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core::scoring::disulfides::FullatomDisulfideEnergyContainer Class Reference

#include <FullatomDisulfideEnergyContainer.hh>

Inheritance diagram for core::scoring::disulfides::FullatomDisulfideEnergyContainer:
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Public Member Functions

 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
 
Size other_neighbor_id (Size resid) const
 
DisulfideAtomIndices const & disulfide_atom_indices (Size resid) const
 
DisulfideAtomIndices const & other_neighbor_atom_indices (Size resid) const
 
void save_energy (Size disulfide_index, EnergyMap const &emap)
 
void mark_energy_computed (Size disulfide_index)
 
void mark_energy_uncomputed (Size disulfide_index)
 
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
 
- Public Member Functions inherited from core::scoring::LREnergyContainer
virtual ~LREnergyContainer ()
 

Static Public Attributes

static Size const NO_DISULFIDE
 Disulfide Energy Container Class Implementation. More...
 

Private Member Functions

void find_disulfides (pose::Pose const &pose)
 
bool disulfides_changed (pose::Pose const &pose)
 
Size num_disulfides () const
 

Private Attributes

utility::vector1< Sizeresid_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_
 

Constructor & Destructor Documentation

core::scoring::disulfides::FullatomDisulfideEnergyContainer::FullatomDisulfideEnergyContainer ( )

Referenced by clone().

core::scoring::disulfides::FullatomDisulfideEnergyContainer::FullatomDisulfideEnergyContainer ( pose::Pose const &  pose)

References find_disulfides().

core::scoring::disulfides::FullatomDisulfideEnergyContainer::~FullatomDisulfideEnergyContainer ( )
virtual

Member Function Documentation

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::accumulate_energy ( Size  disulfide_index,
EnergyMap emap 
) const
LREnergyContainerOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::clone ( ) const
virtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::const_neighbor_iterator_begin ( int  resid) const
virtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::const_neighbor_iterator_end ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

References empty().

ResidueNeighborConstIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::const_upper_neighbor_iterator_begin ( int  resid) const
virtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::const_upper_neighbor_iterator_end ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

References empty().

DisulfideAtomIndices const & core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_atom_indices ( Size  resid) const
bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_bonded ( Size  res1id,
Size  res2id 
) const
bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfides_changed ( pose::Pose const &  pose)
private
bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::empty ( ) const
virtual
bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::energy_computed ( Size  disulfide_index) const

References disulfide_info_.

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::find_disulfides ( pose::Pose const &  pose)
private
Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::lower_neighbor_id ( Size  disulfide_index) const

References disulfide_partners_.

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::mark_energy_computed ( Size  disulfide_index)

References disulfide_info_.

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::mark_energy_uncomputed ( Size  disulfide_index)

References disulfide_info_.

ResidueNeighborIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::neighbor_iterator_begin ( int  resid)
virtual
ResidueNeighborIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::neighbor_iterator_end ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

References empty().

Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::num_disulfides ( ) const
private

References disulfide_partners_.

Referenced by empty().

Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::num_residues ( ) const
DisulfideAtomIndices const & core::scoring::disulfides::FullatomDisulfideEnergyContainer::other_neighbor_atom_indices ( Size  resid) const
Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::other_neighbor_id ( Size  resid) const
Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::other_neighbor_id ( Size  disulfide_index,
Size  resid 
) const

References disulfide_partners_.

bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::residue_forms_disulfide ( Size  resid) const
void core::scoring::disulfides::FullatomDisulfideEnergyContainer::retrieve_energy ( Size  disulfide_index,
EnergyMap emap 
) const
void core::scoring::disulfides::FullatomDisulfideEnergyContainer::save_energy ( Size  disulfide_index,
EnergyMap const &  emap 
)
void core::scoring::disulfides::FullatomDisulfideEnergyContainer::set_num_nodes ( Size  newsize)
virtual
void core::scoring::disulfides::FullatomDisulfideEnergyContainer::update ( pose::Pose const &  pose)
Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::upper_neighbor_id ( Size  disulfide_index) const

References disulfide_partners_.

ResidueNeighborIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::upper_neighbor_iterator_begin ( int  resid)
virtual
ResidueNeighborIteratorOP core::scoring::disulfides::FullatomDisulfideEnergyContainer::upper_neighbor_iterator_end ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

References empty().

Member Data Documentation

utility::vector1< std::pair< DisulfideAtomIndices, DisulfideAtomIndices > > core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_atom_indices_
private
utility::vector1< std::pair< FullatomDisulfideEnergyComponents, bool > > core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_info_
private
utility::vector1< std::pair< Size, Size > > core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_partners_
private
utility::vector1< chemical::ResidueTypeCOP > core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_residue_types_
private
Size const core::scoring::disulfides::FullatomDisulfideEnergyContainer::NO_DISULFIDE
static
utility::vector1< Size > core::scoring::disulfides::FullatomDisulfideEnergyContainer::resid_2_disulfide_index_
private

The documentation for this class was generated from the following files: