FragmentCrmsdResDepth.cc

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// -*- mode:c++;tab-width:2;indent-tabs-mode:t;show-trailing-whitespace:t;rm-trailing-spaces:t -*-
// vi: set ts=2 noet:
//
// This file is part of the Rosetta software suite && is made available under license.
// The Rosetta software is developed by the contributing members of the Rosetta Commons consortium.
// (C) 199x-2009 Rosetta Commons participating institutions && developers.
// For more information, see http://www.rosettacommons.org/.

/// @file   protocols/frag_picker/scores/FragmentCrmsdResDepth.cc
/// @brief  Object that scores a fragment by its crmsd to the native
/// @author David E Kim

#include <protocols/frag_picker/scores/FragmentCrmsdResDepth.hh>
#include <protocols/frag_picker/VallChunk.hh>
#include <protocols/frag_picker/VallResidue.hh>
#include <protocols/frag_picker/VallProvider.hh>
#include <protocols/frag_picker/scores/FragmentScoreMap.hh>
#include <protocols/frag_picker/FragmentCandidate.hh>

// option key includes
#include <basic/options/option.hh>
#include <basic/options/keys/OptionKeys.hh>
#include <basic/options/keys/in.OptionKeys.gen.hh>

#include <core/conformation/Residue.hh>
#include <basic/Tracer.hh>


#include <numeric/model_quality/rms.hh>

// utils
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <basic/prof.hh>

//Auto Headers
#include <core/id/NamedAtomID.hh>
#include <core/import_pose/import_pose.hh>
#include <core/io/pdb/pose_io.hh>
#include <core/pose/Pose.hh>
#include <utility/io/izstream.hh>
#include <iostream>
#include <string>


namespace protocols {
namespace frag_picker {
namespace scores {

using namespace basic::options;
using namespace basic::options::OptionKeys;

static basic::Tracer trRmsScore(
    "protocols.frag_picker.scores.FragmentCrmsdResDepth");

FragmentCrmsdResDepth::~FragmentCrmsdResDepth() {}

FragmentCrmsdResDepth::FragmentCrmsdResDepth(Size priority, Real lowest_acceptable_value,
    bool use_lowest, core::pose::PoseOP reference_pose, utility::vector1<core::Real> & query_residue_depth) :
  CachingScoringMethod(priority, lowest_acceptable_value, use_lowest, "FragmentCrmsdResDepth") {
  reference_pose_ = reference_pose;
  n_atoms_ = reference_pose_->total_residue();
  reference_coordinates_.redimension(3, n_atoms_, 0.0);
  fill_CA_coords(*reference_pose_, reference_coordinates_, n_atoms_);
  weights_.redimension(reference_pose_->total_residue(), 1.0);
  query_residue_depth_ = query_residue_depth;
}

FragmentCrmsdResDepth::FragmentCrmsdResDepth(Size priority, Real lowest_acceptable_value, bool use_lowest,
  utility::vector1< utility::vector1<Real> > xyz, utility::vector1<core::Real> & query_residue_depth)  :
        CachingScoringMethod(priority, lowest_acceptable_value, use_lowest, "FragmentCrmsdResDepth") {

  n_atoms_ = xyz.size();
  reference_coordinates_.redimension(3, n_atoms_, 0.0);
  weights_.redimension(n_atoms_, 1.0);
  for (core::Size i = 1; i <= n_atoms_; i++) {
    trRmsScore.Debug << i<<" ";
    for (core::Size d = 1; d <= 3; ++d) {
      reference_coordinates_(d, i) = xyz[i][d];
      trRmsScore.Debug <<xyz[i][d]<<" ";
    }
    trRmsScore.Debug <<std::endl;
  }
  query_residue_depth_ = query_residue_depth;
}

void FragmentCrmsdResDepth::fill_CA_coords(core::pose::Pose const& pose,
    FArray2_double& coords, Size n_atoms) {

  trRmsScore.Debug << "Copying coordinates from ... The first residues are: "
      << pose.residue(1).name3() << " " << pose.residue(2).name3() << " "
      << pose.residue(3).name3() << std::endl;

  for (core::Size i = 1; i <= n_atoms; i++) {
    id::NamedAtomID idCA("CA", i);
    PointPosition const& xyz = pose.xyz(idCA);
    for (core::Size d = 1; d <= 3; ++d) {
      coords(d, i) = xyz[d - 1];
    }
  }
}

bool FragmentCrmsdResDepth::score(FragmentCandidateOP f, FragmentScoreMapOP empty_map) {

