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IMP Reference Guide  2.13.0
The Integrative Modeling Platform
bond_graph.h
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1 /**
2  * \file IMP/atom/bond_graph.h
3  * \brief Represents a graph of the bonds within an atomic structure
4  *
5  * Copyright 2007-2020 IMP Inventors. All rights reserved.
6  *
7  */
8 
9 #ifndef IMPATOM_BOND_GRAPH_H
10 #define IMPATOM_BOND_GRAPH_H
11 
12 #include "bond_decorators.h"
13 #include "Hierarchy.h"
14 #include "internal/bond_graph_functors.h"
16 #include <IMP/internal/NestedIterator.h>
17 #include <boost/graph/graph_traits.hpp>
18 #include <boost/graph/properties.hpp>
19 #include <boost/iterator/transform_iterator.hpp>
20 
21 #ifndef SWIG
22 
23 IMPATOM_BEGIN_NAMESPACE
24 
25 //! Represent a bond graph as a boost graph
26 /** The BondGraph class implements the following boost graph concepts
27  - bidirectional_graph
28  - adjacency_graph
29  - vertex_list_graph
30  - edge_list_graph.
31 
32  See the
33 \external{http://www.boost.org/doc/libs/1_39_0/libs/graph/doc/table_of_contents.html,
34  Boost.Graph manual} for more details and a list of algorithms.
35 
36  The vertices are Bondeds. The type of the edge_descriptors
37  is internal. You can use the get_bond() method to get the corresponding
38  Bond.
39 
40  And all vertices can be assumed to have internal boost vertex indices.
41  The Boost.PropertyMap to access these can be accessed using the
42  get_vertex_index_map() function.
43 
44  Some usage examples
45  \code
46  boost::isomorphism(a,b,
47  boost::isomorphism_map(BondGraph::VertexVertexPropertyMap(pk))
48  .vertex_index1_map(a.get_vertex_index_map())
49  .vertex_index2_map(b.get_vertex_index_map()));
50 boost::dijkstra_shortest_paths(a, Bonded(),
51  boost::predecessor_map(BondGraph::VertexVertexPropertyMap(pk))
52  .weight_map(BondGraph::EdgeFloatPropertyMap(Bond::get_legnth_key()))
53  .distance_map(BondGraph::VertexFloatPropertyMap(FloatKey("graph distance")))
54  .vertex_index_map(a.get_vertex_index_map()));
55  \endcode
56 
57  \untested{BondGraph}
58  */
59 class IMPATOMEXPORT BondGraph {
60 
61  mutable IntKey index_key_;
62 
63  public:
64  IMP_NO_DOXYGEN(mutable Particles sc_);
65 
66  //! The graph is on the leaves of the atom::Hierarchy
67  /** All the leaves will be made Bonded particles if they are not already.
68  \note The hierarchy must not have any bonds to particles not in the
69  hierarchy.
70  */
71  BondGraph(Hierarchy bd);
72 
73  BondGraph() {}
74 
75  ~BondGraph();
76 
77 #ifndef IMP_DOXYGEN
78 
79  typedef internal::AttributeVertexPropertyMap<FloatKey, Float>
80  VertexFloatPropertyMap;
81  typedef internal::AttributeVertexPropertyMap<IntKey, Int>
82  VertexIntPropertyMap;
83  typedef internal::AttributeVertexPropertyMap<ParticleIndexKey, Bonded>
84  VertexVertexPropertyMap;
85 
86  typedef internal::AttributeEdgePropertyMap<FloatKey, Float>
87  EdgeFloatPropertyMap;
88  typedef internal::AttributeEdgePropertyMap<IntKey, Int> EdgeIntPropertyMap;
89 
90  VertexIntPropertyMap get_vertex_index_map() const;
91 #else
92  /** @name Property maps
93  Boost.Graph makes extensive use of property maps. We define a few maps
94  which use the particle attributes to store their data. Each map is
95  constructed by passing an appropriate attribute key, to specify the
96  attribute used to store the data. Attempt to store to an attribute
97  which the particle does not already have adds the attribute to the
98  particle. More information about property maps can be found in
99 \external{http://www.boost.org/doc/libs/1_39_0/libs/property_map/property_map.html,
100  the Boost.PropertyMap documentation}.
