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*				*	
* @Author: Peter Woo Tae Kim    *
*				*
* Version 1.0			*
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* Graphical Simulation		*
* Designer guidelines
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This document was created to provide guidance for using our new graphical
tool for creating XML simulation specification files.  This tool was
designed to make the simulator more accessible to new users by providing
a graphical interface for automatically generating local rule files
corresponding to icosahedrally-symmetric shells.

There are three steps to using the graphical tool: providing coordinates
of Subunit types, specifying subunit pairs that are capable of binding,
and saving the file to XML.

1. Providing Coordinates

  The user begins by specifying the coordinates of each subunit type 
  relative to the center of one triangular face of an icosahedron.
  This is an equilateral triangle with side length defined to be 1.

		^
	       / \         ^
              /   \	   |  Y direction
             /     \	   |
            /   *   \	   |
           /         \ 	   |		* : center of triangle
          ------------
 	-----------> X direction

  The above diagram shows x and y directions on the triangle.  The z
  direction represents elevation above the face of the triangle.

  When user provides the coordinates of a subunit, the tool generates the 60
  symmetric subunits for the icosahedron and displays them to the user.

2. Connecting Subunits

  To build connections between subunits, the user clicks on the
  corresponding subunits. The first subunit that is clicked will be
  primary subunit and the second subunit will be connecting
  subunit. When the user clicks the two subunits, the tool creates the
  binding sites and determines the symmetries of the binding sites in
  order to create appropriate icosahedrally-symmetric binding sites.

  If the primary and connecting subunits are in same face, the tool will
  copy the bindings using 3-fold symmetry. If they are in different
  faces, the tool will copy the bindings using 5-fold symmetry. 2-fold
  symmetry occurs when two subunits are of the same type and in different
  triangles, and they are equally far apart from the two-fold axis. 

  Although the tool distinguishes 2-fold and 5-fold symmetric binding
  sites for purposes of naming them in the XML file, graphically, they
  will look the same.

3. Writing to XML
  
  The XML file created by graphical tool can be used as it is as
  input to the DESSA simulator.  However, the XML file created by the tool
  has default values, for the <Assembly> element and <BindingInteract>
  elements, so the user should edit those values as needed. 


4. Some examples coordinates

  T=1 virus : 	(0.333333333333, 0, 0)

  T=3 virus : 	(0, 0.4, 0)
		(0, 0.2, 0)
		(0, -0.2, 0)

  T=7 virus :   (0.1, 0, 0)
		(-0.1, 0, 0)
		(-0.1, 0.2, 0)
		(0.1, 0.2, 0)
		(0.05, 0.3, 0)
		(-0.05, 0.3, 0)
		(0, 0.4, 0)


 Permission is hereby granted, free of charge, to any person obtaining
a copy of this software and associated documentation files (the
"Software"), to deal in the Software without restriction, including
without limitation the rights to use, copy, modify, merge, publish,
distribute, sublicense, and/or sell copies of the Software, and to
permit persons to whom the Software is furnished to do so, subject to
the following conditions: The above copyright notice and this
permission notice shall be included in all copies or substantial
portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.