Package: cctk
cctka Python-based computational chemistry toolkitcctksimplifies the computational modeling of organic reactions and small molecule structures by automating routine interactions with quantum chemistry software packages:input file creation: conformer enumeration, job keyword manipulations, constrained potential energy surface creationmethod screening: creating jobs that screen grids of DFT methods and basis setsjob monitoring: identification of job status, progress of optimizations, and resubmission of failed jobsdata extraction: geometries, energies, molecular properties (e.g. charges or NMR shieldings), or geometric parameters (distances, angles, dihedrals) from output filesdata analysis: easy export for statistical analysis or visualizationA quick-start guide isavailable. More documentation ishere.cctkis primarily designed for use withGaussian 16. Some support is provided for other file formats (.xyz,.mol2,.pdb,Schrodingermae, andOrca.inp/.out).InstallationFirst Timecctkis easy to install! It should work on any system where Python works.With Python 3.6 or later, type:pip install cctkorconda install -c conda-forge cctkIf you don't havepipor virtual environments available on your system, then we recommend installing Anaconda first:Go tohttps://www.anaconda.com/distribution/. Download the Python 3 installer appropriate to your system and run it.Create a virtual environment to use withcctk(with whatever version of Python you prefer):conda create --name cctk python=3.8Now activate the virtual environment:conda activate cctkTo usecctk, you will need to place this command at the beginning of your Python scripts:import cctkThedocumentationcontains many examples of how to writecctkscripts.Upgradingcctkis undergoing active development. To upgrade to the latest stable release:pip install --upgrade cctkTo install the development version, which may be unstable, run:$ pip install --upgrade git+git@github.com:ekwan/cctk.git@masterAlternatively, clone the repository. Then, from within the repository folder, run:pip install --upgrade .Building DocumentationIf you want to read thecctkdocumentation locally, you can build it by going to thedocsfolder and typing:make htmlThis command will require thesphinxandsphinx-bootstrap-themepackages to be installed first. Once generated, the documentation will be available locally at:docs/_build/html/index.html.Fine PrintPackage Detailscctk/contains the Python modules forcctkand the accompanying static data files.docs/contains the code needed to generate the documentation.scripts/contains pre-defined scripts that usecctkto quickly analyze and manipulate one or many output files.test/contains code to testcctkand accompanying files.tutorial/contains detailed tutorials on how to usecctkon complex, real-world problems.cctkrequires Python 3.7+,numpy, andnetworkx.
A full list of requirements can be found inenv.yml.External Data:cctkdepends on some external data (cctk/data/):Atomic weights are taken from theNIST websiteand stored incctk/data/isotopes.csv.Covalent radii are taken fromDalton Trans.2008, 2832and stored incctk/data/covalent_radii.csv.
(When multiple atomic types were specified, the one with longer bond distances was adopted for simplicity).van der Waals radii were taken fromJ. Am. Chem. Soc.1983,105, 5220,Inorg. Mater.2001,37, 871, andJ. Phys. Chem. A,2009,113, 5806and stored incctk/data/vdw_radii.csv.Authors and Community:cctkis an ongoing project led by Corin Wagen and Eugene Kwan.There is a Slack workspace forcctkusers and developers: please emailcwagen@g.harvard.eduorekwan16@gmail.comfor access.How to Cite:Wagen, C.C.; Kwan, E.E.cctk2020,www.github.com/ekwan/cctk.License:This project is licensed under the Apache License, Version 2.0.  Please seeLICENSEfor full terms and conditions.Copyright 2020 by Corin Wagen and Eugene Kwan