DiversifyCrmsdByClustering.cc

Go to the documentation of this file.

// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// (c) Copyright Rosetta Commons Member Institutions.
// (c) This file is part of the Rosetta software suite and is made available under license.
// (c) The Rosetta software is developed by the contributing members of the Rosetta Commons.
// (c) For more information, see http://www.rosettacommons.org. Questions about this can be
// (c) addressed to University of Washington UW TechTransfer, email: license@u.washington.edu.

/// @file   protocols/frag_picker/CompositeFragmentSelector.cc
/// @brief provides a selector that picks fragments diferent enough from the fragments that have been already picked
/// @author Dominik Gront (dgront@chem.uw.edu.pl)

#include <protocols/frag_picker/DiversifyCrmsdByClustering.hh>

// package headers
#include <protocols/frag_picker/FragmentCandidate.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.fwd.hh>
#include <core/pose/Pose.hh>

#include <core/id/NamedAtomID.hh>
#include <numeric/model_quality/rms.hh>
#include <basic/Tracer.hh>

// Clustering stuff
#include <numeric/ClusteringTreeNode.hh>
#include <numeric/agglomerative_hierarchical_clustering.hh>

#include <utility/vector1.hh>

namespace protocols {
namespace frag_picker {

using namespace core;

static basic::Tracer trDiversifyCrmsdByClustering(
                "protocols.frag_picker.DiversifyCrmsdByClustering");

void DiversifyCrmsdByClustering::copy_coordinates(FragmentCandidateOP src,FArray2D_double & dst) {

    pose::PoseOP pose = src->get_chunk()->get_pose();
    Size len = src->get_length();
    Size offset = src->get_first_index_in_vall() - 1;
    for (core::Size i = 1; i <= len; i++) {
  id::NamedAtomID idCA("CA", i+offset);
  PointPosition const& xyz = pose->xyz(idCA);
  for (core::Size d = 1; d <= 3; ++d) {
      dst(d, i) = xyz[d - 1];
  }
    }
}


/// @brief  Selects desired number of fragments from a given set of candidates
void DiversifyCrmsdByClustering::select_fragments(
   ScoredCandidatesVector1 const& in,
   ScoredCandidatesVector1& out )
{
  if(in.size()==0) return;

  //-------------- Size of fragments
  Size len = in[1].first->get_length();
  trDiversifyCrmsdByClustering.Debug << "Diversifying fragments of size "<<len<<" #(in) = "<<in.size()<<std::endl;
  //-------------- Resize container for xyz data
  if(in.size() > xyz_.size()) {
      trDiversifyCrmsdByClustering.Trace << "Reallocated: to "<<xyz_.size()<<std::endl;
      xyz_.resize(in.size());
  }
  //-------------- Resize each xyz vector to match fragments' size
  for(Size i=1;i<=in.size();i++) {
      if((Size)xyz_[i].size2() != len) {
    xyz_[i].redimension(3,len,0.0);
      }
  }
  //-------------- Copy xyz coordinates, setup ids
  utility::vector1<Size> ids;
  for(Size i=1;i<=in.size();i++) {
      copy_coordinates(in[i].first,xyz_[i]);
      ids.push_back(i);
  }

  //-------------- Prepare distance matrix
  utility::vector1< utility::vector1<Real> > distances(in.size());
  for(Size i=1;i<=in.size();i++)
      distances[i].resize( in.size() );

  for(Size i=2;i<=in.size();i++) {
          for(Size j=2;j<=in.size();j++) {
    Real val = numeric::model_quality::rms_wrapper(len,xyz_[i],xyz_[j]);
    distances[ i ][ j ] = val;
    distances[ j ][ i ] = val;
      }
      distances[i][i] = 0.0;
  }
  utility::vector1<numeric::ClusteringTreeNodeOP> roots = numeric::average_link_clustering(distances,frags_per_pos());

  //----------- Retrieve clusters
  for(Size i=1;i<=frags_per_pos();i++) {
      utility::vector1<Size> ids_out;
      numeric::get_cluster_data(ids,roots[i],ids_out);
      out.push_back( in[ ids_out[1] ] );
      trDiversifyCrmsdByClustering.Debug << "Fragment "<<i<<" cluster stats: dist="<<roots[i]->distance()
    <<" size="<<roots[i]->size()<<std::endl;
  }

  trDiversifyCrmsdByClustering.Trace<<out.size()<<" fragments passed through DiversifyCrmsdByClustering at query position "
      << in[1].first->get_first_index_in_query()<<std::endl;
}

} // frag_picker
} // protocols