merge_tree_utils.h

Go to the documentation of this file.

/**
 *  \file IMP/multifit/merge_tree_utils.h
 *
 *  Copyright 2007-2015 IMP Inventors. All rights reserved.
 */

#ifndef IMPMULTIFIT_MERGE_TREE_UTILS_H
#define IMPMULTIFIT_MERGE_TREE_UTILS_H

#include <boost/functional/hash.hpp>
#include <boost/graph/adjacency_matrix.hpp>
#include <boost/graph/adjacency_list.hpp>
#include <boost/pending/disjoint_sets.hpp>
#include <boost/graph/graph_utility.hpp>
#include <IMP/multifit/multifit_config.h>
#include <IMP/atom/Hierarchy.h>
#include <boost/unordered_map.hpp>
#include <boost/graph/kruskal_min_spanning_tree.hpp>
#include <boost/graph/prim_minimum_spanning_tree.hpp>

IMPMULTIFIT_BEGIN_NAMESPACE

namespace MTU {
typedef boost::adjacency_matrix<boost::undirectedS, boost::no_property,
                                boost::property<boost::edge_weight_t, double> >
    DependencyGraph;
typedef boost::graph_traits<DependencyGraph>::edge_descriptor DGEdge;
typedef DependencyGraph::edge_property_type DGWeight;
typedef boost::graph_traits<DependencyGraph>::vertex_descriptor DGVertex;
typedef boost::unordered_map<kernel::Particle *, DGVertex> PVMAP;
typedef boost::unordered_map<DGVertex, Particle *> VPMAP;
};

//! A simple Restraint that always returns a score of zero.
class IMPMULTIFITEXPORT DummyRestraint : public kernel::Restraint {
 public:
  DummyRestraint(kernel::Particle *a, kernel::Particle *b)
      : kernel::Restraint(a->get_model(), "DummyRestraint%1%"),
        p1_(a),
        p2_(b) {}
  virtual double unprotected_evaluate(IMP::kernel::DerivativeAccumulator *accum)
      const IMP_OVERRIDE;
  virtual IMP::kernel::ModelObjectsTemp do_get_inputs() const IMP_OVERRIDE;
  IMP_OBJECT_METHODS(DummyRestraint);

 protected:
  kernel::Particle *p1_, *p2_;
};

//! Utility class for building merge trees.
class IMPMULTIFITEXPORT MergeTreeBuilder {
 public:
  MergeTreeBuilder(const atom::Hierarchies &mhs) : g_(mhs.size()), mhs_(mhs) {
    // add mapping from mol to node

    typedef boost::graph_traits<MTU::DependencyGraph>::vertex_iterator
        VertexIterator;
    VertexIterator v_it, v_it_end;
    boost::tie(v_it, v_it_end) = boost::vertices(g_);
    int ind = 0;
    for (; v_it != v_it_end; ++v_it) {
      mol2node_[mhs_[ind]] = *v_it;
      node2mol_[*v_it] = mhs_[ind];
      ind = ind + 1;
    }
  }  // end constructor

  // add +1 to the edge weight, creates the edge if does not exist
  void increase_edge(atom::Hierarchy mh1, atom::Hierarchy mh2) {
    // do not add self edges
    if (mh1.get_particle() == mh2.get_particle()) return;
    // get the corresponding nodes
    MTU::DGVertex u, v;
    u = mol2node_[mh1.get_particle()];
    v = mol2node_[mh2.get_particle()];
    if (!boost::edge(u, v, g_).second) {  // edge does not exist
      boost::add_edge(u, v, MTU::DGWeight(0.), g_);
    }
    // increase edge by one
    MTU::DGEdge e;
    e = boost::edge(u, v, g_).first;
    boost::put(boost::edge_weight_t(), g_, e,
               boost::get(boost::edge_weight_t(), g_, e) - 1);
  }
  void show(std::ostream &out = std::cout) const {
    out << "vertices:";
    typedef boost::graph_traits<MTU::DependencyGraph>::vertex_iterator
        vertex_iter;
    std::pair<vertex_iter, vertex_iter> vp;
    for (vp = vertices(g_); vp.first != vp.second; ++vp.first) {
      out << node2mol_.find(*vp.first)->second->get_name() << " ";
    }
    out << std::endl;
    out << "edges:";
    boost::graph_traits<MTU::DependencyGraph>::edge_iterator ei, ei_end;
    for (boost::tie(ei, ei_end) = edges(g_); ei != ei_end; ++ei)
      out << "(" << node2mol_.find(source(*ei, g_))->second->get_name() << ","
          << node2mol_.find(target(*ei, g_))->second->get_name() << ","
          << boost::get(boost::edge_weight_t(), g_, *ei) << ")" << std::endl;
    out << std::endl;
  }
  kernel::ParticlePairsTemp get_mst_dependency() const {
    std::vector<MTU::DGEdge> mst;
    boost::kruskal_minimum_spanning_tree(g_, std::back_inserter(mst));
    // go over the edges and get the pairs
    kernel::ParticlePairsTemp ret;
    for (int i = 0; i < (int)mst.size(); i++) {
      kernel::ParticlePair pp;
      pp[0] = node2mol_.find(boost::source(mst[i], g_))->second;
      pp[1] = node2mol_.find(boost::target(mst[i], g_))->second;
      ret.push_back(pp);
    }
    return ret;
  }

 protected:
  // the graph
  MTU::DependencyGraph g_;
  atom::Hierarchies mhs_;
  MTU::PVMAP mol2node_;
  MTU::VPMAP node2mol_;
};

IMPMULTIFIT_END_NAMESPACE

#endif /* IMPMULTIFIT_MERGE_TREE_UTILS_H */