101  @{
102  */
103  //! Provide boost access to a Float attribute each vertex
105  //! Provide boost access to an Int attribute each vertex
107  //! Provide boost access to a Particle attribute each vertex
108  /** The particles in question must be Bonded particles. */
110  //! Provide boost access to a Float attribute on the edges such as length
112  //! Provide boost access to an Int attribute on each edge.
114 
115  VertexIntPropertyMap get_vertex_index_map() const;
116 /** @} */
117 #endif
118 
119 #ifndef IMP_DOXYGEN
120  typedef std::pair<Bonded, Bonded> edge_descriptor;
121 #endif
122 
123  Bond get_bond(edge_descriptor d) const {
124  return IMP::atom::get_bond(d.first, d.second);
125  }
126 
127 #ifndef IMP_DOXYGEN
128  struct traversal_category : public virtual boost::adjacency_graph_tag,
129  public virtual boost::vertex_list_graph_tag,
130  public virtual boost::edge_list_graph_tag,
131  // public virtual boost::incidence_graph_tag
132  public virtual boost::bidirectional_graph_tag {};
133  typedef Bonded vertex_descriptor;
134  // typedef undirected_tag directed_category;
135  typedef int vertices_size_type;
136  typedef int edges_size_type;
137  typedef int degree_size_type;
138 
139  typedef boost::transform_iterator<internal::MakeOutEdgeDescriptor,
140  vertex_descriptor::BondIterator>
141  out_edge_iterator;
142  typedef vertex_descriptor::BondedIterator adjacency_iterator;
143  typedef boost::transform_iterator<
144  internal::MakeBonded, IMP::Particles::iterator> vertex_iterator;
145  typedef boost::disallow_parallel_edge_tag edge_parallel_category;
146  typedef boost::undirected_tag directed_category;
147 
148  typedef boost::transform_iterator<internal::MakeInEdgeDescriptor,
149  vertex_descriptor::BondIterator>
150  in_edge_iterator;
151 
152  typedef IMP::internal::NestedIterator<internal::NestedTraits> edge_iterator;
153 
154  struct graph_tag {};
155  typedef Int vertex_property_type;
156 #endif
157 };
158 
159 IMPATOM_END_NAMESPACE
160 
161 #include "internal/bond_graph_boost_functions.h"
162 
163 #endif // IMP_SWIG
164 
165 #endif /* IMPATOM_BOND_GRAPH_H */
EdgeFloatPropertyMap
Provide boost access to a Float attribute on the edges such as length.
Definition: bond_graph.h:111
Store a list of ParticleIndexes.
VertexFloatPropertyMap
Provide boost access to a Float attribute each vertex.
Definition: bond_graph.h:104
EdgeIntPropertyMap
Provide boost access to an Int attribute on each edge.
Definition: bond_graph.h:113
Contains decorators for a bond.
Decorator for helping deal with a hierarchy of molecules.
VertexIntPropertyMap
Provide boost access to an Int attribute each vertex.
Definition: bond_graph.h:106
#define IMP_NO_DOXYGEN(x)
Hide something from doxygen.
The standard decorator for manipulating molecular structures.
A decorator for wrapping a particle representing a molecular bond.
Represent a bond graph as a boost graph.
Definition: bond_graph.h:59
Bond get_bond(Bonded a, Bonded b)
Get the bond between two particles.
int Int
Basic integer value.
Definition: types.h:35
VertexVertexPropertyMap
Provide boost access to a Particle attribute each vertex.
Definition: bond_graph.h:109