Monte-Carlo Simulation of DNA/RNA Helices
HelixMC is a software package for Monte-Carlo (MC) simulations of DNA/RNA helices using the base-pair level model. It provides a powerful tool to understand the flexibility of DNA/RNA helices through numerical simulations.
A working C/C++ compiler. Here we used gcc (4.6.3)
Python (2.7.3) with packages:
numpy >= 1.6.1
matplotlib >= 1.1.0
The easiest way to install is to use pip:
pip install helixmc
Alternatively, one can download the source code from the latest GitHub repository. Simply run:
git clone https://github.com/DasLab/HelixMC.git
After this, you can instal HelixMC using setup.py::
python setup.py build
sudo python setup.py install
Instead of installing using setup.py, 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:/path/to/HelixMC/
export PYTHONPATH=$PYTHONPATH:/path/to/HelixMC/
Then build the Cython extension. Under the helixmc/ folder, run::
python _cython_build.py 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 _c_build.py build_ext --inplace
Now you should be all set. To test the install, simply run::
helixmc-run --help
Copyright © of HelixMC Source Code is described in LICENSE.md.
Developed by Das lab, Leland Stanford Junior University.
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