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MolOP (Molecule OPerator)

MolOP is a Python 3.10+ library and CLI designed to streamline computational chemistry workflows. It bridges the gap between raw calculation outputs and structured, analysis-ready molecular data.

What is MolOP?

  • Unified Parser: A single interface (AutoParser) to read Gaussian logs, GJF, XYZ, SDF, and more.
  • Structure Recovery: Advanced algorithms to reconstruct molecular graphs (bonds) from coordinates, with superior support for radicals and metal complexes.
  • Data Modeling: Pydantic-based models providing type-safe access to energies, vibrations, orbitals, and population analysis.
  • Batch Processor: Parallelized processing of thousands of files with built-in filtering and transformation capabilities.

When to use

  • You need to extract thermodynamic data or properties from hundreds of Gaussian log files.
  • You want to convert between chemical file formats while preserving or recovering bonding information.
  • You are building a machine learning pipeline and need a reliable way to featurize molecular structures from QM outputs.
  • You prefer a “chained” CLI for quick data inspection and manipulation without writing Python scripts.

Non-goals

  • Quantum Solver: MolOP does not perform QM calculations; it parses and processes their results.
  • Visualization: While it integrates with RDKit, it is not a dedicated molecular viewer.
  • Force Field Engine: It is not designed for running molecular dynamics simulations.

Getting Started

Citation

If MolOP helps your research, please cite it as:

MolOP (Molecule OPerator), https://github.com/gentle1999/MolOP