PackstatCalculator.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   core/pose/metrics/PackstatCalculator.cc
/// @brief  packstat calculator class
/// @author Florian Richter

// Unit headers
#include <protocols/toolbox/pose_metric_calculators/PackstatCalculator.hh>
#include <core/scoring/packstat/compute_sasa.hh>

#include <core/chemical/ResidueType.hh>
// AUTO-REMOVED #include <core/pose/metrics/CalculatorFactory.hh>
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <protocols/toolbox/PoseMetricCalculators/NumberHBondsCalculator.hh>
// AUTO-REMOVED #include <protocols/toolbox/PoseMetricCalculators/SasaCalculator.hh>
#include <protocols/toolbox/pose_manipulation.hh>



// Utility headers
#include <basic/Tracer.hh>
#include <utility/exit.hh>
#include <utility/stream_util.hh>
#include <utility/string_util.hh>
#include <basic/MetricValue.hh>


#include <cassert>

#include <utility/vector1.hh>



using namespace core;
using namespace core::pose;
using namespace core::pose::metrics;

static basic::Tracer TR("protocols/toolbox/PoseMetricCalculators/PackstatCalculator");

namespace protocols{
namespace toolbox {
namespace pose_metric_calculators {


PackstatCalculator::PackstatCalculator(
  core::Size oversample,
  bool remove_nonprotein_res
) : total_packstat_(0),
    special_region_packstat_(0),
    oversample_(oversample),
    remove_nonprotein_res_(remove_nonprotein_res)
{
  special_region_.clear();
  residue_packstat_.clear();
}


PackstatCalculator::PackstatCalculator(
  std::set< core::Size > const & special_region,
  core::Size oversample,
  bool remove_nonprotein_res
) : total_packstat_(0),
    special_region_packstat_(0),
    oversample_(oversample),
    remove_nonprotein_res_(remove_nonprotein_res),
    special_region_( special_region )
{
  residue_packstat_.clear();
}


void
PackstatCalculator::lookup(
  std::string const & key,
  basic::MetricValueBase * valptr
) const
{

   if ( key == "total_packstat" ) {
     basic::check_cast( valptr, &total_packstat_, "total_packstat expects to return a real" );
     (static_cast<basic::MetricValue<Real> *>(valptr))->set( total_packstat_ );

   } else if ( key == "special_region_packstat" ) {
     basic::check_cast( valptr, &special_region_packstat_, "special_region_packstat expects to return a real" );
     (static_cast<basic::MetricValue<Real> *>(valptr))->set( special_region_packstat_ );

   } else if ( key == "residue_packstat" ) {
     basic::check_cast( valptr, &residue_packstat_, "residue_packstat expects to return a utility::vector1< Real >" );
     (static_cast<basic::MetricValue<utility::vector1< Real > > *>(valptr))->set( residue_packstat_ );

   } else {
     basic::Error() << "PackstatCalculator cannot compute the requested metric " << key << std::endl;
     utility_exit();
   }

} //lookup



std::string
PackstatCalculator::print( std::string const & key ) const
{

  if ( key == "total_packstat" ) {
    return utility::to_string( total_packstat_ );
  } else if ( key == "special_region_packstat" ) {
    return utility::to_string( special_region_packstat_ );
  } else if ( key == "residue_packstat" ) {
    return utility::to_string( residue_packstat_ );
  }

  basic::Error() << "PackstatCalculator cannot compute metric " << key << std::endl;
  utility_exit();
  return "";

} //print


/// @brief this function doesn't actually recompute anything by itself, but calls the
/// @brief stuff in the packstat code
void
PackstatCalculator::recompute( Pose const & this_pose )
{
  using namespace core::scoring::packstat;

  if( remove_nonprotein_res_ ){

    bool has_nonprot_res(false);

    for( core::Size i = 1; i <= this_pose.total_residue(); ++i){
      if( ! this_pose.residue_type(i).is_protein() ){
        has_nonprot_res = true;
        break;
      }
    }

    if( has_nonprot_res ){

      PoseOP pureprotpose = new Pose( this_pose );

      pose_manipulation::remove_non_protein_residues( *pureprotpose );

      total_packstat_ = compute_packing_score( *pureprotpose, oversample_ );
      residue_packstat_ = compute_residue_packing_scores( *pureprotpose, oversample_ );
      runtime_assert( pureprotpose->total_residue() == residue_packstat_.size() );
    }
    else{
      total_packstat_ = compute_packing_score( this_pose, oversample_ );
      residue_packstat_ = compute_residue_packing_scores( this_pose, oversample_ );
      runtime_assert( this_pose.total_residue() == residue_packstat_.size() );
    }
  }

  else{
    total_packstat_ = compute_packing_score( this_pose, oversample_ );
    residue_packstat_ = compute_residue_packing_scores( this_pose, oversample_ );
    runtime_assert( this_pose.total_residue() == residue_packstat_.size() );
  }


  core::Real respackstat_sum(0.0);
  core::Real special_region_sum(0.0);
  for( Size i = 1; i <= residue_packstat_.size(); ++i){

    respackstat_sum = respackstat_sum + residue_packstat_[i];
    if( special_region_.find( i ) != special_region_.end() ) special_region_sum = special_region_sum + residue_packstat_[i];

  }

  //runtime_assert( total_packstat_ == ( respackstat_sum / residue_packstat_.size() ) );
  //std::cerr << "total packstat is " << total_packstat_ << ", average residue packstat is " << respackstat_sum / residue_packstat_.size() << std::endl;

  special_region_packstat_ = ( special_region_sum / special_region_.size() );

} //recompute


} //namespace pose_metric_calculators
} //namespace toolbox
} //namespace protocols