Capriqorn (CAlculation of P(R) and I(Q) Of macRomolecules in solutioN) is a molecular dynamics (MD) data analysis package written in Python. It calculates the radial particle-pair distribution function p(r) and the intensity I(q) from MD frames.
Capriqorn requires the Cadishi package to perform distance histogram calculations.
Capriqorn was developed, built, and tested on SUSE Linux Enterprise Server 11 SP 4, Ubuntu Linux 14.04 LTS, and Scientific Linux 7 using cPython 2.7.11 from the Anaconda Python distribution. It requires NumPy, SciPy, h5py, MDAnalysis and Cadishi (https://github.com/bio-phys/cadishi) .
Documentation is available at http://capriqorn.readthedocs.io/en/latest/. Alternatively, you may access the local copy at doc/html/index.html after having cloned the repository.
The package is installed in the Pythonic way e.g. as follows:
$ python setup.py install --user # install into the user's home directoryMake sure to add $HOME/.local/bin to your PATH environment variable.
Capriqorn provides a single executable capriq that gives access to the calculations. Run capriq --help to get an overview on the available commands and options.
To run an example calculation based on the data set included in Capriqorn proceed as follows:
- Run capriq example to generate the necessary YAML input files for the preprocessor, the histogram calculation, and the postprocessor. Optionally, inspect and adapt the parameter files.
- Run the preprocessor capriq preproc.
- Run capriq histo
- Run capriq postproc
Note that the step 2 is equivalent to the cadishi commands.
Capriqorn is released under the GPLv2 license. See the file LICENSE.txt for details.
Copyright 2015 - 2017: Juergen Koefinger, Klaus Reuter, Max Linke
Please cite
Jürgen Köfinger and Gerhard Hummer
Phys. Rev. E 87, 052712 (2013)
For your convenience, we provide citations in the bibtex format and the endnote format in the folder doc/citations.