core::scoring::disulfides::CentroidDisulfideNeighborIterator Class Reference

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

#include <CentroidDisulfideEnergyContainer.hh>

Inheritance diagram for core::scoring::disulfides::CentroidDisulfideNeighborIterator:

Public Member Functions
	CentroidDisulfideNeighborIterator (CentroidDisulfideEnergyContainer *owner, Size focused_node, Size disulfide_index)
	constructor More...
	CentroidDisulfideNeighborIterator (CentroidDisulfideEnergyContainer *owner)
	constructor, default to no disulfide bond More...
	~CentroidDisulfideNeighborIterator () override
ResidueNeighborIterator &	operator= (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 CentroidDisulfideEnergyContainer associated with this iterator. More...
void	retrieve_energy (EnergyMap &) const override
	Get the energies for the current disulfide bond from the CentroidDisulfideEnergyContainer associated with this iterator. More...
void	accumulate_energy (EnergyMap &) const override
	Add some energies to the totals already in CentroidDisulfideEnergyContainer. 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
CentroidDisulfideNeighborIterator &	operator= (CentroidDisulfideNeighborIterator const &)

Private Attributes
CentroidDisulfideEnergyContainer *	owner_
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

CentroidDisulfideNeighborIterator() [1/2]

core::scoring::disulfides::CentroidDisulfideNeighborIterator::CentroidDisulfideNeighborIterator	(	CentroidDisulfideEnergyContainer *	owner,
		Size	focused_node,
		Size	disulfide_index
	)

constructor

CentroidDisulfideNeighborIterator() [2/2]

core::scoring::disulfides::CentroidDisulfideNeighborIterator::CentroidDisulfideNeighborIterator

(

CentroidDisulfideEnergyContainer *

owner

)

constructor, default to no disulfide bond

~CentroidDisulfideNeighborIterator()

core::scoring::disulfides::CentroidDisulfideNeighborIterator::~CentroidDisulfideNeighborIterator ( )

overridedefault

Member Function Documentation

accumulate_energy()

void core::scoring::disulfides::CentroidDisulfideNeighborIterator::accumulate_energy ( EnergyMap &  emap ) const

overridevirtual

Add some energies to the totals already in CentroidDisulfideEnergyContainer.

Implements core::scoring::ResidueNeighborIterator.

References core::scoring::disulfides::CentroidDisulfideEnergyContainer::accumulate_energy(), disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, and owner_.

energy_computed()

bool core::scoring::disulfides::CentroidDisulfideNeighborIterator::energy_computed ( ) const

overridevirtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::energy_computed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, and owner_.

lower_neighbor_id()

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::lower_neighbor_id ( ) const

overridevirtual

Get the lower-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::lower_neighbor_id(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, and owner_.

mark_energy_computed()

void core::scoring::disulfides::CentroidDisulfideNeighborIterator::mark_energy_computed ( )

overridevirtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::mark_energy_computed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, and owner_.

mark_energy_uncomputed()

void core::scoring::disulfides::CentroidDisulfideNeighborIterator::mark_energy_uncomputed ( )

overridevirtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::mark_energy_uncomputed(), core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, and owner_.

neighbor_id()

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::neighbor_id ( ) const

overridevirtual

Which residue is disulfide bonded to the current residue?

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::other_neighbor_id(), and owner_.

operator!=()

bool core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator!= ( ResidueNeighborIterator const &  rhs ) const

overridevirtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

operator++()

ResidueNeighborIterator const & core::scoring::disulfides::CentroidDisulfideNeighborIterator::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::CentroidDisulfideEnergyContainer::NO_DISULFIDE.

operator=() [1/2]

CentroidDisulfideNeighborIterator& core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator= ( CentroidDisulfideNeighborIterator const &  )

private

operator=() [2/2]

ResidueNeighborIterator & core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator= ( ResidueNeighborIterator const &  rhs )

overridevirtual

Assignment.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

operator==()

bool core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator== ( ResidueNeighborIterator const &  rhs ) const

overridevirtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

residue_iterated_on()

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::residue_iterated_on ( ) const

overridevirtual

Which residue are we looking for disulfide bonds to?

Implements core::scoring::ResidueNeighborIterator.

References focused_residue_.

retrieve_energy()

void core::scoring::disulfides::CentroidDisulfideNeighborIterator::retrieve_energy ( EnergyMap &  emap ) const

overridevirtual

Get the energies for the current disulfide bond from the CentroidDisulfideEnergyContainer associated with this iterator.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, owner_, and core::scoring::disulfides::CentroidDisulfideEnergyContainer::retrieve_energy().

save_energy()

void core::scoring::disulfides::CentroidDisulfideNeighborIterator::save_energy ( EnergyMap const &  emap )

overridevirtual

Save the specified energies for this disulfide to the CentroidDisulfideEnergyContainer associated with this iterator.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, owner_, and core::scoring::disulfides::CentroidDisulfideEnergyContainer::save_energy().

upper_neighbor_id()

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::upper_neighbor_id ( ) const

overridevirtual

Get the higher-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, core::scoring::disulfides::CentroidDisulfideEnergyContainer::NO_DISULFIDE, owner_, and core::scoring::disulfides::CentroidDisulfideEnergyContainer::upper_neighbor_id().

Member Data Documentation

disulfide_index_

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::disulfide_index_

private

Referenced by accumulate_energy(), energy_computed(), lower_neighbor_id(), mark_energy_computed(), mark_energy_uncomputed(), neighbor_id(), operator!=(), operator++(), operator=(), operator==(), retrieve_energy(), save_energy(), and upper_neighbor_id().

focused_residue_

Size core::scoring::disulfides::CentroidDisulfideNeighborIterator::focused_residue_

private

Referenced by neighbor_id(), operator!=(), operator++(), operator=(), operator==(), and residue_iterated_on().

owner_

CentroidDisulfideEnergyContainer* core::scoring::disulfides::CentroidDisulfideNeighborIterator::owner_

private

Referenced by accumulate_energy(), energy_computed(), lower_neighbor_id(), mark_energy_computed(), mark_energy_uncomputed(), neighbor_id(), operator!=(), operator=(), operator==(), retrieve_energy(), save_energy(), and upper_neighbor_id().

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

• src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.hh
• src/core/scoring/disulfides/CentroidDisulfideEnergyContainer.cc