<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/1.0b19/"><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
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"description": "<a href=\"https://badge.fury.io/py/AaronTools\"><img src=\"https://badge.fury.io/py/AaronTools.svg\" alt=\"PyPI version\"></a>\r\n<a href='https://aarontools.readthedocs.io/en/latest/?badge=latest'>\r\n <img src='https://readthedocs.org/projects/aarontools/badge/?version=latest' alt='Documentation Status' />\r\n</a>\r\n<a href=\"https://pypi.org/project/AaronTools/1.0b19/\"><img src=\"https://img.shields.io/pypi/dm/aarontools.svg\"></a>\r\n<a href=\"https://doi.org/10.1002/wcms.1510\"><img src=\"https://img.shields.io/badge/DOI-10.1002/wcms.1510-blue\"></a>\r\n\r\n# AaronTools.py\r\nAaronTools provides a collection of tools for automating routine tasks encountered when running quantum chemistry computations.\r\n\r\nThese tools can be used either directly within a Python script using AaronTools objects, or via a series of command-line scripts. \r\n\r\n## Documentation\r\nAaronTools 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>.\r\n\r\n## Installation\r\n* with pypi: <code>pip install AaronTools</code>\r\n\r\nSee 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.\r\n\r\n## Citation\r\nIf you use AaronTools, please cite:\r\n\r\nV. 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>\r\n\r\n## Features\r\nAaronTools 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:\r\n\r\n* Calculating steric parameters\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n* Molecular Structure Editing\r\n * 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>)\r\n * 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>)\r\n* Generating Molecular Structures\r\n * 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>)\r\n * 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>)\r\n* Quantum Computation Setup and Processing\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n * 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>)\r\n* 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>)\r\n * Gaussian\r\n * ORCA\r\n * Psi4\r\n * Q-Chem\r\n * NBO\r\n * xTB\r\n\r\nFeatures are explained in more detail in the <a href=\"https://aarontools.readthedocs.io/en/latest/\">documentation and in docstrings of the Python API. \r\n\r\n\r\n## Other Versions\r\n\r\n### ChimeraX Plugin\r\nThe 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>.\r\n\r\n### Perl\r\nA Perl implementation of AaronTools is also <a href=\"https://github.com/QChASM/AaronTools\">available here.</a>\r\nHowever, 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.\r\n\r\n\r\n## Contact\r\nIf you have any questions or would like to discuss bugs or additional needed features, feel free to contact us at qchasm@uga.edu\r\n",
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