Basic Installation¶

git clone https://github.com/msmbuilder/msmbuilder
cd msmbuilder
python setup.py install

Dependencies¶

MSMBuilder is a python package that heavily leans on other components of the scientific python ecosystem. To use msmbuilder, the following libraries and software will need to be installed.

Linux, or Mac OS X

We develop mainly on 64-bit Linux and Mac machines. Windows is not well supported.

Python >= 2.6

The development package (python-dev or python-devel on most Linux distributions) is recommended.

NumPy >= 1.6.0

Numpy is the base package for numerical computing in python.

SciPy >= 0.11.0

We use scipy for sparse matrix, numerical linear algebra and optimization.

scikit-learn >= 0.14.0

Many of the models in msmbuilder build off base classes in scikit-learn.

MDTraj >= 0.8.0

MDTraj is a library for handing molecular dynamics trajectories.

Pandas >= 0.9.0

Pandas is pretty cool

cython >= 0.18.0

This is needed to compile the package.

cvxopt

Only one module in MSMBuilder uses cvxopt. TODO: make cvxopt optional.

Optional packages:

nose

Recommended, to run the test-suite.

Git

To download the source code

I get a wierd error during compilation with pip install or python setup.py install. What’s wrong?¶

We’ve received a couple reports of incorrect code generation on earlier versions of cython with python3.4. Try upgrading to the latest verion of cython, and reinstalling. If that doesn’t work, open an issue on the github issue tracker.