chemtoolkit

Cheminformatics and computational chemistry utilities providing helper functions built on top of RDKit, OpenConf, and ORCA to streamline molecular manipulation, 2D structure alignment, conformer generation, and quantum chemical workflows.

Features

• Molecular Utilities (chemtoolkit.mol):

  • Atom Reordering: Reorder atomic indices sequentially based on SMILES mapping tags (:1, :2, etc.).
  • 2D Structure Alignment & Rendering: Draw molecules in 2D while maintaining spatial orientation aligned with a reference template.
  • Conformer Search & Parsing: Generate conformer ensembles via OpenConf and automatically extract the lowest energy frame.
  • Format Conversion: Export structures to .xyz format and strip atom mappings into canonical SMILES.

• ORCA Integration (chemtoolkit.orca):

  • Input File Generation: Easily write .inp calculation files with custom route parameters, memory allocation, and processor configurations.
  • Output Parsing: Extract final single-point energies and optimized 3D geometries directly from ORCA .out log files.

Installation

From PyPI

pip install chemtoolkit