DisulfideMatchingEnergyContainer.hh

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// vi: set ts=2 sw=2 noet:
//
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/// @file   core/scoring/disulfides/DisulfideMatchingEnergyContainer.hh
/// @brief  Disulfide Energy Container class declaration
/// @author rvernon@u.washington.edu
/// @todo This file was taken with minimal modifications from FullatomDisulfideEnergyContainer.hh.
/// It might be a good idea to move some code into a superclass inheritted by both.

#ifndef INCLUDED_core_scoring_disulfides_DisulfideMatchingEnergyContainer_hh
#define INCLUDED_core_scoring_disulfides_DisulfideMatchingEnergyContainer_hh

// Unit headers
#include <core/scoring/disulfides/DisulfideMatchingEnergyContainer.fwd.hh>

#ifdef WIN32
#include <core/scoring/disulfides/DisulfideAtomIndices.hh>
#endif

// Package headers
#include <core/scoring/LREnergyContainer.hh>

// Project headers
#include <core/chemical/ResidueType.fwd.hh>

#include <core/scoring/EnergyMap.fwd.hh>
// AUTO-REMOVED #include <core/scoring/ScoreFunction.fwd.hh>

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

#include <core/pose/Pose.fwd.hh>

#include <core/scoring/disulfides/DisulfideAtomIndices.fwd.hh>
#include <utility/vector1.hh>


namespace core {
namespace scoring {
namespace disulfides {

/** @brief An iterator over the disulfide bonds a residue forms
 *
 * When scoring a pose, a long range energy container must be able to iterate
 * over all the residues which interact with a particular residue. For
 * disulfide bonds, this is either zero or one items depending on whether the
 * residue specified forms a disulfide bond or not.
 *
 * @todo Given the proper options, include all residues in the vicinity which
 * could form a bond, not just the best one. Maybe even include non-cysteines!
 */
class DisulfideMatchingNeighborIterator : public ResidueNeighborIterator {
public:

  DisulfideMatchingNeighborIterator(
    DisulfideMatchingEnergyContainerAP owner,
    Size focused_node,
    Size disulfide_index
  );

  DisulfideMatchingNeighborIterator(
    DisulfideMatchingEnergyContainerAP owner
  );

  virtual ~DisulfideMatchingNeighborIterator();

  virtual ResidueNeighborIterator const & operator = ( ResidueNeighborIterator const & );
  virtual ResidueNeighborIterator const & operator ++ ();
  virtual bool operator == ( ResidueNeighborIterator const & ) const;
  virtual bool operator != ( ResidueNeighborIterator const & ) const;

  virtual Size upper_neighbor_id() const;
  virtual Size lower_neighbor_id() const;

  virtual Size residue_iterated_on() const;
  virtual Size neighbor_id() const;

  virtual void save_energy( EnergyMap const & );
  virtual void retrieve_energy( EnergyMap & ) const;
  virtual void accumulate_energy( EnergyMap & ) const;

  virtual void mark_energy_computed();
  virtual void mark_energy_uncomputed();

  virtual bool energy_computed() const;

private:
  DisulfideMatchingEnergyContainerAP owner_;
  Size focused_residue_;
  Size disulfide_index_;
};

/// @brief Just a const version of DisulfideMatchingNeighborIterator
class DisulfideMatchingNeighborConstIterator : public ResidueNeighborConstIterator {
public:
  DisulfideMatchingNeighborConstIterator(
    DisulfideMatchingEnergyContainerCAP owner,
    Size focused_node,
    Size disulfide_index
  );

  DisulfideMatchingNeighborConstIterator( DisulfideMatchingEnergyContainerCAP owner );

  virtual ~DisulfideMatchingNeighborConstIterator();

  virtual ResidueNeighborConstIterator const & operator = ( ResidueNeighborConstIterator const & );
  virtual ResidueNeighborConstIterator const & operator ++ ();
  virtual bool operator == ( ResidueNeighborConstIterator const & ) const;
  virtual bool operator != ( ResidueNeighborConstIterator const & ) const;

  virtual Size upper_neighbor_id() const;
  virtual Size lower_neighbor_id() const;

  virtual Size residue_iterated_on() const;
  virtual Size neighbor_id() const;

  virtual void retrieve_energy( EnergyMap & ) const;
  virtual void accumulate_energy( EnergyMap & ) const;

  virtual bool energy_computed() const;

private:
  DisulfideMatchingEnergyContainerCAP owner_;
  Size focused_residue_;
  Size disulfide_index_;

