https://github.com/ekwan/cctk
Python-based library for working with computational chemistry files
https://github.com/ekwan/cctk
Last synced: about 1 month ago
JSON representation
Python-based library for working with computational chemistry files
- Host: GitHub
- URL: https://github.com/ekwan/cctk
- Owner: ekwan
- License: apache-2.0
- Created: 2019-10-11T19:41:32.000Z (over 6 years ago)
- Default Branch: master
- Last Pushed: 2025-10-29T14:51:28.000Z (4 months ago)
- Last Synced: 2025-10-29T16:40:39.701Z (4 months ago)
- Language: Python
- Size: 67.7 MB
- Stars: 21
- Watchers: 1
- Forks: 4
- Open Issues: 6
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-python-chemistry - cctk - A library for computational chemistry (DFT) for input file generation, data extraction, method screening and analysis. (Simulations)
README
# cctk
[](https://pypi.python.org/pypi/cctk/)
[](https://anaconda.org/conda-forge/cctk)
[](https://cctk.rtfd.io)
[](https://pypi.python.org/pypi/cctk/)
*a Python-based computational chemistry toolkit*
*cctk* simplifies 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 creation
- **method screening**: creating jobs that screen grids of DFT methods and basis sets
- **job monitoring**: identification of job status, progress of optimizations, and resubmission of failed jobs
- **data extraction**: geometries, energies, molecular properties (e.g. charges or NMR shieldings), or geometric parameters (distances, angles, dihedrals) from output files
- **data analysis**: easy export for statistical analysis or visualization
A quick-start guide is [available](https://cctk.readthedocs.io/en/latest/quick-start.html). More documentation is [here](https://cctk.readthedocs.io/).
*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`).
## Installation
### First Time
*cctk* is easy to install! It should work on any system where Python works.
With Python 3.6 or later, type:
```
pip install cctk
```
or
```
conda install -c conda-forge cctk
```
If you don't have [pip](https://pypi.org/project/pip/) or virtual environments available on your system, then we recommend installing Anaconda first:
1. Go to [https://www.anaconda.com/distribution/](https://www.anaconda.com/distribution/). Download the Python 3 installer appropriate to your system and run it.
2. Create a virtual environment to use with *cctk* (with whatever version of Python you prefer):
```
conda create --name cctk python=3.8
```
3. Now activate the virtual environment:
```
conda activate cctk
```
To use *cctk*, you will need to place this command at the beginning of your Python scripts:
```
import cctk
```
The [documentation](https://cctk.readthedocs.io/) contains many examples of how to write *cctk* scripts.
### Upgrading
*cctk* is undergoing active development. To upgrade to the latest stable release:
```
pip install --upgrade cctk
```
To install the development version, which may be unstable, run:
```
$ pip install --upgrade git+git@github.com:ekwan/cctk.git@master
```
Alternatively, clone the repository. Then, from within the repository folder, run:
```
pip install --upgrade .
```
### Building Documentation
If you want to read the *cctk* documentation locally, you can build it by going to the `docs` folder and typing:
```
make html
```
This 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`.
## Fine Print
### Package Details
- `cctk/` contains the Python modules for *cctk* and the accompanying static data files.
- `docs/` contains the code needed to generate the documentation.
- `scripts/` contains pre-defined scripts that use *cctk* to quickly analyze and manipulate one or many output files.
- `test/` contains code to test *cctk* and accompanying files.
- `tutorial/` contains detailed tutorials on how to use *cctk* on complex, real-world problems.
*cctk* requires Python 3.7+, [`numpy`](https://numpy.org/), and [`networkx`](https://networkx.github.io/).
A full list of requirements can be found in `env.yml`.
### External Data:
*cctk* depends on some external data (`cctk/data/`):
- Atomic weights are taken from the
[NIST website](https://physics.nist.gov/cgi-bin/Compositions/stand_alone.pl?ele=&all=all&ascii=ascii2&isotype=some)
and stored in `cctk/data/isotopes.csv`.
- Covalent radii are taken from
[*Dalton Trans.* **2008**, 2832](https://pubs.rsc.org/en/content/articlelanding/2008/dt/b801115j#!divAbstract)
and stored in `cctk/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 from
[*J. Am. Chem. Soc.* **1983**, *105*, 5220](https://pubs.acs.org/doi/10.1021/ja00354a007),
[*Inorg. Mater.* **2001**, *37*, 871](https://link.springer.com/article/10.1023/A:1011625728803), and
[*J. Phys. Chem. A*, **2009**, *113*, 5806](https://pubs.acs.org/doi/10.1021/jp8111556) and stored in `cctk/data/vdw_radii.csv`.
### Authors and Community:
*cctk* is an ongoing project led by Corin Wagen and Eugene Kwan.
There is a Slack workspace for *cctk* users and developers: please email ``cwagen@g.harvard.edu`` or ``ekwan16@gmail.com`` for access.
### How to Cite:
Wagen, C.C.; Kwan, E.E. *cctk* **2020**, [www.github.com/ekwan/cctk](https://www.github.com/ekwan/cctk).
### License:
This project is licensed under the Apache License, Version 2.0. Please see `LICENSE` for full terms and conditions.
*Copyright 2020 by Corin Wagen and Eugene Kwan*