ContactMapEvaluator.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:
//
// (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/simple_filters/ContactMapEvaluator.cc
/// @brief
/// @author James Thompson

// libRosetta headers

#include <core/types.hh>
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/io/silent/SilentStruct.hh>

#include <protocols/simple_filters/ContactMapEvaluator.hh>

#include <ObjexxFCL/string.functions.hh>
#include <boost/dynamic_bitset.hpp>
#include <algorithm>

#include <utility/vector1.hh>


namespace protocols {
namespace simple_filters {

boost::dynamic_bitset<>
get_contact_features(
  core::pose::Pose const & pose,
  core::Real const dist_threshold,
  std::string const & atom_name,
  core::Size const min_seqsep = 12,
  core::Size const skip_res   = 0
) {
  using core::Size;
  using core::Real;
  using utility::vector1;
  using boost::dynamic_bitset;

  Real const dist_threshold_sq( dist_threshold * dist_threshold );

  Size const N( pose.total_residue() );
  dynamic_bitset<> features( (N*N - N) / 2 );
  Size feat_idx(1);
  Size const step_size( 1 + skip_res );
  for ( Size ii = 1; ii <= pose.total_residue(); ii += step_size ) {
  for ( Size jj = ii + min_seqsep; jj <= pose.total_residue(); jj += step_size ) {
    Real const dist_sq(
      pose.residue(ii).xyz(atom_name).distance_squared(
        pose.residue(jj).xyz(atom_name)
      )
    );

    if ( dist_sq < dist_threshold_sq ) {
      features[feat_idx] = 1;
    }
    feat_idx++;
  } // jj
  } // ii

  return features;
}

core::Real pct_features_in_common(
  boost::dynamic_bitset<> const & set1,
  boost::dynamic_bitset<> const & set2
) {
  using core::Real;

  boost::dynamic_bitset<> result = (set1 & set2);
    //( set1 &  set2) |
    //(~set1 & ~set2);
  //std::string s1, s2;
  //boost::to_string(set1,s1);
  //boost::to_string(set2,s2);
  //std::cout << s1 << " cmp " << s2 << std::endl;
  Real const dist(
    static_cast< Real >( result.count() ) /
    //static_cast< Real >( std::max( set1.count(),set2.count() ) )
    static_cast< Real >( set2.count() )
  );
  //std::cout << result.count() << " " << result.size() << std::endl;
  return dist;
}

ContactMapEvaluator::ContactMapEvaluator(
  core::pose::Pose const & native_pose,
  core::Real const max_dist,
  core::Size const min_seqsep
) :
  evaluation::SingleValuePoseEvaluator< core::Real >( "contact_map" ),
  max_dist_(max_dist),
  min_seqsep_(min_seqsep),
  native_(native_pose)
{}

void ContactMapEvaluator::apply(
  core::pose::Pose & pose,
  std::string,
  core::io::silent::SilentStruct & ss
) const {
  using ObjexxFCL::string_of;
  using core::pose::Pose;

  boost::dynamic_bitset<> native_features = get_contact_features(
    native_, max_dist_, "CA", min_seqsep_
  );
  boost::dynamic_bitset<> features = get_contact_features( pose, max_dist_, "CA", min_seqsep_ );
  core::Real const cm_score(
    pct_features_in_common(features,native_features)
  );
  std::string const output_name(
    "contact_score_" + string_of(max_dist_) + "_" + string_of(min_seqsep_)
  );
  ss.add_energy( output_name, cm_score );
}

} // simple_filter
} // protocols