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core::scoring::disulfides::DisulfideMatchingEnergyContainer Class Reference

#include <DisulfideMatchingEnergyContainer.hh>

Inheritance diagram for core::scoring::disulfides::DisulfideMatchingEnergyContainer:
Inheritance graph
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Public Member Functions

 DisulfideMatchingEnergyContainer ()
 
 DisulfideMatchingEnergyContainer (pose::Pose const &)
 
void update (pose::Pose const &)
 
 ~DisulfideMatchingEnergyContainer () override
 
bool empty () const override
 
LREnergyContainerOP clone () const override
 
bool any_neighbors_for_residue (int resid) const override
 
bool any_upper_neighbors_for_residue (int resid) const override
 
ResidueNeighborConstIteratorOP const_neighbor_iterator_begin (int resid) const override
 
ResidueNeighborConstIteratorOP const_neighbor_iterator_end (int resid) const override
 
ResidueNeighborConstIteratorOP const_upper_neighbor_iterator_begin (int resid) const override
 
ResidueNeighborConstIteratorOP const_upper_neighbor_iterator_end (int resid) const override
 
ResidueNeighborIteratorOP neighbor_iterator_begin (int resid) override
 
ResidueNeighborIteratorOP neighbor_iterator_end (int resid) override
 
ResidueNeighborIteratorOP upper_neighbor_iterator_begin (int resid) override
 
ResidueNeighborIteratorOP upper_neighbor_iterator_end (int resid) override
 
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
 
- Public Member Functions inherited from core::scoring::LREnergyContainer
 ~LREnergyContainer () override
 
virtual void set_num_nodes (Size)
 

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
< DisulfideMatchingEnergyComponents,
bool > > 
disulfide_info_
 

Constructor & Destructor Documentation

core::scoring::disulfides::DisulfideMatchingEnergyContainer::DisulfideMatchingEnergyContainer ( )
default
core::scoring::disulfides::DisulfideMatchingEnergyContainer::DisulfideMatchingEnergyContainer ( pose::Pose const &  pose)

References find_disulfides().

core::scoring::disulfides::DisulfideMatchingEnergyContainer::~DisulfideMatchingEnergyContainer ( )
overridedefault

Member Function Documentation

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::accumulate_energy ( Size  disulfide_index,
EnergyMap emap 
) const
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::any_neighbors_for_residue ( int  resid) const
overridevirtual
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::any_upper_neighbors_for_residue ( int  resid) const
overridevirtual
LREnergyContainerOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::clone ( ) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_neighbor_iterator_begin ( int  resid) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_neighbor_iterator_end ( int  resid) const
overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_upper_neighbor_iterator_begin ( int  resid) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_upper_neighbor_iterator_end ( int  resid) const
overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

DisulfideAtomIndices const & core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_atom_indices ( Size  resid) const
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_bonded ( Size  res1id,
Size  res2id 
) const
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed ( pose::Pose const &  pose)
private
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::empty ( ) const
overridevirtual
bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::energy_computed ( Size  disulfide_index) const
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides ( pose::Pose const &  pose)
private
Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::lower_neighbor_id ( Size  disulfide_index) const
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::mark_energy_computed ( Size  disulfide_index)
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::mark_energy_uncomputed ( Size  disulfide_index)
ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::neighbor_iterator_begin ( int  resid)
overridevirtual
ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::neighbor_iterator_end ( int  resid)
overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

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

References disulfide_partners_.

Referenced by empty(), and find_disulfides().

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

References disulfide_partners_.

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::residue_forms_disulfide ( Size  resid) const
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::retrieve_energy ( Size  disulfide_index,
EnergyMap emap 
) const
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::save_energy ( Size  disulfide_index,
EnergyMap const &  emap 
)
void core::scoring::disulfides::DisulfideMatchingEnergyContainer::update ( pose::Pose const &  pose)
Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_id ( Size  disulfide_index) const
ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_iterator_begin ( int  resid)
overridevirtual
ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_iterator_end ( int  resid)
overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

Member Data Documentation

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

Disulfide Energy Container Class Implementation.

Referenced by core::scoring::disulfides::DisulfideMatchingNeighborIterator::accumulate_energy(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::accumulate_energy(), any_neighbors_for_residue(), any_upper_neighbors_for_residue(), const_neighbor_iterator_begin(), const_upper_neighbor_iterator_begin(), disulfide_atom_indices(), disulfide_bonded(), disulfides_changed(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::energy_computed(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::energy_computed(), find_disulfides(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::lower_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::lower_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_computed(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_uncomputed(), neighbor_iterator_begin(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator++(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::operator++(), other_neighbor_atom_indices(), residue_forms_disulfide(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::retrieve_energy(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::retrieve_energy(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::save_energy(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::upper_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::upper_neighbor_id(), and upper_neighbor_iterator_begin().

utility::vector1< Size > core::scoring::disulfides::DisulfideMatchingEnergyContainer::resid_2_disulfide_index_
private

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