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core::scoring::disulfides::DisulfideMatchingNeighborIterator Class Reference

An iterator over the disulfide bonds a residue forms. More...

#include <DisulfideMatchingEnergyContainer.hh>

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

 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainer *owner, Size focused_node, Size disulfide_index)
 constructor More...
 
 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainer *owner)
 constructor, default to no disulfide bond More...
 
 ~DisulfideMatchingNeighborIterator () override
 
ResidueNeighborIteratoroperator= (ResidueNeighborIterator const &) override
 Assignment. More...
 
ResidueNeighborIterator const & operator++ () override
 
bool operator== (ResidueNeighborIterator const &) const override
 
bool operator!= (ResidueNeighborIterator const &) const override
 
Size upper_neighbor_id () const override
 Get the higher-numbered residue for this disulfide bond. More...
 
Size lower_neighbor_id () const override
 Get the lower-numbered residue for this disulfide bond. More...
 
Size residue_iterated_on () const override
 Which residue are we looking for disulfide bonds to? More...
 
Size neighbor_id () const override
 Which residue is disulfide bonded to the current residue? More...
 
void save_energy (EnergyMap const &) override
 Save the specified energies for this disulfide to the DisulfideMatchingEnergyContainer associated with this iterator. More...
 
void retrieve_energy (EnergyMap &) const override
 Get the energies for the current disulfide bond from the DisulfideMatchingEnergyContainer associated with this iterator. More...
 
void accumulate_energy (EnergyMap &) const override
 Add some energies to the totals already in DisulfideMatchingEnergyContainer. More...
 
void mark_energy_computed () override
 
void mark_energy_uncomputed () override
 
bool energy_computed () const override
 
- Public Member Functions inherited from core::scoring::ResidueNeighborIterator
 ~ResidueNeighborIterator () override
 

Private Member Functions

DisulfideMatchingNeighborIteratoroperator= (DisulfideMatchingNeighborIterator const &src)
 

Private Attributes

DisulfideMatchingEnergyContainerowner_
 
Size focused_residue_
 
Size disulfide_index_
 

Detailed Description

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!

Constructor & Destructor Documentation

core::scoring::disulfides::DisulfideMatchingNeighborIterator::DisulfideMatchingNeighborIterator ( DisulfideMatchingEnergyContainer owner,
Size  focused_node,
Size  disulfide_index 
)

constructor

core::scoring::disulfides::DisulfideMatchingNeighborIterator::DisulfideMatchingNeighborIterator ( DisulfideMatchingEnergyContainer owner)

constructor, default to no disulfide bond

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

Member Function Documentation

void core::scoring::disulfides::DisulfideMatchingNeighborIterator::accumulate_energy ( EnergyMap emap) const
overridevirtual
bool core::scoring::disulfides::DisulfideMatchingNeighborIterator::energy_computed ( ) const
overridevirtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::lower_neighbor_id ( ) const
overridevirtual
void core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_computed ( )
overridevirtual
void core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_uncomputed ( )
overridevirtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::neighbor_id ( ) const
overridevirtual
bool core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator!= ( ResidueNeighborIterator const &  rhs) const
overridevirtual
ResidueNeighborIterator const & core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator++ ( )
overridevirtual
Note
Incrementing an iterator in a list with exactly one element moves that iterator off the end of the list.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

DisulfideMatchingNeighborIterator& core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator= ( DisulfideMatchingNeighborIterator const &  src)
private
ResidueNeighborIterator & core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator= ( ResidueNeighborIterator const &  rhs)
overridevirtual
bool core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator== ( ResidueNeighborIterator const &  rhs) const
overridevirtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::residue_iterated_on ( ) const
overridevirtual

Which residue are we looking for disulfide bonds to?

Implements core::scoring::ResidueNeighborIterator.

References focused_residue_.

void core::scoring::disulfides::DisulfideMatchingNeighborIterator::retrieve_energy ( EnergyMap emap) const
overridevirtual
void core::scoring::disulfides::DisulfideMatchingNeighborIterator::save_energy ( EnergyMap const &  emap)
overridevirtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::upper_neighbor_id ( ) const
overridevirtual

Member Data Documentation

Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::disulfide_index_
private
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::focused_residue_
private
DisulfideMatchingEnergyContainer* core::scoring::disulfides::DisulfideMatchingNeighborIterator::owner_
private

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