  PROF_START( basic::CA_RMSD_EVALUATION );

  Real depth_score = 0;

  if ((Size) fragment_coordinates_.size2() < f->get_length()) {
    fragment_coordinates_.redimension(3, f->get_length(), 0.0);
    frag_pos_coordinates_.redimension(3, f->get_length(), 0.0);
  }
  for (Size i = 1; i <= f->get_length(); i++) {
    Size qindex = i + f->get_first_index_in_query() - 1;
    VallChunkOP chunk = f->get_chunk();
    VallResidueOP r = chunk->at( f->get_first_index_in_vall() + i - 1 );
    fragment_coordinates_(1, i) = r->x();
    frag_pos_coordinates_(1, i) = reference_coordinates_(1, qindex);
    fragment_coordinates_(2, i) = r->y();
    frag_pos_coordinates_(2, i) = reference_coordinates_(2, qindex);
    fragment_coordinates_(3, i) = r->z();
    frag_pos_coordinates_(3, i) = reference_coordinates_(3, qindex);
    // residue depth similarity score from Zhou and Zhou, Proteins 2005
    // (exp( - Dquery / 2.8) - exp( - Dtemplate / 2.8))**2
    Real depthdiff = exp(-1*query_residue_depth_[qindex]/2.8) - exp(-1*r->depth()/2.8);
    depth_score += depthdiff*depthdiff;
  }
  Real rms = numeric::model_quality::rms_wrapper(f->get_length(),
      fragment_coordinates_, frag_pos_coordinates_);

  // similarity score from Zhou and Zhou, Proteins 2005
  // rmsd**2 + weight*depth_score  with weight = 10
  Real totalScore = rms*rms + 10*depth_score;

  empty_map->set_score_component(totalScore, id_);
  PROF_STOP( basic::CA_RMSD_EVALUATION );
  if ((rms > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;

  return true;
}


void FragmentCrmsdResDepth::do_caching(VallChunkOP current_chunk) {

  chunk_coordinates_.redimension(3, current_chunk->size());
  for (core::Size i = 1; i <= current_chunk->size(); i++) {
    VallResidueOP r = current_chunk->at(i);
    chunk_coordinates_(1, i) = r->x();
    chunk_coordinates_(2, i) = r->y();
    chunk_coordinates_(3, i) = r->z();
  }
}

bool FragmentCrmsdResDepth::cached_score(FragmentCandidateOP fragment,
    FragmentScoreMapOP scores) {

  std::string tmp = fragment->get_chunk()->chunk_key();
  if (tmp.compare(cached_scores_id_) != 0)
    do_caching(fragment->get_chunk());

  Real depth_score = 0;

  PROF_START( basic::CA_RMSD_EVALUATION );
  Size frag_len = fragment->get_length();
  if ((Size) fragment_coordinates_.size2() < frag_len)
    fragment_coordinates_.redimension(3, frag_len, 0.0);
  if ((Size) frag_pos_coordinates_.size2() < frag_len)
    frag_pos_coordinates_.redimension(3, frag_len, 0.0);

  for (core::Size i = 1; i <= frag_len; ++i) {
    Size qindex = i + fragment->get_first_index_in_query() - 1;
    Size vindex = i + fragment->get_first_index_in_vall() - 1;
    for (core::Size d = 1; d <= 3; ++d) {
      fragment_coordinates_(d, i) = chunk_coordinates_(d, vindex);
      frag_pos_coordinates_(d, i) = reference_coordinates_(d, qindex);
    }
    // residue depth similarity score from Zhou and Zhou, Proteins 2005
    // (exp( - Dquery / 2.8) - exp( - Dtemplate / 2.8))**2
    Real depthdiff = exp(-1*query_residue_depth_[qindex]/2.8) -
        exp(-1*fragment->get_chunk()->at( vindex )->depth()/2.8);
    depth_score += depthdiff*depthdiff;
  }

