FullatomDisulfideEnergyContainer.hh

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// 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
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/// @file   core/scoring/disulfides/FullatomDisulfideEnergyContainer.hh
/// @brief  Disulfide Energy Container class declaration
/// @author Andrew Leaver-Fay

#ifndef INCLUDED_core_scoring_disulfides_FullatomDisulfideEnergyContainer_hh
#define INCLUDED_core_scoring_disulfides_FullatomDisulfideEnergyContainer_hh

// Unit headers
#include <core/scoring/disulfides/FullatomDisulfideEnergyContainer.fwd.hh>
// AUTO-REMOVED #include <core/scoring/disulfides/DisulfideAtomIndices.hh>

// 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 {

class DisulfResNeighbIterator : public ResidueNeighborIterator {
public:

  DisulfResNeighbIterator(
    FullatomDisulfideEnergyContainerAP owner,
    Size focused_node,
    Size disulfide_index
  );

  DisulfResNeighbIterator(
    FullatomDisulfideEnergyContainerAP owner
  );

  virtual ~DisulfResNeighbIterator();

  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:
  FullatomDisulfideEnergyContainerAP owner_;
  Size focused_residue_;
  Size disulfide_index_;
};

class DisulfResNeighbConstIterator : public ResidueNeighborConstIterator {
public:
  DisulfResNeighbConstIterator(
    FullatomDisulfideEnergyContainerCAP owner,
    Size focused_node,
    Size disulfide_index
  );

  DisulfResNeighbConstIterator( FullatomDisulfideEnergyContainerCAP owner );

  virtual ~DisulfResNeighbConstIterator();

  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:
  FullatomDisulfideEnergyContainerCAP owner_;
  Size focused_residue_;
  Size disulfide_index_;

};

class FullatomDisulfideEnergyComponents
{
public:
  FullatomDisulfideEnergyComponents() :
    dslf_ss_dst_( 0.0 ),
    dslf_cs_ang_( 0.0 ),
    dslf_ss_dih_( 0.0 ),
    dslf_ca_dih_( 0.0 ),
    dslf_cbs_ds_( 0.0 )
  {}

  Energy dslf_ss_dst() const { return dslf_ss_dst_;}
  Energy dslf_cs_ang() const { return dslf_cs_ang_;}
  Energy dslf_ss_dih() const { return dslf_ss_dih_;}
  Energy dslf_ca_dih() const { return dslf_ca_dih_;}
  Energy dslf_cbs_ds() const { return dslf_cbs_ds_;}

  Energy & dslf_ss_dst() { return dslf_ss_dst_;}
  Energy & dslf_cs_ang() { return dslf_cs_ang_;}
  Energy & dslf_ss_dih() { return dslf_ss_dih_;}
  Energy & dslf_ca_dih() { return dslf_ca_dih_;}
  Energy & dslf_cbs_ds() { return dslf_cbs_ds_;}

private:

  Energy dslf_ss_dst_;
  Energy dslf_cs_ang_;
  Energy dslf_ss_dih_;
  Energy dslf_ca_dih_;
  Energy dslf_cbs_ds_;
};

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

public:
  FullatomDisulfideEnergyContainer();

  FullatomDisulfideEnergyContainer( pose::Pose const & );

  void
  update( pose::Pose const & );

  virtual
  ~FullatomDisulfideEnergyContainer();

  virtual
  bool empty() const;

  virtual
  LREnergyContainerOP clone() const;

  virtual
  void
  set_num_nodes( Size );

  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;
  Size num_residues() 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< FullatomDisulfideEnergyComponents, bool > > disulfide_info_;

};

}
}
}

#endif