RNA_SugarCloseEnergy.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.
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// (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
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/// @file   core/scoring/methods/RNA_SugarCloseEnergy.cc
/// @brief  RNA_SugarClose energy method class implementation
/// @author Rhiju Das

// Unit Headers
#include <core/scoring/rna/RNA_SugarCloseEnergy.hh>
#include <core/scoring/rna/RNA_SugarCloseEnergyCreator.hh>

// Package Headers
#include <core/scoring/rna/RNA_Util.hh>
#include <core/scoring/rna/RNA_FittedTorsionInfo.hh>
// AUTO-REMOVED #include <core/scoring/ScoringManager.hh>
#include <core/scoring/constraints/HarmonicFunc.hh>
#include <core/scoring/constraints/HarmonicFunc.fwd.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/FadeFunc.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <basic/options/keys/rna.OptionKeys.gen.hh>


// Project headers
#include <core/pose/Pose.hh>

// Utility headers
#include <numeric/conversions.hh>
// AUTO-REMOVED #include <numeric/xyz.functions.hh>

#include <core/conformation/Residue.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>


// C++


namespace core {
namespace scoring {
namespace rna {

/// @details This must return a fresh instance of the RNA_SugarCloseEnergy class,
/// never an instance already in use
methods::EnergyMethodOP
RNA_SugarCloseEnergyCreator::create_energy_method(
  methods::EnergyMethodOptions const &
) const {
  return new RNA_SugarCloseEnergy;
}

ScoreTypes
RNA_SugarCloseEnergyCreator::score_types_for_method() const {
  ScoreTypes sts;
  sts.push_back( rna_sugar_close );
  return sts;
}


/// ctor
RNA_SugarCloseEnergy::RNA_SugarCloseEnergy() :
  parent( new RNA_SugarCloseEnergyCreator ),
  scale_rna_torsion_tether_( 0.05 ), // THIS IS A SCALING FACTOR FOR ALL CONSTRAINTS.
  scale_rna_torsion_sd_( 1.0 / std::sqrt( scale_rna_torsion_tether_ ) ),
  o4star_c1star_bond_length_( 1.414 ),
  o4star_c1star_sd_( 0.01 ),
  o4star_c1star_dist_harm_func_( new constraints::HarmonicFunc( o4star_c1star_bond_length_, scale_rna_torsion_sd_ * o4star_c1star_sd_ )),
  angle_sd_( numeric::conversions::radians( 1.0 ) ),
  o4star_c1star_c2star_bond_angle_( numeric::conversions::radians( 106.39 ) ),
  o4star_c1star_c2star_angle_harm_func_(
    new constraints::HarmonicFunc( o4star_c1star_c2star_bond_angle_, scale_rna_torsion_sd_ * angle_sd_ ) ),
  o4star_c1star_first_base_bond_angle_( numeric::conversions::radians( 108.2 ) ),
  o4star_c1star_first_base_angle_harm_func_(
    new constraints::HarmonicFunc( o4star_c1star_first_base_bond_angle_, angle_sd_ ) ),
  c4star_o4star_c1star_bond_angle_( numeric::conversions::radians( 110.4 ) ),
  c4star_o4star_c1star_angle_harm_func_(
                                        new constraints::HarmonicFunc( c4star_o4star_c1star_bond_angle_, scale_rna_torsion_sd_ * angle_sd_ ) ),
  //phenix_based_sugar_close params
  use_phenix_sugar_close_( basic::options::option[ basic::options::OptionKeys::rna::corrected_geo ]() ),
  o4star_c1star_bond_north_(1.412),
  o4star_c1star_bond_south_(1.415),
  bond_sd_(0.015),
  o4star_c1star_c2star_angle_north_( numeric::conversions::radians(107.6) ),
  o4star_c1star_c2star_angle_south_( numeric::conversions::radians(105.8) ),
  o4star_c1star_n1_9_angle_north_( numeric::conversions::radians(108.5) ),
  o4star_c1star_n1_9_angle_south_( numeric::conversions::radians(108.2) ),
  c4star_o4star_c1star_angle_north_( numeric::conversions::radians(109.7) ),
  c4star_o4star_c1star_angle_south_( numeric::conversions::radians(109.9) ),
  angle_sd1_( numeric::conversions::radians(1.0) ),
  angle_sd2_( numeric::conversions::radians(1.5) )
{}

RNA_SugarCloseEnergy::~RNA_SugarCloseEnergy() {}

/// clone
methods::EnergyMethodOP
RNA_SugarCloseEnergy::clone() const
{
  return new RNA_SugarCloseEnergy;
}


///////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::setup_for_derivatives( pose::Pose & pose, ScoreFunction const & ) const
{
  setup_sugar_ring_closure_constraints( pose );
}


///////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::residue_energy(
    conformation::Residue const & rsd,
    EnergyMap & emap  ) const {

  constraints::ConstraintSet residue_rna_sugar_close_constraints;
  add_sugar_ring_closure_constraints( rsd, residue_rna_sugar_close_constraints );
  residue_rna_sugar_close_constraints.eval_intrares_energy( rsd, emap );

}

///////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::residue_energy(
    conformation::Residue const & rsd,
    pose::Pose const &,
    EnergyMap & emap  ) const {
  return residue_energy( rsd, emap );
}

///////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::eval_atom_derivative(
  id::AtomID const & id,
  pose::Pose const & pose,
  kinematics::DomainMap const &, // domain_map,
  ScoreFunction const & sfxn,
  EnergyMap const & weights,
  Vector & F1,
  Vector & F2
) const
{
  //rna_sugar_close_constraints_->eval_atom_derivative( id, pose, sfxn, weights, F1, F2 );
  // eval_atom_derivative became deprecated while I was working in another branch -- need to find a replacement?
  rna_sugar_close_constraints_->deprecated_eval_atom_derivative( id, pose, sfxn, weights, F1, F2 );
}


