chemtoolkit

A Python utility library designed for computational chemists and cheminformatics workflows. It provides streamlined helper functions built on top of RDKit, OpenConf, and ORCA to handle molecular structure reordering, 2D depiction alignment, conformer generation, ORCA input automation, orbital analysis, and 3D surface plotting.

Features

• Molecular Utilities (chemtoolkit.mol):

  • Atom Reordering: Renumber atomic indices based on SMILES mapping tags (:1, :2, etc.).
  • 2D Structure Alignment & Depiction: Render 2D molecular structures aligned spatially to a reference template.
  • Conformer Search & Extraction: Run conformer sampling via OpenConf and automatically extract lowest-energy structures.
  • Format Conversion: Convert SMILES to canonical representations and export RDKit structures to .xyz format.

• ORCA Integration (chemtoolkit.orca):

  • Input File Generation: Generate complete .inp files automatically from .xyz files with custom routes, memory allocation, and parallel execution parameters.
  • HOMO/LUMO Analysis: Parse .out log files to extract orbital indices or orbital energies (in eV).
  • Orbital & Density Plotting: Drive orca_plot non-interactively to export 3D Gaussian .cube files for HOMO, LUMO, or spin density.

Installation

From PyPI

pip install chemtoolkit