| 1 | /*
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| 2 | * Project: MoleCuilder
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| 3 | * Description: creates and alters molecular systems
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| 4 | * Copyright (C) 2010 University of Bonn. All rights reserved.
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| 5 | * Please see the LICENSE file or "Copyright notice" in builder.cpp for details.
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| 6 | */
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| 7 |
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| 8 | /**
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| 9 | * \file mainpage.dox
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| 10 | *
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| 11 | * Here, the mainpage (index.html) for the doxygen documentation resides.
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| 12 | *
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| 13 | * Created on: Oct 11, 2011
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| 14 | * Author: heber
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| 15 | */
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| 16 |
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| 17 | /*! \page copyright Copyright notice
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| 18 | *
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| 19 | * MoleCuilder - to create and alter molecular systems
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| 20 | * Copyright (C) 2010 University Bonn. All rights reserved.
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| 21 | *
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| 22 | */
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| 23 |
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| 24 | /** \mainpage MoleCuilder - a molecular set builder
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| 25 | *
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| 26 | * This is the main page of the Doxygen documentation of \e MoleCuilder. We give
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| 27 | * a brief description what the program is intended to do and then branch via
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| 28 | * the contents of this documentation into various topics.
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| 29 | *
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| 30 | * \section about About the Program
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| 31 | *
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| 32 | * MoleCuilder is a program, written entirely in C++, that enables the
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| 33 | * construction of a coordinate set for the atoms making up a molecular system. It
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| 34 | * allows for both building of simple molecules by adding atom-wise giving bond
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| 35 | * angles and distances or absolute coordinates, but also using them as
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| 36 | * templates. Regions can be specified and ordered to be filled with a molecule
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| 37 | * in a certain manner. Greater conglomerations of molecules can be tesselated
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| 38 | * and recognized as a region themselves to be subsequently surrounded by other
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| 39 | * (surface solvated) molecules.
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| 40 | * Once initial configurations have been created, empirical potential functions
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| 41 | * can be fitted to ab-initio calculations -- calculated quickly via the BOSSANOVA
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| 42 | * scheme -- to enable subsequent (classical) molecular dynamics simulations.
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| 43 | *
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| 44 | * For copyright see \ref copyright.
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| 45 | *
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| 46 | * \section idea The central idea behind the program
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| 47 | *
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| 48 | * What are the central ideas?
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| 49 | *
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| 50 | * - Testedness: See \ref tests-policy which is meant \e seriously. Nothing is
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| 51 | * worse than one version behaving different to the next with respect to
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| 52 | * output.
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| 53 | * - Re-usability: Every piece of functionality should be easy to re-use at
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| 54 | * someplace else. Say no to specialized one-purpose scripts, say yes to
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| 55 | * a LEGO-like system of building your world.
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| 56 | * - Extendability: It's easy to add a new piece to the code. And it is even
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| 57 | * more so, if you have read this documentation and know what's all already
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| 58 | * in place.
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| 59 | * - Userfriendliness: Every Action can be undone, every Action gives lots
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| 60 | * of output (if desired) to tell you what's going on. It's easy to save
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| 61 | * files in between. There are also three kinds of GUIs, each of which
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| 62 | * have the same functionality.
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| 63 | * - Scriptability: Eventually, you want to create lots of configurations with
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| 64 | * only small differences. A session can be stored as either command-line or
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| 65 | * python script and extended to create all of the configurations in a straight-
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| 66 | * forward manner.
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| 67 | *
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| 68 | * \section contents Contents
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| 69 | *
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| 70 | * This manual is divided into the following sections:
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| 71 | * \li \ref install
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| 72 | * \li \ref tests
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| 73 | * \li \ref launch
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| 74 | * \li \ref data
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| 75 | * \li \ref debug
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| 76 | * \li \ref code
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| 77 | * \li \ref fileformats
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| 78 | * \li \ref userguide
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| 79 | *
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| 80 | * \date 2014-04-18
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| 81 | *
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| 82 | */
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| 83 |
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| 84 |
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| 85 |
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