RNA_Mg_KnowledgeBasedPotential.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/scoring/rna/RNA_Mg_KnowledgeBasedPotential.hh
/// @brief
/// @author Rhiju Das


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

// Package headers
#include <core/scoring/rna/RNA_ScoringInfo.hh>

// Project headers
#include <core/pose/Pose.hh>
#include <core/conformation/Residue.hh>
#include <core/chemical/ResidueType.hh>
#include <core/chemical/AtomType.hh>

// Utility headers
#include <utility/vector1.hh>
#include <basic/Tracer.hh>


static basic::Tracer tr("core.scoring.rna.RNA_Mg_KnowledgeBasedPotential");

namespace core {
namespace scoring {
namespace rna {

/// @details ctor
RNA_Mg_KnowledgeBasedPotential::RNA_Mg_KnowledgeBasedPotential():
  gaussian_parameter_phosphate_oxygen_(-5.93, 2.22, 0.55 ), // amplitude, center, width
  gaussian_parameter_imine_           (-3.41, 2.40, 0.33 ),
  gaussian_parameter_exocyclic_oxygen_(-4.20, 2.33, 0.43 ), // Reduced this from 5.2 to 3.4 after seeing too many close interactions.
  gaussian_parameter_o2star_          (-3.88, 2.54, 0.34 ),
  gaussian_parameter_phosphate_p_     ( 5.00, 2.00, 0.25 ), //this is a penalty!
  gaussian_parameter_polar_H_         ( 5.00, 2.25, 0.50 ), //this is a penalty!
  gaussian_parameter_nonpolar_H_      ( 5.00, 2.00, 0.50 ), //this is a penalty!
  //gaussian_parameter_aromatic_H_      ( 5.00, 2.00, 0.50 ), //assume no penalty here. Just a guess.

  gaussian_parameter_phosphate_oxygen_indirect_(-1.96, 4.07, 0.51 ), // longer-range, water-mediated interactions
  gaussian_parameter_imine_indirect_           (-1.24, 4.18, 0.28 ),
  gaussian_parameter_exocyclic_oxygen_indirect_(-1.93, 4.08, 0.45 ),
  gaussian_parameter_o2star_indirect_          (-1.28, 4.10, 0.37 ),

  gaussian_parameter_costheta_phosphate_oxygen_( 1.00, -0.91, 0.49 ), // amplitude, center, width of angular 'form factor'
  gaussian_parameter_costheta_imine_           ( 1.00, -0.97, 0.18 ), // note how sharp this is!
  gaussian_parameter_costheta_exocyclic_oxygen_( 1.00, -0.79, 0.34 ),
  gaussian_parameter_costheta_o2star_          ( 1.00, -0.91, 0.49 ), // not enough stats, copy from phosphate_oxygen
  gaussian_parameter_costheta_polar_H_         ( 1.00, -1.00, 0.25 ), //guess
  gaussian_parameter_costheta_nonpolar_H_      ( 1.00, -1.00, 0.25 ), //guess

  gaussian_parameter_costheta_phosphate_oxygen_indirect_( 1.00, -0.74, 0.55 ), // amplitude, center, width of angular 'form factor'
  gaussian_parameter_costheta_imine_indirect_           ( 1.00, -0.94, 0.46 ),
  gaussian_parameter_costheta_exocyclic_oxygen_indirect_( 1.00, -0.56, 0.61 ),
  gaussian_parameter_costheta_o2star_indirect_          ( 1.00, -0.74, 0.55 ) // not enough stats, copy from phosphate_oxygen

{
}

//////////////////////////////////////////////////////////////////
Gaussian_parameter
RNA_Mg_KnowledgeBasedPotential::get_mg_potential_gaussian_parameter( core::conformation::Residue const & rsd, Size const j ) const{
  bool is_phosphate_oxygen( false );
  return get_mg_potential_gaussian_parameter( rsd, j, is_phosphate_oxygen );
}


/////////////////////////////////
// This is actually pretty general, and would even work for non-RNA residues, but
// for now stick to RNA where I've tried to derive a reasonable low resolution potential
// from the available PDB statistics in the RNA09 set.
Gaussian_parameter
RNA_Mg_KnowledgeBasedPotential::get_mg_potential_gaussian_parameter( core::conformation::Residue const & rsd, Size const j, bool & is_phosphate_oxygen ) const{

  is_phosphate_oxygen = false;

  if ( rsd.is_RNA() ) {

    std::string const atom_type_name = rsd.atom_type( j ).name();

    //tr << "atom check: " << j << " " << atom_type_name << "." << std::endl;

    // This information should probably go into a special RNA_Mg_Potential.cc function or something.
    if ( atom_type_name == "OOC" ) { // This is a  O1P or O2P nonbridging phosphate oxygen
      is_phosphate_oxygen = true;
      return gaussian_parameter_phosphate_oxygen_;
    } else if ( atom_type_name == "Nhis" ) { // imine nitrogens
      return gaussian_parameter_imine_;
    } else if ( atom_type_name == "OCbb" ) { // exocyclic oxygens
      return gaussian_parameter_exocyclic_oxygen_;
    } else if ( rsd.atom_name( j ) == " O2*" ){
      return gaussian_parameter_o2star_;
    } else if ( rsd.atom_name(j) == " P  " ){
      return gaussian_parameter_phosphate_p_;
    } else if ( atom_type_name == "Hpol" ){
      return gaussian_parameter_polar_H_;
    } else if ( atom_type_name == "Hapo" ) { //|| atom_type_name == "Haro" ){
      return gaussian_parameter_nonpolar_H_;
    }
  }

  return Gaussian_parameter( 0.0, 0.0, 0.0 );
}


/////////////////////////////////
Gaussian_parameter
RNA_Mg_KnowledgeBasedPotential::get_mg_potential_indirect_gaussian_parameter( core::conformation::Residue const & rsd, Size const j ) const{

  if ( rsd.is_RNA() ) {

    std::string const atom_type_name = rsd.atom_type( j ).name();

