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cctk\n\n[![PyPI version](https://badge.fury.io/py/cctk.svg)](https://pypi.python.org/pypi/cctk/)\n[![Anaconda version](https://anaconda.org/conda-forge/cctk/badges/version.svg)](https://anaconda.org/conda-forge/cctk)\n[![Doc status](https://readthedocs.org/projects/pip/badge/)](https://cctk.rtfd.io)\n[![Downloads](https://img.shields.io/pypi/dm/cctk.svg)](https://pypi.python.org/pypi/cctk/)\n\n*a Python-based computational chemistry toolkit*\n\n*cctk* simplifies the computational modeling of organic reactions and small molecule structures by automating routine interactions with quantum chemistry software packages:\n\n - **input file creation**: conformer enumeration, job keyword manipulations, constrained potential energy surface creation\n - **method screening**: creating jobs that screen grids of DFT methods and basis sets\n - **job monitoring**: identification of job status, progress of optimizations, and resubmission of failed jobs\n - **data extraction**: geometries, energies, molecular properties (e.g. charges or NMR shieldings), or geometric parameters (distances, angles, dihedrals) from output files\n - **data analysis**: easy export for statistical analysis or visualization\n\nA quick-start guide is [available](https://cctk.readthedocs.io/en/latest/quick-start.html). More documentation is [here](https://cctk.readthedocs.io/).\n \n*cctk* is primarily designed for use with [Gaussian 16](https://gaussian.com). Some support is provided for other file formats (`.xyz`, `.mol2`, `.pdb`, [Schrodinger](https://www.schrodinger.com) `mae`, and [Orca](https://sites.google.com/site/orcainputlibrary/) `.inp`/`.out`).\n\n## Installation\n\n### First Time\n\n*cctk* is easy to install! It should work on any system where Python works.\n\nWith Python 3.6 or later, type:\n\n```\npip install cctk\n```\n\nor\n\n```\nconda install -c conda-forge cctk\n```\n\nIf you don't have [pip](https://pypi.org/project/pip/) or virtual environments available on your system, then we recommend installing Anaconda first:\n\n1. Go to [https://www.anaconda.com/distribution/](https://www.anaconda.com/distribution/). Download the Python 3 installer appropriate to your system and run it.\n\n2. Create a virtual environment to use with *cctk* (with whatever version of Python you prefer):\n\n ```\n conda create --name cctk python=3.8\n ```\n\n3. Now activate the virtual environment:\n\n ```\n conda activate cctk\n ```\n\nTo use *cctk*, you will need to place this command at the beginning of your Python scripts:\n\n```\nimport cctk\n```\n\nThe [documentation](https://cctk.readthedocs.io/) contains many examples of how to write *cctk* scripts.\n\n### Upgrading\n\n*cctk* is undergoing active development. To upgrade to the latest stable release:\n\n```\npip install --upgrade cctk\n```\n\nTo install the development version, which may be unstable, run:\n\n```\n$ pip install --upgrade git+git@github.com:ekwan/cctk.git@master \n```\n\nAlternatively, clone the repository. Then, from within the repository folder, run:\n\n```\npip install --upgrade .\n```\n\n### Building Documentation\n\nIf you want to read the *cctk* documentation locally, you can build it by going to the `docs` folder and typing:\n\n```\nmake html\n```\n\nThis command will require the `sphinx` and `sphinx-bootstrap-theme` packages to be installed first. Once generated, the documentation will be available locally at: `docs/_build/html/index.html`.\n\n## Fine Print\n\n### Package Details \n\n- `cctk/` contains the Python modules for *cctk* and the accompanying static data files.  \n- `docs/` contains the code needed to generate the documentation.  \n- `scripts/` contains pre-defined scripts that use *cctk* to quickly analyze and manipulate one or many output files.  \n- `test/` contains code to test *cctk* and accompanying files.  \n- `tutorial/` contains detailed tutorials on how to use *cctk* on complex, real-world problems.  \n\n*cctk* requires Python 3.7+, [`numpy`](https://numpy.org/), and [`networkx`](https://networkx.github.io/).\nA full list of requirements can be found in `env.yml`. \n\n### External Data:\n\n*cctk* depends on some external data (`cctk/data/`):\n\n- Atomic weights are taken from the \n[NIST website](https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=\u0026all=all\u0026ascii=ascii2\u0026isotype=some) \nand stored in `cctk/data/isotopes.csv`.\n- Covalent radii are taken from \n[*Dalton Trans.* **2008**, 2832](https://pubs.rsc.org/en/content/articlelanding/2008/dt/b801115j#!divAbstract) \nand stored in `cctk/data/covalent_radii.csv`.\n(When multiple atomic types were specified, the one with longer bond distances was adopted for simplicity).\n- van der Waals radii were taken from\n[*J. Am. Chem. Soc.* **1983**, *105*, 5220](https://pubs.acs.org/doi/10.1021/ja00354a007), \n[*Inorg. Mater.* **2001**, *37*, 871](https://link.springer.com/article/10.1023/A:1011625728803), and\n[*J. Phys. Chem. A*, **2009**, *113*, 5806](https://pubs.acs.org/doi/10.1021/jp8111556) and stored in `cctk/data/vdw_radii.csv`.\n\n### Authors and Community:\n\n*cctk* is an ongoing project led by Corin Wagen and Eugene Kwan.\n\nThere is a Slack workspace for *cctk* users and developers: please email ``cwagen@g.harvard.edu`` or ``ekwan16@gmail.com`` for access.\n\n### How to Cite:\n\nWagen, C.C.; Kwan, E.E. *cctk* **2020**, [www.github.com/ekwan/cctk](https://www.github.com/ekwan/cctk).\n\n### License:\n\nThis project is licensed under the Apache License, Version 2.0.  Please see `LICENSE` for full terms and conditions. \n\n*Copyright 2020 by Corin Wagen and Eugene Kwan*\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fekwan%2Fcctk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fekwan%2Fcctk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fekwan%2Fcctk/lists"}