Welcome to the AaronTools Documentation!

AaronTools is a Python module for facilitating many tasks in computational quantum chemistry workflows

Pages:

• Installation Guide
• Tutorials
• List of Command Line Scripts
• Customization
• Python API Documentation
• Advanced Topics

Note that this documentation corresponds to the version of AaronTools on GitHub. The version available via pip is usually slightly behind.

Citation

If you use AaronTools, please cite:

V. M. Ingman, A. J. Schaefer, L. R. Andreola, and S. E. Wheeler “QChASM: Quantum Chemistry Automation and Structure Manipulation” WIREs Comp. Mol. Sci. 11, e1510 (2021)

Contact

For questions, feature requests, etc. please contact the developers.

Overview of Features

Below are some of the more popular features in AaronTools, with links to the relevant command line scripts and/or Python API.

Data can be processed from several popular quantum chemsitry software packages including Gaussian, ORCA, Psi4, and xTB.

See Tutorials to get started using AaronTools.

Steric Parameters

Sterimol parameters

• substituentSterimol.py

• ligandSterimol.py

• AaronTools.substituent.Substituent.sterimol()

• AaronTools.component.Component.sterimol()

• AaronTools.geometry.Geometry.sterimol()

Buried Volume

• percentVolumeBuried.py

• AaronTools.geometry.Geometry.percent_buried_volume()

Steric Maps

• stericMap.py

• AaronTools.geometry.Geometry.steric_map()

Ligand Solid Angles

• solidAngle.py

• AaronTools.component.Component.solid_angle()

Ligand Cone Angles

• coneAngle.py

• AaronTools.component.Component.cone_angle()

Structure Operations

Add/Modify Substituents

• substitute.py

• multiSubstitute.py

• AaronTools.geometry.Geometry.substitute()

Swap Ligands

• mapLigand.py

• AaronTools.geometry.Geometry.map_ligand()

Fetch by Name/SMILES

• fetchMolecule.py

• AaronTools.geometry.Geometry.from_string()

Generate Coordination Complexes

• getCoordinationComplexes.py

• AaronTools.geometry.Geometry.get_coordination_complexes()

Quantum Chemistry Setup and Processing

Making Input Files

• makeInput.py

• makeCrestInput.py

• AaronTools.geometry.Geometry.write()

• AaronTools.theory.Theory()

Parsing Data

• printInfo.py

• AaronTools.fileIO.FileReader()

Free Energy (RRHO, Quasi-RRHO, Quasi-Harmonic)

• grabThermo.py

• AaronTools.comp_output.CompOutput()

Vibrational Frequency Analysis

• plotIR.py

• plotAverageIR.py

• follow.py

• printFreq.py

• AaronTools.spectra.Frequency()

Valence Excitations

• plotUVVis.py

• plotAverageUVVis.py

• AaronTools.spectra.ValenceExcitations()

Orbital Data

• printCube.py

• AaronTools.orbitals.Orbitals()

ChimeraX Plugin

The majority of these features are also available with a graphical interface in the SEQCROW plugin for ChimeraX.

Perl

A Perl implementation of AaronTools is also available here. However, users are strongly urged to use the Python version since it has far more powerful features and, unlike the Perl version, will continue to be developed and supported.

Indices and tables

• Index

• Module Index

• Search Page