Download the code in a ZIP file or using GIT version control from the buttons at the right side. GIT way is recommended. The program is still in beta-testing and updates will be easier to install if using GIT.
Many of these dependencies are common packages used by python scientific community and probably you will find some of them already installed by default with some Linux distributions. Check the instructions below for further instructions on the installation process.
- Numpy for numerical arrays handling and math operation on large data
- Scipy for clustering, distance metrics, KDTrees and other spatial nice stuff needed for analysis
- ScientificPython (also needed for Biskit Installation). I highly recommend to install it with NetCDF support (check at the website the compilation instructions).
- Biskit. Nice module for dealing with PDB files and other features.
- Matplotlib. Plotting capabilities.
- AMBER software: Ambertools is opensource and distributed without charge. It is needed for all the process of preparation and analysis of the simulations. The MDs can be run using AMBER itself (license required) or NAMD (distributed without charge). See User Guide.
Although not mandatory, NetCDF libraries provide faster access to trajectory data and reduce disk space usage.
- NetCDF libraries. System-wide libraries for dealing with NetCDF formatted files. Please check your system installation instructions and the easiest way to install in your machine. This should be built before installing ScientificPython module.
Dependencies installation, in principle, should be automatic. When installing pyMDMix, setup.py will try to download and install all dependencies not found (aside Ambertools which is not a python module). This will work for most of the dependencies listed above BUT for Biskit:
Biskit auto installation is not properly working and one should install it before-hand. Biskit shares most of the dependencies with pyMDMix and therefore when installing Biskit you are done also with pyMDMix. Most important dependency to Biskit is ScientificPython.
Install ScientificPython making sure it binds NetCDF libraries and is able to read NetCDF files. You can try the following command after installation to test if NetCDF was correctly bound:
Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Scientific.IO.NetCDF as ncdf >>>
You should not get any error. E.g. like this one in my Mac OSX:
Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import Scientific.IO.NetCDF as ncdf Traceback (most recent call last): File "
", line 1, in File "/Library/Python/2.7/site-packages/Scientific/IO/NetCDF.py", line 169, in from Scientific_netcdf import * ImportError: dlopen(/Library/Python/2.7/site-packages/Scientific/darwin/Scientific_netcdf.so, 2): Symbol not found: _ncerr Referenced from: /Library/Python/2.7/site-packages/Scientific/darwin/Scientific_netcdf.so Expected in: flat namespace in /Library/Python/2.7/site-packages/Scientific/darwin/Scientific_netcdf.so
Set $AMBERHOME environmental variable if you have not done it already when installing AMBER/AmberTools. This should point to the installation directory. In bash should be something like this:
daniel@pulp:~> export AMBERHOME=/path/to/amber_installation
If installing in Windows, follow these instructions to set the variable.
After installing all the dependencies and downloading the package, unpack the zip file or get the repo version using git, move to the recently created folder and install using python.
daniel@pulp:~> unzip pyMDMix-XXXX.zip daniel@pulp:~> cd pyMDMix-XXXX/ daniel@pulp_pyMDMix-XXXX/~> python setup.py install
Or using git
daniel@pulp:~> git clone git://git.code.sf.net/p/mdmix/code pymdmix daniel@pulp:~> cd pymdmix/ daniel@pulp:mdmix/~> python setup.py install
You may require root privileges when installing the python package.
If you do not have root access, run a local installation using:
daniel@pulp:pymdmix/~> python setup.py install --user
If installation process was successful, you should be able to enter a python interactive console and load pyMDMix.
daniel@pulp:/~> python Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> >>> import pyMDMix >>>
Sometimes Biskit yields some warning messages which you should not worry if they refer to
Python 2.7.3 (default, Apr 14 2012, 08:58:41) [GCC] on linux2 Type "help", "copyright", "credits" or "license" for more information. >>> import pyMDMix Warning (ignored): Could not import PVM (Parallel Virtual Machine) modules. Please check that PVM and pypvm are installed! Parallelisation is not available. cudm was not imported Warning (ignored): Could not import biggles module -- plotting is not available.
in /home/daniel/.local/lib/python2.7/site-packages/Biskit/__init__.py line 120: ('No module named biggles',).