Installation

MSMBuilder is a python package that uses a number of components from the “scientific python” stack. These packages include numpy and scipy for array manipulation and numerical linear algebra, PyTables for storing binary data, and others.

Note

MSMBuilder is runs on Python 2.7 and Python 3.3. Use whichever you prefer. Other version like Python 2.6 and Python 3.2 probably will work, but are not explicitly supported .

Easily with conda

The easiest way to install MSMBuilder is with the python package manager conda. conda is an open-source cross-platform binary package manager integrated with the scientific python stack. It’s built into the Anaconda python distribution produced by Continuum Analytics, which is a python installer that comes shipped with many of the python packages needed for science.

Warning

We strongly recommend using Anaconda. Installing the scientific stack by hand can be quite tricky.

If you don’t want to get Anaconda, you can also install conda into an existing python interpreter. Once you have conda, install MSMBuilder with

conda config --add channels http://conda.binstar.org/omnia
conda install msmbuilder

Note

For windows users, we recommend using the 32-bit version of Anaconda.

Medium With pip

MSMBuilder can be instaleld with pip, but pip is not fantastic at installing the dependencies. If you’ve already got the dependencies installed (see below), then you can download and install MSMBuilder:

pip install msmbuilder

Hard Way by Hand

If you use conda, all of this will be done automatically. If you prefer to do things by hand, keep reading.

You’ll need to get the following python packages:

On a debian-based linux, you can get most of them with

$ sudo apt-get install libhdf5-serial-dev python-dev python-numpy \
python-scipy python-setuptools python-nose python-tables \
python-matplotlib python-yaml swig ipython python-pip

Download MSMBuilder, unzip, move to the msmbuilder directory. Then, use pip to install any remaining dependencies

$ pip install -r requirements.txt

Then install MSMBuilder with setup.py

$ python setup.py install

You may need root privileges during the install step; alternatively, you can specify an alternative install path via –prefix=XXX. If you performed the install step with –prefix=XXX, you need to ensure that

  1. XXX/bin is included in your PATH
  2. XXX/lib/python2.7/site-packages/ is included in your PYTHONPATH

Step (1) ensures that you can run MSMBuilder scripts without specifying their location. Step (2) ensures that your Python can locate the MSMBuilder libraries.

Versions