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

#include <CentroidDisulfideEnergyContainer.hh>

Public Member Functions
	CentroidDisulfideNeighborIterator (CentroidDisulfideEnergyContainerAP owner, Size focused_node, Size disulfide_index)
	constructor More...

	CentroidDisulfideNeighborIterator (CentroidDisulfideEnergyContainerAP owner)
	constructor, default to no disulfide bond More...

virtual	~CentroidDisulfideNeighborIterator ()

virtual ResidueNeighborIterator const &	operator= (ResidueNeighborIterator const &)
	Assignment. More...

virtual ResidueNeighborIterator const &	operator++ ()

virtual bool	operator== (ResidueNeighborIterator const &) const

virtual bool	operator!= (ResidueNeighborIterator const &) const

virtual Size	upper_neighbor_id () const
	Get the higher-numbered residue for this disulfide bond. More...

virtual Size	lower_neighbor_id () const
	Get the lower-numbered residue for this disulfide bond. More...

virtual Size	residue_iterated_on () const
	Which residue are we looking for disulfide bonds to? More...

virtual Size	neighbor_id () const
	Which residue is disulfide bonded to the current residue? More...

virtual void	save_energy (EnergyMap const &)
	Save the specified energies for this disulfide to the CentroidDisulfideEnergyContainer associated with this iterator. More...

virtual void	retrieve_energy (EnergyMap &) const
	Get the energies for the current disulfide bond from the CentroidDisulfideEnergyContainer associated with this iterator. More...

virtual void	accumulate_energy (EnergyMap &) const
	Add some energies to the totals already in CentroidDisulfideEnergyContainer. More...

virtual void	mark_energy_computed ()

virtual void	mark_energy_uncomputed ()

virtual bool	energy_computed () const

Public Member Functions inherited from core::scoring::ResidueNeighborIterator
virtual	~ResidueNeighborIterator ()

Private Attributes
CentroidDisulfideEnergyContainerAP	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

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

constructor

core::scoring::disulfides::CentroidDisulfideNeighborIterator::CentroidDisulfideNeighborIterator ( CentroidDisulfideEnergyContainerAP owner )

constructor, default to no disulfide bond

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

virtual

Member Function Documentation

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

virtual

Add some energies to the totals already in CentroidDisulfideEnergyContainer.

Implements core::scoring::ResidueNeighborIterator.

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

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

virtual

Implements core::scoring::ResidueNeighborIterator.

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

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

virtual

Get the lower-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

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

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

virtual

Implements core::scoring::ResidueNeighborIterator.

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

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

virtual

Implements core::scoring::ResidueNeighborIterator.

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

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

virtual

Which residue is disulfide bonded to the current residue?

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

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

virtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

ResidueNeighborIterator const & core::scoring::disulfides::CentroidDisulfideNeighborIterator::operator++ ( )

virtual

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.

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

virtual

Assignment.

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

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

virtual

Implements core::scoring::ResidueNeighborIterator.

References disulfide_index_, focused_residue_, and owner_.

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

virtual

Which residue are we looking for disulfide bonds to?

Implements core::scoring::ResidueNeighborIterator.

References focused_residue_.

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

virtual

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, and owner_.

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

virtual

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, and owner_.

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

virtual

Get the higher-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

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

Member Data Documentation

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().

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

private

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

CentroidDisulfideEnergyContainerAP 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().

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

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

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation