DesignVsNativeComparison.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 stuff to compare designs against the native pdb
/// @brief
/// @author Florian Richter, floric@u.washington.edu

// Unit headers
#include <protocols/enzdes/DesignVsNativeComparison.hh>
#include <protocols/enzdes/enzdes_util.hh>

// Project headers
#include <core/pose/Pose.hh>
// AUTO-REMOVED #include <core/io/pdb/pose_io.hh>
#include <basic/options/option.hh>
//#include <core/pose/metrics/PoseMetricCalculatorBase.fwd.hh>
#include <core/scoring/Energies.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/MetricValue.hh>
#include <protocols/toolbox/pose_manipulation.hh>

#include <core/scoring/constraints/ConstraintSet.hh> //temporary include

// Utility Headers
// AUTO-REMOVED #include <utility/io/izstream.hh>
// AUTO-REMOVED #include <utility/string_util.hh>

#include <basic/Tracer.hh>


// option key includes

#include <basic/options/keys/enzdes.OptionKeys.gen.hh>

#include <core/import_pose/import_pose.hh>
#include <utility/vector1.hh>



static basic::Tracer tr("protocols.enzdes.DesignVsNativeComparison");

namespace protocols {
namespace enzdes {


DesignVsNativeComparison::DesignVsNativeComparison(){
  native_poses_.clear();
}

DesignVsNativeComparison::~DesignVsNativeComparison(){}

void
DesignVsNativeComparison::compare_to_native(
  core::pose::Pose const & pose,
  utility::vector1< std::pair< std::string, std::string > > const & calculators,
  core::scoring::ScoreFunctionCOP scorefxn,
  utility::vector1< core::io::silent::SilentEnergy > & silent_Es)
{

  //first, extract the pdb code from the pose input tag
  std::string pdb_code = enzutil::get_pdb_code_from_pose_tag( pose );

  std::map<  std::string, core::pose::PoseOP >::iterator map_it = native_poses_.find( pdb_code );

  if( map_it == native_poses_.end() ){

    std::string native_path = basic::options::option[basic::options::OptionKeys::enzdes::compare_native].value();

    std::string native_filename = native_path + pdb_code + ".pdb";
    core::pose::PoseOP new_native = new core::pose::Pose();

    core::import_pose::pose_from_pdb( *new_native, native_filename );

    //need to score the native, in case the calculators rely on cached energies
    //also need to remove non protein residues, just to make sure
    toolbox::pose_manipulation::remove_non_protein_residues( *new_native );

    (*scorefxn)(*new_native);

    native_poses_.insert( std::pair< std::string, core::pose::PoseOP >( pdb_code, new_native ) );

    map_it = native_poses_.find( pdb_code );

  }

  core::pose::PoseOP native = map_it->second;

  core::Real native_totalE = native->energies().total_energies().dot( native->energies().weights() );

  //remove the ligand from the pose, so the comparison makes sense
  core::pose::PoseOP pureprotpose = new core::pose::Pose( pose );

  toolbox::pose_manipulation::remove_non_protein_residues( *pureprotpose );

  //arrghh, bug, when scoring a pose where one of the deleted residues was constrained, program crashes
  //because the deleted residue survives in the long range energy containers:(
  //temporary hack workaround: put an empty constraint set into the pureprotpose
  pureprotpose->constraint_set( new core::scoring::constraints::ConstraintSet() );
  core::Real pose_totalE = (*scorefxn)(*pureprotpose );

  //ok, we have our native, now use each of the calculators to compare
  //and of course we're also looking at the total energy
  silent_Es.push_back( core::io::silent::SilentEnergy( "NaCo_dTotE", pose_totalE - native_totalE, 1, 12) );

  basic::MetricValue< core::Real > mval_real;
  basic::MetricValue< core::Size > mval_size;

  core::Real poseval, nativeval;

  for( utility::vector1< std::pair< std::string, std::string > >::const_iterator calc_it = calculators.begin();
       calc_it != calculators.end(); ++calc_it ){


    if( calc_it->first == "hbond_pm" || calc_it->first == "burunsat_pm" || calc_it->first == "NLconts_pm" || calc_it->second == "total_pos_charges" || calc_it->second == "total_neg_charges" ){
      pureprotpose->metric( calc_it->first, calc_it->second, mval_size );
      poseval = mval_size.value();

      native->metric( calc_it->first, calc_it->second, mval_size );
      nativeval = mval_size.value();
    }
    else{
      pureprotpose->metric( calc_it->first, calc_it->second, mval_real );
      poseval = mval_real.value();

      native->metric( calc_it->first, calc_it->second, mval_real );
      nativeval = mval_real.value();
    }

    //std::cerr << "For " << calc_it->first << ", design val is " << poseval << " and nativeval is " << nativeval << std::endl;

    //now create a silent energy out of the calculated value
    core::Real native_diff = poseval - nativeval;
    std::string se_name = "NaCo_"+calc_it->first;
    if( calc_it->first == "charges_pm" ) se_name = "NaCo_" + calc_it->second;
    int width = std::max( 10, (int) se_name.length() + 3 );

    //core::io::SilentEnergy se( se_name , native_diff, 1, width );
    silent_Es.push_back( core::io::silent::SilentEnergy ( se_name , native_diff, 1, width ) );

  } //loop over calculators


} //compare_to_native


}//enzdes
}//protocols