    // This information should probably go into a special RNA_Mg_Potential.cc function or something.
    if ( atom_type_name == "OOC" ) { // This is a  O1P or O2P nonbridging phosphate oxygen
      return gaussian_parameter_phosphate_oxygen_indirect_;
    } else if ( atom_type_name == "Nhis" ) { // imine nitrogens
      return gaussian_parameter_imine_indirect_;
    } else if ( atom_type_name == "OCbb" ) { // exocyclic oxygens
      return gaussian_parameter_exocyclic_oxygen_indirect_;
    } else if ( rsd.atom_name( j ) == " O2*" ){
      return gaussian_parameter_o2star_indirect_;
    }
  }

  return Gaussian_parameter( 0.0, 0.0, 0.0 );
}


/////////////////////////////////
Gaussian_parameter
RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_gaussian_parameter( core::conformation::Residue const & rsd, Size const j ) const{

  if ( rsd.is_RNA() ) {

    std::string const atom_type_name = rsd.atom_type( j ).name();

    // This information should probably go into a special RNA_Mg_Potential.cc function or something.
    if ( atom_type_name == "OOC" ) { // This is a  O1P or O2P nonbridging phosphate oxygen
      return gaussian_parameter_costheta_phosphate_oxygen_;
    } else if ( atom_type_name == "Nhis" ) { // imine nitrogens
      return gaussian_parameter_costheta_imine_;
    } else if ( atom_type_name == "OCbb" ) { // exocyclic oxygens
      return gaussian_parameter_costheta_exocyclic_oxygen_;
    } else if ( rsd.atom_name( j ) == " O2*" ){
      return gaussian_parameter_costheta_o2star_;
    } else if ( atom_type_name == "Hpol" ){
      return gaussian_parameter_costheta_polar_H_;
    } else if ( atom_type_name == "Hapo" ) { //|| atom_type_name == "Haro" ){
      return gaussian_parameter_costheta_nonpolar_H_;
    }
  }

  return Gaussian_parameter( 0.0, 0.0, 0.0 );
}

/////////////////////////////////
Gaussian_parameter
RNA_Mg_KnowledgeBasedPotential::get_mg_potential_costheta_indirect_gaussian_parameter( core::conformation::Residue const & rsd, Size const j ) const{

  if ( rsd.is_RNA() ) {

    std::string const atom_type_name = rsd.atom_type( j ).name();

    // This information should probably go into a special RNA_Mg_Potential.cc function or something.
    if ( atom_type_name == "OOC" ) { // This is a  O1P or O2P nonbridging phosphate oxygen
      return gaussian_parameter_costheta_phosphate_oxygen_indirect_;
    } else if ( atom_type_name == "Nhis" ) { // imine nitrogens
      return gaussian_parameter_costheta_imine_indirect_;
    } else if ( atom_type_name == "OCbb" ) { // exocyclic oxygens
      return gaussian_parameter_costheta_exocyclic_oxygen_indirect_;
    } else if ( rsd.atom_name( j ) == " O2*" ){
      return gaussian_parameter_costheta_o2star_indirect_;
    }
  }

  return Gaussian_parameter( 0.0, 0.0, 0.0 );
}


//////////////////////////////////////////////////////////////////////////////////////////
void
RNA_Mg_KnowledgeBasedPotential::setup_info_for_mg_calculation( pose::Pose & pose ) const
{
  //We don't know a priori which atom numbers correspond to which
  // atom names (e.g., O2* on an adenosine could be different depending
  // on whether its at a chainbreak, terminus, etc.)
  //Better to do a quick setup every time to pinpoint atoms that require
  //  monitoring for Mg binding.

  rna::RNA_ScoringInfo & rna_scoring_info( rna::nonconst_rna_scoring_info_from_pose( pose ) );

  if ( rna_scoring_info.mg_calculation_annotated_sequence() == pose.annotated_sequence() ) {
    //    tr << "matching sequence -- early return from setup_info_for_mg_calculation" << std::endl;
    return; // should be up to date
  }
  rna_scoring_info.set_mg_calculation_annotated_sequence( pose.annotated_sequence() );

  utility::vector1< bool > & is_magnesium = rna_scoring_info.nonconst_is_magnesium();
  utility::vector1< utility::vector1< Size > > &
      atom_numbers( rna_scoring_info.nonconst_atom_numbers_for_mg_calculation() );

  Size const total_residue( pose.total_residue() );

  atom_numbers.resize( total_residue );
  is_magnesium.resize( total_residue );

  for (Size i = 1; i <= total_residue; i++ ) {

    conformation::Residue const & rsd( pose.residue( i ) );
    is_magnesium[ i ] = false;
    atom_numbers[ i ].clear();

    if ( rsd.is_RNA() ) {


      // we go over all atoms, because we are putting in some repulsions (from polar hydrogens & phosphorus)
      for (Size j = 1; j <= rsd.natoms(); j++ ){
        Gaussian_parameter gaussian_parameter = get_mg_potential_gaussian_parameter( rsd, j );
        //tr << j << rsd.atom_name(j) << " ==> gaussian parameter " << gaussian_parameter.center << std::endl;
        if ( gaussian_parameter.center > 0.0 ) atom_numbers[ i ].push_back( j );
      }

    } else if ( rsd.name3() == " MG" ){
      is_magnesium[ i ] = true;
    }

    //tr << rsd.name3() << ' ' << i << ' ' << is_magnesium[ i ] << std::endl;

  }
}


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