| 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 molecules.dox
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| 10 | *
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| 11 | * Created on: Oct 31, 2011
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| 12 | * Author: heber
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| 13 | */
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| 14 |
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| 15 | /**
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| 16 | * \page molecules Molecules
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| 17 | *
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| 18 | * Molecule is the next important structure to atom.
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| 19 | *
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| 20 | * Molecule are especially important for \ref fragmentation and lots of
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| 21 | * their (old) code comes from this theme.
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| 22 | *
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| 23 | * Basically, a molecule is just a conglomerate of atoms whose nodes form a
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| 24 | * connected subgraph of the entire molecular system.
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| 25 | *
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| 26 | * A molecule has its own internal array of atoms that may be traversed.
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| 27 | * Similar concepts as with the World with regards to const and non-const
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| 28 | * traversal, the former involving an Observer mechanism, come into play here
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| 29 | * as well.
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| 30 | *
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| 31 | * \section molecules-atoms Atoms
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| 32 | *
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| 33 | * Atoms are added to the molecule via molecule::AddAtom() and removed via
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| 34 | * molecule::RemoveAtom(). Therein, the atom receives a unique ParticleInfo::Nr
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| 35 | * that is useful only within the molecule and is displayed in the atoms name,
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| 36 | * i.e. atom names only vary within the molecule.
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| 37 | *
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| 38 | * The molecule only stores the atoms global id and uses a boost::transform_iterator
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| 39 | * to map the ids to the true refs obtained from the World.
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| 40 | *
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| 41 | * \section molecules-formula Formula
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| 42 | *
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| 43 | * One important concept of molecules is the associated Formula. It, as well
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| 44 | * as the AtomCount, are implemented as Cachables, i.e. they are aware of
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| 45 | * changes to the contained atoms via the Observer mechanism but update
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| 46 | * themselves only when requested.
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| 47 | *
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| 48 | * Formulas are very powerful because they can also be used as a Descriptor
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| 49 | * (\ref descriptors) to access only a certain subsets of molecules, e.g.
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| 50 | * "H2O" selects all water molecules.
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| 51 | *
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| 52 | * \section molecules-bondgraph Notes on the BondGraph
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| 53 | *
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| 54 | * Note that molecules are very volatile: Changing the bond graph also changes
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| 55 | * most of the present molecules at this time as so far there is no update
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| 56 | * mechanism. Hence, be aware of it.
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| 57 | *
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| 58 | *
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| 59 | * \date 2011-10-31
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| 60 | *
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| 61 | */
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