};

/**
 * @brief Storage for Disulfide Energy Terms
 */
class DisulfideMatchingEnergyComponents
{
public:
  DisulfideMatchingEnergyComponents() :
    dslfc_rot_( 0.0 ),
    dslfc_trans_( 0.0 ),
    dslfc_RT_( 0.0 )
  {}

  Energy dslfc_rot() const { return dslfc_rot_;}
  Energy dslfc_trans() const { return dslfc_trans_;}
  Energy dslfc_RT() const { return dslfc_RT_;}

  Energy & dslfc_rot() { return dslfc_rot_;}
  Energy & dslfc_trans() { return dslfc_trans_;}
  Energy & dslfc_RT() { return dslfc_RT_;}

private:
  Energy dslfc_rot_;
  Energy dslfc_trans_;
  Energy dslfc_RT_;
};

class DisulfideMatchingEnergyContainer : public LREnergyContainer {
public:
  static Size const NO_DISULFIDE;

public:
  DisulfideMatchingEnergyContainer();

  DisulfideMatchingEnergyContainer( pose::Pose const & );

  void
  update( pose::Pose const & );

  virtual
  ~DisulfideMatchingEnergyContainer();

  virtual
  bool empty() const;

  virtual
  LREnergyContainerOP clone() const;

  virtual
  ResidueNeighborConstIteratorOP
  const_neighbor_iterator_begin( int resid ) const;

  virtual
  ResidueNeighborConstIteratorOP
  const_neighbor_iterator_end( int resid ) const;

  virtual
  ResidueNeighborConstIteratorOP
  const_upper_neighbor_iterator_begin( int resid ) const;

  virtual
  ResidueNeighborConstIteratorOP
  const_upper_neighbor_iterator_end( int resid ) const;

  virtual
  ResidueNeighborIteratorOP
  neighbor_iterator_begin( int resid );

  virtual
  ResidueNeighborIteratorOP
  neighbor_iterator_end( int resid );

  virtual
  ResidueNeighborIteratorOP
  upper_neighbor_iterator_begin( int resid );

  virtual
  ResidueNeighborIteratorOP
  upper_neighbor_iterator_end( int resid );

  bool
  disulfide_bonded( Size res1id, Size res2id ) const;

  bool residue_forms_disulfide( Size resid ) const;

  // What residue is resid forming a disulfide with?
  Size other_neighbor_id( Size resid ) const;

  DisulfideAtomIndices const &
  disulfide_atom_indices( Size resid ) const;

  DisulfideAtomIndices const &
  other_neighbor_atom_indices( Size resid ) const;

// Read and write access granted to Disulf Iterators. Other classes should not use these methods.
public:

  // Mutators
  void save_energy( Size disulfide_index, EnergyMap const & emap );
  void mark_energy_computed( Size disulfide_index );
  void mark_energy_uncomputed( Size disulfide_index );

  // Accessors
  Size lower_neighbor_id( Size disulfide_index ) const;
  Size upper_neighbor_id( Size disulfide_index ) const;
  Size other_neighbor_id( Size disulfide_index, Size resid ) const;

  void accumulate_energy( Size disulfide_index, EnergyMap & emap ) const;
  void retrieve_energy( Size disulfide_index, EnergyMap & emap ) const;
  bool energy_computed( Size disulfide_index ) const;

private:
  void find_disulfides( pose::Pose const & pose );
  bool disulfides_changed( pose::Pose const & pose );
  Size num_disulfides() const;
private:
  utility::vector1< Size > resid_2_disulfide_index_;
  utility::vector1< chemical::ResidueTypeCOP > disulfide_residue_types_;
  utility::vector1< std::pair< Size, Size > > disulfide_partners_;
  utility::vector1< std::pair< DisulfideAtomIndices, DisulfideAtomIndices > > disulfide_atom_indices_;
  utility::vector1< std::pair< DisulfideMatchingEnergyComponents, bool > > disulfide_info_;
};

}
}
}

#endif