IMP  2.2.1
The Integrative Modeling Platform
merge_tree_utils.h
Go to the documentation of this file.
1 /**
2  * \file IMP/multifit/merge_tree_utils.h
3  *
4  * Copyright 2007-2014 IMP Inventors. All rights reserved.
5  */
6 
7 #ifndef IMPMULTIFIT_MERGE_TREE_UTILS_H
8 #define IMPMULTIFIT_MERGE_TREE_UTILS_H
9 
10 #include <boost/graph/adjacency_matrix.hpp>
11 #include <boost/graph/adjacency_list.hpp>
12 #include <boost/pending/disjoint_sets.hpp>
13 #include <boost/graph/graph_utility.hpp>
14 #include <IMP/multifit/multifit_config.h>
15 #include <IMP/atom/Hierarchy.h>
16 #include <boost/unordered_map.hpp>
17 #include <boost/graph/kruskal_min_spanning_tree.hpp>
18 #include <boost/graph/prim_minimum_spanning_tree.hpp>
19 
20 IMPMULTIFIT_BEGIN_NAMESPACE
21 
22 namespace MTU {
23 typedef boost::adjacency_matrix<boost::undirectedS, boost::no_property,
24  boost::property<boost::edge_weight_t, double> >
26 typedef boost::graph_traits<DependencyGraph>::edge_descriptor DGEdge;
27 typedef DependencyGraph::edge_property_type DGWeight;
28 typedef boost::graph_traits<DependencyGraph>::vertex_descriptor DGVertex;
29 typedef boost::unordered_map<kernel::Particle *, DGVertex> PVMAP;
30 typedef boost::unordered_map<DGVertex, Particle *> VPMAP;
31 };
32 
33 //! A simple Restraint that always returns a score of zero.
34 class IMPMULTIFITEXPORT DummyRestraint : public kernel::Restraint {
35  public:
37  : kernel::Restraint(a->get_model(), "DummyRestraint%1%"),
38  p1_(a),
39  p2_(b) {}
40  virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
41  const IMP_OVERRIDE;
42  virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
44 
45  protected:
46  kernel::Particle *p1_, *p2_;
47 };
48 
49 //! Utility class for building merge trees.
50 class IMPMULTIFITEXPORT MergeTreeBuilder {
51  public:
52  MergeTreeBuilder(const atom::Hierarchies &mhs) : g_(mhs.size()), mhs_(mhs) {
53  // add mapping from mol to node
54 
55  typedef boost::graph_traits<MTU::DependencyGraph>::vertex_iterator
56  VertexIterator;
57  VertexIterator v_it, v_it_end;
58  boost::tie(v_it, v_it_end) = boost::vertices(g_);
59  int ind = 0;
60  for (; v_it != v_it_end; ++v_it) {
61  mol2node_[mhs_[ind]] = *v_it;
62  node2mol_[*v_it] = mhs_[ind];
63  ind = ind + 1;
64  }
65  } // end constructor
66 
67  // add +1 to the edge weight, creates the edge if does not exist
68  void increase_edge(atom::Hierarchy mh1, atom::Hierarchy mh2) {
69  // do not add self edges
70  if (mh1.get_particle() == mh2.get_particle()) return;
71  // get the corresponding nodes
72  MTU::DGVertex u, v;
73  u = mol2node_[mh1.get_particle()];
74  v = mol2node_[mh2.get_particle()];
75  if (!boost::edge(u, v, g_).second) { // edge does not exist
76  boost::add_edge(u, v, MTU::DGWeight(0.), g_);
77  }
78  // increase edge by one
79  MTU::DGEdge e;
80  e = boost::edge(u, v, g_).first;
81  boost::put(boost::edge_weight_t(), g_, e,
82  boost::get(boost::edge_weight_t(), g_, e) - 1);
83  }
84  void show(std::ostream &out = std::cout) const {
85  out << "vertices:";
86  typedef boost::graph_traits<MTU::DependencyGraph>::vertex_iterator
87  vertex_iter;
88  std::pair<vertex_iter, vertex_iter> vp;
89  for (vp = vertices(g_); vp.first != vp.second; ++vp.first) {
90  out << node2mol_.find(*vp.first)->second->get_name() << " ";
91  }
92  out << std::endl;
93  out << "edges:";
94  boost::graph_traits<MTU::DependencyGraph>::edge_iterator ei, ei_end;
95  for (boost::tie(ei, ei_end) = edges(g_); ei != ei_end; ++ei)
96  out << "(" << node2mol_.find(source(*ei, g_))->second->get_name() << ","
97  << node2mol_.find(target(*ei, g_))->second->get_name() << ","
98  << boost::get(boost::edge_weight_t(), g_, *ei) << ")" << std::endl;
99  out << std::endl;
100  }
101  kernel::ParticlePairsTemp get_mst_dependency() const {
102  std::vector<MTU::DGEdge> mst;
103  boost::kruskal_minimum_spanning_tree(g_, std::back_inserter(mst));
104  // go over the edges and get the pairs
106  for (int i = 0; i < (int)mst.size(); i++) {
108  pp[0] = node2mol_.find(boost::source(mst[i], g_))->second;
109  pp[1] = node2mol_.find(boost::target(mst[i], g_))->second;
110  ret.push_back(pp);
111  }
112  return ret;
113  }
114 
115  protected:
116  // the graph
117  MTU::DependencyGraph g_;
118  atom::Hierarchies mhs_;
119  MTU::PVMAP mol2node_;
120  MTU::VPMAP node2mol_;
121 };
122 
123 IMPMULTIFIT_END_NAMESPACE
124 
125 #endif /* IMPMULTIFIT_MERGE_TREE_UTILS_H */
boost::graph DependencyGraph
A directed graph on the interactions between the various objects in the model.
Class for adding derivatives from restraints to the model.
Particle * get_particle() const
Utility class for building merge trees.
A class to store an fixed array of same-typed values.
Definition: base/Array.h:33
Decorator for helping deal with a hierarchy of molecules.
The standard decorator for manipulating molecular structures.
A restraint is a term in an IMP ScoringFunction.
#define IMP_OBJECT_METHODS(Name)
Define the basic things needed by any Object.
Class to handle individual model particles.
void show(Hierarchy h, std::ostream &out=std::cout)
Print out a molecular hierarchy.
virtual ModelObjectsTemp do_get_inputs() const =0
IMP::kernel::Restraint Restraint
A simple Restraint that always returns a score of zero.