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‎README.md

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<a href="https://badge.fury.io/py/AaronTools"><img src="https://badge.fury.io/py/AaronTools.svg" alt="PyPI version" height="18"></a>
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<a href="https://badge.fury.io/py/AaronTools"><img src="https://badge.fury.io/py/AaronTools.svg" alt="PyPI version"></a>
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<a href="https://doi.org/10.1002/wcms.1510"><img src="https://img.shields.io/badge/DOI-10.1002/wcms.1510-blue"></a>
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# AaronTools.py
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AaronTools provides a collection of tools for automating routine tasks encountered when running quantum chemistry computations.
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These tools can be used either directly within a Python script using AaronTools objects, or via a series of command-line scripts.
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See the <a href="https://github.com/QChASM/AaronTools.py/wiki">Wiki</a> for installation and usage.
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## Installation
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AaronTools is described in
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"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>.
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AaronTools can be installed from <a href="https://pypi.org/project/AaronTools/">PyPI</a> or from GitHub. See the <a href="https://github.com/QChASM/AaronTools.py/wiki">Wiki</a> for installation details and usage.
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A Perl implementation of AaronTools is also <a href="https://github.com/QChASM/AaronTools">available here.</a>
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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.
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## Citation
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If you use the Python AaronTools, please cite:
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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>
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## Features
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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:
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* Calculating steric parameters
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* Sterimol Parameters, including Sterimol2Vec (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-substituentSterimol">substituent CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-ligandSterimol">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>)
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* Buried Volume (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-percentVolumeBuried">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L2408">API</a>)
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* Steric Maps (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-stericMap">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L2739">API</a>)
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* Ligand Solid Angle (<a href="">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/component.py#L901">API</a>)
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* Ligand Cone Angle - Tolman for asymmetric mono- and bidentate ligands, as well as exact cone angles (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-coneAngle">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/component.py#L456">API</a>)
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* Molecular Structure Editing
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* add or modify substituents (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-substitute">single CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-multiSubstitute">batch CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L3979">single API</a>)
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* swap ligands (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-mapLigand">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L4907">API</a>)
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* Generating Molecular Structures
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* coordination complexes (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-getCoordinationComplexes">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L271">API</a>)
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* organic molecules from SMILES or IUPAC (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-fetchMolecule">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/geometry.py#L154">API</a>)
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* Quantum Computation Setup and Processing
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* making input files for Gaussian, ORCA, Psi4, Q-Chem, xTB, and SQM (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-makeInput">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/fileIO.py#L190">API</a>)
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* parsing data from output files (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-printInfo">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/fileIO.py#L1077">API</a>)
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* thermochemistry based on Boltzmann-populated vibrational modes (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-grabThermo">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/comp_output.py#L36">API</a>)
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* normal vibrational modes (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-follow">displace along mode CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-printFreq">print data CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-plotIR">IR or VCD spectrum CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/spectra.py#L691">API</a>)
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* valence excitations (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#user-content-plotUVVispy">UV/vis or ECD spectrum CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/ff461166927faff684d6d16e4deb1e4a45375eae/spectra.py#L1327">API</a>)
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* orbitals, electron density, and Fukui functions (<a href="https://github.com/QChASM/AaronTools.py/wiki/Command-Line-Scripts#printcube">CLS</a>, <a href="https://github.com/QChASM/AaronTools.py/blob/e5f218341e47c74e41df3340ab6a31d3cadcaf6a/orbitals.py#L14">API</a>)
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* Parse output from output files of several popular quantum chemistry programs (<a href="https://github.com/QChASM/AaronTools.py/wiki/Tutorials:-Coding-with-FileReaders">wiki</a>)
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* Gaussian
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* ORCA
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* Psi4
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* Q-Chem
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* NBO
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* xTB
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Features are explained in more detail on various pages of the wiki, on help pages for various CLSs, and in docstrings of the Python API.
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## Other Versions
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### ChimeraX Plugin
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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>.
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### Perl
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A Perl implementation of AaronTools is also <a href="https://github.com/QChASM/AaronTools">available here.</a>
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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.
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## Contact
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If you have any questions or would like to discuss bugs or additional needed features, feel free to contact us at [email protected]

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