/////////////////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::setup_sugar_ring_closure_constraints( pose::Pose & pose ) const{
  rna_sugar_close_constraints_ = constraints::ConstraintSetOP( new constraints::ConstraintSet );

  for (Size i = 1; i <= pose.total_residue(); i++ ){
    add_sugar_ring_closure_constraints( pose.residue( i ), *rna_sugar_close_constraints_ );
  }

}

/////////////////////////////////////////////////////////////////////////////////////////
void
RNA_SugarCloseEnergy::add_sugar_ring_closure_constraints( conformation::Residue const & rsd, constraints::ConstraintSet & cst_set ) const {

  using namespace core::scoring::constraints;

  if ( !rsd.is_RNA() ) return;

  Size const & i( rsd.seqpos() );

  //fast look up!
  Size const o4star_index=rsd.RNA_type().o4star_atom_index();
  Size const c1star_index=rsd.RNA_type().c1star_atom_index();
  Size const c2star_index=rsd.RNA_type().c2star_atom_index();
  Size const c4star_index=rsd.RNA_type().c4star_atom_index(); 

  //consistency_check
  if(o4star_index!=7)  utility_exit_with_message("o4star_id="+ObjexxFCL::string_of(o4star_index) + "!=7");
  if(c1star_index!=10) utility_exit_with_message("c1star_id="+ObjexxFCL::string_of(c1star_index) +"!=10");
  if(c2star_index!=11) utility_exit_with_message("c2star_id="+ObjexxFCL::string_of(c2star_index) +"!=11");
  if(c4star_index!=6)  utility_exit_with_message("c4star_id="+ObjexxFCL::string_of(c4star_index) +"!=16");

  id::AtomID const o4star_id( o4star_index, i );
  id::AtomID const c1star_id( c1star_index, i );
  id::AtomID const c2star_id( c2star_index, i );
  id::AtomID const c4star_id( c4star_index, i );
  id::AtomID const first_base_atom_id( first_base_atom_index( rsd ),  i );

  constraints::ConstraintOP dist_cst, angle1, angle2, angle3;
  if (use_phenix_sugar_close_) {
    Real const delta = rsd.mainchain_torsion( DELTA );
    RNA_FittedTorsionInfo rna_torsion_fitted_info;
    Real const delta_cutoff = rna_torsion_fitted_info.delta_cutoff();
    if ( delta < delta_cutoff ) { //NORTH
      dist_cst = new AtomPairConstraint( o4star_id, c1star_id, 
        new HarmonicFunc( o4star_c1star_bond_north_, scale_rna_torsion_sd_ * bond_sd_ ) , rna_sugar_close );
      angle1 = new AngleConstraint( o4star_id, c1star_id, c2star_id,
        new HarmonicFunc( o4star_c1star_c2star_angle_north_, scale_rna_torsion_sd_ * angle_sd1_ ), rna_sugar_close );
      angle2 = new AngleConstraint( c4star_id, o4star_id, c1star_id,
        new HarmonicFunc( c4star_o4star_c1star_angle_north_, scale_rna_torsion_sd_ * angle_sd1_ ), rna_sugar_close );
      angle3 = new AngleConstraint( o4star_id, c1star_id, first_base_atom_id,
        new HarmonicFunc( o4star_c1star_n1_9_angle_north_, scale_rna_torsion_sd_ * angle_sd2_ ), rna_sugar_close );
    } else { //SOUTH
      dist_cst = new AtomPairConstraint( o4star_id, c1star_id, 
        new HarmonicFunc( o4star_c1star_bond_south_, scale_rna_torsion_sd_ * bond_sd_ ) , rna_sugar_close );
      angle1 = new AngleConstraint( o4star_id, c1star_id, c2star_id,
        new HarmonicFunc( o4star_c1star_c2star_angle_south_, scale_rna_torsion_sd_ * angle_sd1_ ), rna_sugar_close );
      angle2 = new AngleConstraint( c4star_id, o4star_id, c1star_id,
        new HarmonicFunc( c4star_o4star_c1star_angle_south_, scale_rna_torsion_sd_ * angle_sd1_ ), rna_sugar_close );
      angle3 = new AngleConstraint( o4star_id, c1star_id, first_base_atom_id,
        new HarmonicFunc( o4star_c1star_n1_9_angle_south_, scale_rna_torsion_sd_ * angle_sd2_ ), rna_sugar_close );
    }
  } else {
    dist_cst = 
      new AtomPairConstraint( o4star_id, c1star_id, o4star_c1star_dist_harm_func_, rna_sugar_close );
    angle1 = 
      new AngleConstraint( o4star_id, c1star_id, c2star_id, o4star_c1star_c2star_angle_harm_func_, rna_sugar_close );
    angle2 = 
      new AngleConstraint( c4star_id, o4star_id, c1star_id, c4star_o4star_c1star_angle_harm_func_, rna_sugar_close );
    angle3 = 
      new AngleConstraint( o4star_id, c1star_id, first_base_atom_id, o4star_c1star_first_base_angle_harm_func_, rna_sugar_close );
  }

  cst_set.add_constraint( dist_cst );
  cst_set.add_constraint( angle1 ); //Note to Rhiju (12/25/2011): Previously in Trunk version, angle1 was not added to the cst_set!
  cst_set.add_constraint( angle2 );
  cst_set.add_constraint( angle3 );

}



void RNA_SugarCloseEnergy::indicate_required_context_graphs( utility::vector1< bool > & ) const{}

core::Size
RNA_SugarCloseEnergy::version() const
{
  return 1; // A new torsion potential (integration from Das lab branch -- Aug 2011)
}


} // rna
} // scoring
} // core