NonResidueTypeConstraint.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   core/scoring/constraints/NonResidueTypeConstraint.cc
///
/// @brief
/// @author Sarel Fleishman


#include <core/scoring/constraints/NonResidueTypeConstraint.hh>

#include <core/conformation/Residue.hh>
//#include <core/io/pdb/pose_io.hh> -- REALLY?
// AUTO-REMOVED #include <core/options/option.hh>
// AUTO-REMOVED #include <core/options/keys/OptionKeys.hh>
#include <core/scoring/ScoreType.hh>
// AUTO-REMOVED #include <core/scoring/constraints/ConstraintSet.hh>
#include <basic/Tracer.hh>

#include <core/id/SequenceMapping.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/constraints/XYZ_Func.hh>
#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace constraints {


static basic::Tracer non_residue_type_constraint_tracer("core.scoring.constraints.NonResidueTypeConstraint");


NonResidueTypeConstraint::NonResidueTypeConstraint(
  core::pose::Pose const & pose,
  Size seqpos,
  core::Real favor_non_native_bonus
):
  Constraint( core::scoring::res_type_constraint ),
  seqpos_( seqpos ),
  rsd_type_name3_( pose.residue_type( seqpos ).name3() ),
  favor_non_native_bonus_( favor_non_native_bonus )
{}


NonResidueTypeConstraint::NonResidueTypeConstraint(
  core::pose::Pose const &,
  Size seqpos,
  std::string AAname,
  core::Real favor_non_native_bonus
):
  Constraint( core::scoring::res_type_constraint ),
  seqpos_( seqpos ),
  rsd_type_name3_( AAname ),
  favor_non_native_bonus_( favor_non_native_bonus )
{}

NonResidueTypeConstraint::NonResidueTypeConstraint(
    Size seqpos,
    std::string aa_in,
    std::string name3_in,
    core::Real bonus_in
):
  Constraint( core::scoring::res_type_constraint ),
  seqpos_( seqpos ),
  AAname( aa_in ),
  rsd_type_name3_( name3_in ),
  favor_non_native_bonus_( bonus_in )
{}


NonResidueTypeConstraint::~NonResidueTypeConstraint() {}

ConstraintOP
NonResidueTypeConstraint::clone() const
{
  return ConstraintOP( new NonResidueTypeConstraint( *this ) );
}

utility::vector1< core::Size >
NonResidueTypeConstraint::residues() const {
  utility::vector1< core::Size > pos_list(1, seqpos_); // length 1 containing "all" seqpos_ values
  return pos_list;
}

void
NonResidueTypeConstraint::show( std::ostream & out ) const {
  out << "NonResidueTypeConstraint; ";
  out << "seqpos: " << seqpos_;
  out << "; AAname: "<< AAname;
  out << "; rsd_type_name3: "<< rsd_type_name3_;
  out << "; favor_non_native_bonus: "<< favor_non_native_bonus_;
}

ConstraintOP
NonResidueTypeConstraint::remap_resid( core::id::SequenceMapping const &seqmap ) const
{
  core::Size newseqpos = seqmap[ seqpos_ ];
  if ( newseqpos != 0 ) {
    return ConstraintOP( new NonResidueTypeConstraint(  newseqpos, AAname, rsd_type_name3_, favor_non_native_bonus_ ) );
  } else {
    return NULL;
  }
}


// Calculates a score for this constraint using XYZ_Func, and puts the UNWEIGHTED score into
// emap. Although the current set of weights currently is provided, Constraint objects
// should put unweighted scores into emap.
void
NonResidueTypeConstraint::score( XYZ_Func const & xyz_func, EnergyMap const & weights, EnergyMap & emap ) const
{
  Real const weight(weights[ this->score_type() ] );
  if( weight == 0 ) return; // what's the point?

  conformation::Residue const & rsd( xyz_func.residue(seqpos_) );
  if( rsd.type().name3() == rsd_type_name3_ )
    emap[ this->score_type() ] -= favor_non_native_bonus_;
  // no match, don't adjust score
}


void
NonResidueTypeConstraint::fill_f1_f2(
  AtomID const & ,//atom,
  XYZ_Func const &,
  Vector & ,//F1,
  Vector & ,//F2,
  EnergyMap const & //weights
) const
{
  // Do nothing.
  // Derivative of this restraint is effectively zero
  // so we just "add zero" to F1 and F2.
}

} // namespace constraints
} // namespace scoring
} // namespace core