<a href="https://badge.fury.io/py/AaronTools"><img src="https://badge.fury.io/py/AaronTools.svg" alt="PyPI version"></a> <a href='https://aarontools.readthedocs.io/en/latest/?badge=latest'> <img src='https://readthedocs.org/projects/aarontools/badge/?version=latest' alt='Documentation Status' /> </a> <a href="https://pypi.org/project/AaronTools/1.1/"><img src="https://img.shields.io/pypi/dm/aarontools.svg"></a> <a href="https://doi.org/10.1002/wcms.1510"><img src="https://img.shields.io/badge/DOI-10.1002/wcms.1510-blue"></a>

AaronTools.py

AaronTools provides a collection of tools for automating routine tasks encountered when running quantum chemistry computations.

These tools can be used either directly within a Python script using AaronTools objects, or via a series of command-line scripts.

Documentation

AaronTools documenation, including tutorials on the Python API, can be found on our <a href="https://aarontools.readthedocs.io/en/latest/">Read-the-Docs Page</a>.

Installation

• with pypi: <code>pip install AaronTools</code>

See the <a href="https://aarontools.readthedocs.io/en/latest/tutorials/install.html">installation guide</a> for more details, including how to manually install from this GitHub repository.

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" <a href="http://dx.doi.org/10.1002/wcms.1510" target="_blank"><i>WIREs Comp. Mol. Sci.</i> <b>11</b>, e1510 (2021)</a>

Features

AaronTools has a wide variety of features that can be accessed through the Python API as well as command line scripts (CLSs). These features include, but are not limited to:

• Calculating steric parameters
  • Sterimol Parameters, including Sterimol2Vec (<a href="https://aarontools.readthedocs.io/en/latest/cls/substituentSterimol.html">substituent CLS</a>, <a href="https://aarontools.readthedocs.io/en/latest/cls/ligandSterimol.html">ligand CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/substituent.py#L504">substituent API</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/component.py#L219">ligand API</a>)
  • Buried Volume (<a href="https://aarontools.readthedocs.io/en/latest/cls/percentVolumeBuried.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L2408">API</a>)
  • Steric Maps (<a href="https://aarontools.readthedocs.io/en/latest/cls/stericMap.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L2739">API</a>)
  • Ligand Solid Angle (<a href="https://aarontools.readthedocs.io/en/latest/cls/solidAngle.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/component.py#L901">API</a>)
  • Ligand Cone Angle - Tolman for asymmetric mono- and bidentate ligands, as well as exact cone angles (<a href="https://aarontools.readthedocs.io/en/latest/cls/coneAngle.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/component.py#L456">API</a>)
• Molecular Structure Editing
  • add or modify substituents (<a href="https://aarontools.readthedocs.io/en/latest/cls/substitute.html">single CLS</a>, <a href="https://aarontools.readthedocs.io/en/latest/cls/multiSubstitute.html">batch CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L3979">single API</a>)
  • swap ligands (<a href="https://aarontools.readthedocs.io/en/latest/cls/mapLigand.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L4907">API</a>)
• Generating Molecular Structures
  • coordination complexes (<a href="https://aarontools.readthedocs.io/en/latest/cls/getCoordinationComplexes.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L271">API</a>)
  • organic molecules from SMILES or IUPAC (<a href="https://aarontools.readthedocs.io/en/latest/cls/fetchMolecule.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L154">API</a>)
• Quantum Computation Setup and Processing
  • making input files for Gaussian, ORCA, Psi4, Q-Chem, xTB, and SQM (<a href="https://aarontools.readthedocs.io/en/latest/cls/makeInput.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/fileIO.py#L190">API</a>)
  • parsing data from output files (<a href="https://aarontools.readthedocs.io/en/latest/cls/printInfo.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/fileIO.py#L1077">API</a>)
  • thermochemistry based on Boltzmann-populated vibrational modes (<a href="https://aarontools.readthedocs.io/en/latest/cls/grabThermo.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/comp_output.py#L36">API</a>)
  • normal vibrational modes (<a href="https://aarontools.readthedocs.io/en/latest/cls/follow.html">displace along mode CLS</a>, <a href="https://aarontools.readthedocs.io/en/latest/cls/printFreq.html">print data CLS</a>, <a href="https://aarontools.readthedocs.io/en/latest/cls/plotIR.html">IR or VCD spectrum CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/spectra.py#L691">API</a>)
  • valence excitations (<a href="https://aarontools.readthedocs.io/en/latest/cls/plotUVVis.html">UV/vis or ECD spectrum CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/spectra.py#L1327">API</a>)
  • orbitals, electron density, and Fukui functions (<a href="https://aarontools.readthedocs.io/en/latest/cls/printCube.html">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/e5f218341e47c74e41df3340ab6a31d3cadcaf6a/orbitals.py#L14">API</a>)
• Parse data from output files of several popular quantum chemistry programs (<a href="https://aarontools.readthedocs.io/en/latest/tutorials/coding_with_filereaders.html">Read-the-Docs Tutorial</a>)
  • Gaussian
  • ORCA
  • Psi4
  • Q-Chem
  • NBO
  • xTB

Features are explained in more detail in the <a href="https://aarontools.readthedocs.io/en/latest/">documentation and in docstrings of the Python API.

Other Versions

ChimeraX Plugin

The majority of these features are also available with a graphical interface in the <a href="https://cxtoolshed.rbvi.ucsf.edu/apps/seqcrow">SEQCROW plugin</a> for <a href="https://www.cgl.ucsf.edu/chimerax/">ChimeraX</a>.

Perl

A Perl implementation of AaronTools is also <a href="https://github.com/QChASM/AaronTools">available here.</a> However, users are <em>strongly urged</em> to use the Python version since it has far more powerful features and, unlike the Perl version, will continue to be developed and supported.

Contact

If you have any questions or would like to discuss bugs or additional needed features, feel free to contact us at qchasm@uga.edu