently Asked Questions about chemical-file-converter

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

FAQPage Schema
How do I convert XYZ files to Gaussian input formats for computational chemistry workflows?▼

You can convert XYZ files to Gaussian input files (.gjf/.com) using this tool with default Gaussian settings or by customizing parameters. It leverages RDKit or Open Babel to transform single files or batch convert chemical datasets for computational chemistry workflows.

What chemical file formats are supported by RDKit and Open Babel for interconversion?▼

Supported chemical file formats include XYZ, Gaussian input (.gjf/.com), MDL Molfile (.mol), Structure Data (.sdf/.sd), PDB, Tripos Mol2 (.mol2), SMILES (.smi/.smiles), CML, and MOPAC formats. Conversions leverage RDKit or Open Babel for cheminformatics workflow compatibility.

Does this chemical file converter handle coordinate transformations during format conversion?▼

Yes, coordinate handling is included during chemical file format transformations. The tool leverages RDKit or Open Babel to accurately transform molecular coordinates when converting between formats like XYZ, MOL, PDB, and MOL2 for cheminformatics applications.

Can I customize Gaussian parameters when converting molecular structures to .gjf input files?▼

Yes, Gaussian parameter customization is supported when converting molecular structures to .gjf or .com input files. You can specify computational chemistry settings during the chemical file format conversion process to generate properly formatted Gaussian inputs.

Related Skills

Explore More Software Engineering Skills→
RamanEbrahimiRamanEbrahimi
3

datamol

Automate cheminformatics tasks with Python's RDKit library.

Community
Advanced
galeepgaleep

molfeat

Convert SMILES strings and RDKit molecules into numerical features for machine learning.

Community
Advanced
ovachieverovachiever
52

rdkit

Analyze and manipulate molecules with RDKit for cheminformatics workflows.

Community
Advanced
pradyumnasagarpradyumnasagar
6

molecular-io

Read and write molecular file formats with RDKit and Open Babel.

Community
Intermediate