GenBornPotential.hh

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/GenBornPotential.fwd.hh
/// @brief
/// @author


#ifndef INCLUDED_core_scoring_GenBornPotential_hh
#define INCLUDED_core_scoring_GenBornPotential_hh

#include <core/scoring/GenBornPotential.fwd.hh>

#include <core/types.hh>
// AUTO-REMOVED #include <core/scoring/types.hh>

#include <basic/datacache/CacheableData.hh>

#include <core/conformation/Residue.hh>
#include <core/pose/Pose.fwd.hh>
//#include <core/pack/task/PackerTask.fwd.hh>
//#include <core/pack/rotamer_set/RotamerSet.fwd.hh>
#include <core/conformation/RotamerSetBase.fwd.hh>
#include <core/id/AtomID.fwd.hh>
#include <core/kinematics/DomainMap.fwd.hh>
//#include <core//.fwd.hh>

// AUTO-REMOVED #include <utility/vector1.hh>
#include <utility/pointer/owning_ptr.hh>
#include <utility/pointer/ReferenceCount.hh>

#include <utility/vector1.hh>


//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
/**

   This is a reimplementation of Jim Havranek's original rosetta++ Gen Born code.
   source files: rosetta++/gb_elec*

**/
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////
//////////////////////////////////////////////////////////////////////////////////

namespace core {
namespace scoring {

////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////

class GenBornResidueInfo : public utility::pointer::ReferenceCount {

public:
  typedef conformation::Residue Residue;

public:
  virtual ~GenBornResidueInfo();

  GenBornResidueInfoOP
  clone() const
  {
    return new GenBornResidueInfo( *this );
  }


  ///
  GenBornResidueInfo( Residue const & rsd )
  {
    initialize( rsd );
  }

  ///
  Size
  size() const
  {
    return atomic_radius_.size();
  }

  ///
  Real
  atomic_radius( Size const atm ) const
  {
    return atomic_radius_[ atm ];
  }

  ///
  Real &
  atomic_radius( Size const atm )
  {
    return atomic_radius_[ atm ];
  }

  ///
  Real
  born_radius( Size const atm ) const
  {
    return born_radius_[ atm ];
  }

  ///
  Real &
  born_radius( Size const atm )
  {
    return born_radius_[ atm ];
  }

  ///
  Real
  scale_factor( Size const atm ) const
  {
    return scale_factor_[ atm ];
  }

  ///
  Real &
  scale_factor( Size const atm )
  {
    return scale_factor_[ atm ];
  }

  ///
  void
  initialize( Residue const & rsd );

private:
  utility::vector1< Real > atomic_radius_;
  utility::vector1< Real > born_radius_;
  utility::vector1< Real > scale_factor_;

};


////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////

class GenBornPoseInfo : public basic::datacache::CacheableData {

public:
  typedef conformation::Residue   Residue;
  typedef conformation::ResidueOP ResidueOP;

public:

  GenBornPoseInfo() {};

  GenBornPoseInfo( GenBornPoseInfo const & src );

  basic::datacache::CacheableDataOP
  clone() const
  {
    return new GenBornPoseInfo( *this );
  }

  ///
  Size
  size() const
  {
    return residue_info_.size();
  }

  ///
  GenBornResidueInfo &
  residue_info( Size const i )
  {
    return *residue_info_[i];
  }

  ///
  GenBornResidueInfo const &
  residue_info( Size const i ) const
  {
    return *residue_info_[i];
  }

  ///
  bool
  being_packed( Size const seqpos ) const
  {
    return being_packed_[ seqpos ];
  }

  ///
  void
  set_placeholder( Size const i, ResidueOP rsd, GenBornResidueInfoOP info );


  ///
  GenBornResidueInfo const &
  placeholder_info( Size const seqpos ) const
  {
    assert( placeholder_info_[ seqpos ] );
    return *placeholder_info_[ seqpos ];
  }

  ///
  Residue const &
  placeholder_residue( Size const seqpos ) const
  {
    assert( placeholder_residue_[ seqpos ] );
    return *placeholder_residue_[ seqpos ];
  }

  ///
  void
  initialize( pose::Pose const & pose );


  ///
  void
  set_repack_list( utility::vector1< bool > const & repacking_residues );

private:

  // these are allocated in initialize
  utility::vector1< GenBornResidueInfoOP > residue_info_;

  // these may be null pointers
  utility::vector1< ResidueOP > placeholder_residue_;
  utility::vector1< GenBornResidueInfoOP > placeholder_info_;

  // stores info from the packertask when setup_for_packing calls set_repack_list
  utility::vector1< bool > being_packed_;

};


////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////

class GenBornRotamerSetInfo : public basic::datacache::CacheableData {


public:
  typedef conformation::Residue        Residue;
  typedef conformation::ResidueOP      ResidueOP;
  typedef conformation::RotamerSetBase RotamerSetBase;

public:

  ///
  GenBornRotamerSetInfo( GenBornRotamerSetInfo const & src ):
    CacheableData()
  {
    residue_info_.resize( src.size() );
    for ( Size i=1; i<= src.size(); ++i ) {
      residue_info_[i] = src.residue_info_[i]->clone();
    }
  }