  Real rms = numeric::model_quality::rms_wrapper(frag_len,
      fragment_coordinates_, frag_pos_coordinates_);

  // similarity score from Zhou and Zhou, Proteins 2005
  // rmsd**2 + weight*depth_score  with weight = 10
  Real totalScore = rms*rms + 10*depth_score;

  scores->set_score_component(totalScore, id_);
  PROF_STOP( basic::CA_RMSD_EVALUATION );
  if ((rms > lowest_acceptable_value_) && (use_lowest_ == true))
    return false;

  return true;
}

void FragmentCrmsdResDepth::clean_up() {
}

FragmentScoringMethodOP MakeFragmentCrmsdResDepth::make(Size priority,
    Real lowest_acceptable_value, bool use_lowest, FragmentPickerOP picker, std::string) {

  if (option[in::file::native].user()) {
    trRmsScore
        << "Reference structure to score fragments by crmsd loaded from: "
        << option[in::file::native]() << std::endl;
    core::pose::PoseOP nativePose = new core::pose::Pose;
    core::import_pose::pose_from_pdb(*nativePose, option[in::file::native]());

    if (nativePose->total_residue() != picker->get_query_residue_depth().size())
      utility_exit_with_message("MakeFragmentCrmsdResDepth native total residue != query residue depth length");

    return (FragmentScoringMethodOP) new FragmentCrmsdResDepth(priority,
        lowest_acceptable_value, use_lowest, nativePose, picker->get_query_residue_depth());
  }
  if (option[in::file::s].user()) {
    trRmsScore
        << "Reference structure to score fragments by crmsd loaded from: "
        << option[in::file::s]()[1] << std::endl;
    core::pose::PoseOP nativePose = new core::pose::Pose;
    core::import_pose::pose_from_pdb(*nativePose, option[in::file::s]()[1]);

    if (nativePose->total_residue() != picker->get_query_residue_depth().size())
      utility_exit_with_message("MakeFragmentCrmsdResDepth native total residue != query residue depth length");

    return (FragmentScoringMethodOP) new FragmentCrmsdResDepth(priority,
        lowest_acceptable_value, use_lowest, nativePose, picker->get_query_residue_depth());
  }
  if (option[in::file::xyz].user()) {

    trRmsScore
        << "Reference structure to score fragments by crmsd loaded from: "
        << option[in::file::xyz]().c_str() << std::endl;
                std::string line;
                utility::vector1< utility::vector1< Real > > xyz;
                // std::istream & input = utility::io::izstream( option[ in::file::xyz ]().c_str() );
    std::ifstream input( option[ in::file::xyz ]().c_str() );

    while( getline( input, line ) ) {
      trRmsScore.Warning << line<<std::endl;
      if ( line.substr(0,1) == "#" ) continue;
      std::istringstream line_stream( line );
      utility::vector1<Real> row;
      Real x,y,z;
      line_stream >> x >> y >> z;
      row.push_back(x);
      row.push_back(y);
      row.push_back(z);
      xyz.push_back( row );
    }
    trRmsScore <<  xyz.size() << " atoms found in the reference" << std::endl;

    if (xyz.size() != picker->get_query_residue_depth().size())
      utility_exit_with_message("MakeFragmentCrmsdResDepth xyz size != query residue depth length");

    return (FragmentScoringMethodOP) new FragmentCrmsdResDepth(priority,
        lowest_acceptable_value, use_lowest, xyz, picker->get_query_residue_depth());
  }
  utility_exit_with_message(
      "Can't read a reference structure. Provide it with in::file::s flag");

  return NULL;
}

} // scores
} // frag_picker
} // protocols