Rosetta Core  2014.35
Public Member Functions | Private Attributes | List of all members
core::scoring::disulfides::DisulfideMatchingNeighborIterator Class Reference

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

#include <DisulfideMatchingEnergyContainer.hh>

Public Member Functions

 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainerAP owner, Size focused_node, Size disulfide_index)
 constructor More...
 
 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainerAP owner)
 constructor, default to no disulfide bond More...
 
virtual ~DisulfideMatchingNeighborIterator ()
 
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 DisulfideMatchingEnergyContainer associated with this iterator. More...
 
virtual void retrieve_energy (EnergyMap &) const
 Get the energies for the current disulfide bond from the DisulfideMatchingEnergyContainer associated with this iterator. More...
 
virtual void accumulate_energy (EnergyMap &) const
 Add some energies to the totals already in DisulfideMatchingEnergyContainer. 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

DisulfideMatchingEnergyContainerAP 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::DisulfideMatchingNeighborIterator::DisulfideMatchingNeighborIterator ( DisulfideMatchingEnergyContainerAP  owner,
Size  focused_node,
Size  disulfide_index 
)

constructor

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

constructor, default to no disulfide bond

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

Member Function Documentation

void core::scoring::disulfides::DisulfideMatchingNeighborIterator::accumulate_energy ( EnergyMap emap) const
virtual
bool core::scoring::disulfides::DisulfideMatchingNeighborIterator::energy_computed ( ) const
virtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::lower_neighbor_id ( ) const
virtual

Get the lower-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

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

void core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_computed ( )
virtual
void core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_uncomputed ( )
virtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::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::DisulfideMatchingNeighborIterator::operator!= ( ResidueNeighborIterator const &  rhs) const
virtual
ResidueNeighborIterator const & core::scoring::disulfides::DisulfideMatchingNeighborIterator::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::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

ResidueNeighborIterator const & core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator= ( ResidueNeighborIterator const &  rhs)
virtual
bool core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator== ( ResidueNeighborIterator const &  rhs) const
virtual
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::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::DisulfideMatchingNeighborIterator::retrieve_energy ( EnergyMap emap) const
virtual

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

Implements core::scoring::ResidueNeighborIterator.

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

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

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

Implements core::scoring::ResidueNeighborIterator.

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

Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::upper_neighbor_id ( ) const
virtual

Get the higher-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

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

Member Data Documentation

Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::disulfide_index_
private
Size core::scoring::disulfides::DisulfideMatchingNeighborIterator::focused_residue_
private
DisulfideMatchingEnergyContainerAP core::scoring::disulfides::DisulfideMatchingNeighborIterator::owner_
private

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