=============
DMG-Îą Project
=============

DMG-Îą library is an attempt to grant researchers in the field of computational 
biology access to open-sourced, easy to use and intuitive package for performing
fine-grained geometric analysis of molecular systems, especially multi-molecular
systems such as lipid bilayer Molecular Dynamics simulations. The package is 
capable of computing Power Diagrams (Weighted Voronoi Diagrams) in three 
dimensions with various periodic boundary conditions, computing approximate 
projective 2D Voronoi Diagrams on arbitrary surfaces, performing shape 
properties recognition using Alpha Shape theory and can do exact Solvent 
Accessible Surface Area (SASA) computation. The software is written mainly as 
template-based C++ library for greater performance, but rich Python interface is
provided as an easiest and preferred way to manipulate package routines.

**This work is supported by Polish National Science Centre under grant no. 2011/01/N/ST6/07173**

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					<h1>Power Diagrams in 3D</h1>
					<p style = "color: white; font-size: 1.1em; text-align: justify;">
						DMG-Alpha is capable of computing Power Diagrams in 3D for box geometries with 
						arbitrary periodic information. All geometry constructs are easyli accessible, 
						and all kinds of attributes can be simply computed, e.g. areas of cell 
						sides, volumes of cells, neighbouring information.
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					<h1>Projective geometries</h1>
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						DMG-Alpha allows for simple computations of projections of particles 
						to arbitrary shapes (approximated with triangulated surface)
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				<img src="_static/shapes.png" alt="Slide 3">
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					<h1>Geometric properties</h1>
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						DMG-Alpha can compute Alpha-Shape-like constructs based on Power Cells instead of standard dual 
						concept of Regular Triangulations. It allows for shape recognition, blocked pathways, exact 
						Solvent Accessible Surface Area (SASA) computation and more.
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						DMG-Alpha is written mainly in C++ for greater performance, but it's main goal is 
						to provide rich and easy to use and intuitive Python iterface. Python interface 
						also cames with embedded simple graphicas tools which allows to visualise 
						computation effects. Export to standard PDB and PyMol formats is also supported. 
					</p>
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Components
==========

.. toctree::
   :maxdepth: 2

   licinst.rst
   dmga.rst
   dmga2py.rst
   pydmga.rst
   examples.rst
   programs.rst
   gallery.rst



Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`