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Python-based Monte Carlo simulator for DNA/RNA duplexes.

Project description



HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model, coded with Python. HelixMC is distributed under the GPLv3 licence.

The project is authored by Fang-Chieh Chou in 2013, under the supervison of Dr. Rhiju Das, at the Biochemistry Department of Stanford Unviersity.


The required dependencies to build the software are Python >= 2.7, Numpy >= 1.6, Matplotlib >= 1.1.0, and a working C/C++ compiler.


The easiest way to install is to use pip install:

$ pip install helixmc

Alternatively, one can download the source code from the latest GitHub repository. And install using

$ python build
$ sudo python install

Instead of installing using, you can just add your HelixMC folder into the system’s $PATH and $PYTHONPATH. In bash this can be done by adding the following lines to your ~/.bashrc:

export PATH=$PATH:<HelixMC Path>

Then build the Cython extension. Under the helixmc/ folder, run:

$ python build_ext --inplace

Note that this requires you to have Cython installed. Otherwise you can choose to build the c source file, then you do not need Cython:

$ python build_ext --inplace

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