  ///
  basic::datacache::CacheableDataOP
  clone() const
  {
    return new GenBornRotamerSetInfo( *this );
  }

  ///
  Size
  size() const
  {
    return residue_info_.size();
  }

  ///
  GenBornResidueInfo &
  residue_info( Size const i )
  {
    return *residue_info_[i];
  }

  ///
  GenBornResidueInfo const &
  residue_info( Size const i ) const
  {
    return *residue_info_[i];
  }


  ///
  GenBornRotamerSetInfo( RotamerSetBase const & rotamer_set )
  {
    initialize( rotamer_set );
  }

  /// dont forget to 0 the born_radii
  void
  initialize( RotamerSetBase const & rotamer_set );


private:
  utility::vector1< GenBornResidueInfoOP > residue_info_;
};


////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////
////////////////////////////////////////////////////////////////////////////////////////////////////

class GenBornPotential : public utility::pointer::ReferenceCount {
public:
  typedef conformation::Residue Residue;

public:
  /// ctor
  GenBornPotential():
    // Dielectric constants for protein (Ep) and for solvent (Ew)
    Ep( 4.0 ),
    Ew( 80.0 ),
    // Parameters for determination of Generalized Born radii
    ParamS( 0.09 ),
    ParamD( 1.00 ),
    ParamB( 0.80 ),
    ParamG( 4.850000 ),

    // More parameters for GB burial
    Param_TA ( 0.333333333333333 ),
    Param_TB ( 0.4 ),
    Param_TC ( 0.42857142857142857143 ),
    Param_TD ( 0.444444444444444 ),
    Param_TDD( 0.45454545454545454545 ),
    Param_TE ( 1.333333333333333 ),
    Param_TF ( 2.4 ),
    Param_TG ( 3.42857142857142857143 ),
    Param_TH ( 4.44444444444444444 ),
    Param_THH( 5.45454545454545454545 ),

    dummy_radius( 2.39 ),
    dummy_scale( 0.80 ),
    dummy_distance( 2.44 )
  {}



  /// called prior to scoring, eg
  void
  get_all_born_radii( pose::Pose & pose ) const;

  ///
  void
  setup_for_packing(
    pose::Pose & pose,
    utility::vector1< bool > const & repacking_residues
  ) const;


  ///
  void
  update_residue_for_packing(
    pose::Pose & pose,
    Size const seqpos
  ) const;

  ///
  void
  get_rotamers_born_radii(
    pose::Pose const & pose,
    conformation::RotamerSetBase & rotamer_set
  ) const;

  ///
  Real
  get_res_res_elecE(
    Residue const & rsd1,
    GenBornResidueInfo const & gb1,
    Residue const & rsd2,
    GenBornResidueInfo const & gb2
  ) const;

  ///
  void
  eval_atom_derivative(
    id::AtomID const & id,
    Real const weight,
    pose::Pose const & pose,
    kinematics::DomainMap const & domain_map,
    bool const exclude_DNA_DNA,
    Vector & F1,
    Vector & F2
  ) const;

private: // these dont all *have* to be private, just not called by anyone else right now

  ///
  void
  res_res_burial(
    Residue const & rsd1,
    GenBornResidueInfo & gb1,
    Residue const & rsd2,
    GenBornResidueInfo const & gb2
  ) const;

  /// helper
  void
  finalize_born_radii( GenBornResidueInfo & gb_info ) const;

  ///
  Real
  gb_shell_intxn(
    Real const qai,
    Real const rai,
    Real const qbi,
    Real const rbi,
    Real const dist
  ) const;


  ///
  Real
  gb_shell_intxn_deriv(
    Real const qai,
    Real const rai,
    Real const qbi,
    Real const rbi,
    Real const dist
  ) const;


  ///
  void
  get_single_rotamer_born_radii(
    Residue const & rsd1,
    pose::Pose const & pose,
    GenBornPoseInfo const & gb_info,
    GenBornResidueInfo & gb1
  ) const;

  ///
  void
  get_template_born_radii(
    pose::Pose const & pose,
    GenBornPoseInfo & gb_info
  ) const;

  ///
  void
  build_placeholders(
    pose::Pose const & pose,
    GenBornPoseInfo & gb_info
  ) const;

private:

  // Dielectric constants for protein (Ep) and for solvent (Ew)
  Real const Ep;
  Real const Ew;

  // Parameters for determination of Generalized Born radii
  Real const ParamS;
  Real const ParamD;
  Real const ParamB;
  Real const ParamG;

  // More parameters for GB burial
  Real const Param_TA;
  Real const Param_TB;
  Real const Param_TC;
  Real const Param_TD;
  Real const Param_TDD;
  Real const Param_TE;
  Real const Param_TF;
  Real const Param_TG;
  Real const Param_TH;
  Real const Param_THH;

  Real const dummy_radius;
  Real const dummy_scale;
  Real const dummy_distance; // also implicitly defined by the gb placeholder params file

};





} // scoring
} // core

#endif