README

MD

MD is a python toolkit to analyze molecular dynamics
trajectories in xyz format. 
Typicall use case is file oputput from hoomd in the form of
.dcd and .mol2. Catdcd is used to convert them into xyz.txt
catdcd is from vmd.

MD allows one to read molecular dynamics trajectories and access the
atomic coordinates through numpy arrays. This provides a flexible and
relatively fast framework for complex analysis tasks. 

Citation
--------
When using MD in published work, please cite
 	Knorowski, C.
 Thanks!

Dependecies:
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 numpy, networkx, scipy, matplotlib, python >  2.4 but not 3.0+, catdcd(included)

Documentation
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DOcumentation is generated using Doxygen. To generate documentation simply run

doxygen Doxyfile

 Getting started
 ---------------

 Import the package::
 
  >>> import MD


 Examples
 --------

see dna_scripts