Rosetta 3.4
Public Member Functions
core::scoring::disulfides::DisulfideMatchingNeighborIterator Class Reference

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

#include <DisulfideMatchingEnergyContainer.hh>

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List of all members.

Public Member Functions

 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainerAP owner, Size focused_node, Size disulfide_index)
 constructor
 DisulfideMatchingNeighborIterator (DisulfideMatchingEnergyContainerAP owner)
 constructor, default to no disulfide bond
virtual ~DisulfideMatchingNeighborIterator ()
virtual
ResidueNeighborIterator const & 
operator= (ResidueNeighborIterator const &)
 Assignment.
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.
virtual Size lower_neighbor_id () const
 Get the lower-numbered residue for this disulfide bond.
virtual Size residue_iterated_on () const
 Which residue are we looking for disulfide bonds to?
virtual Size neighbor_id () const
 Which residue is disulfide bonded to the current residue?
virtual void save_energy (EnergyMap const &)
 Save the specified energies for this disulfide to the DisulfideMatchingEnergyContainer associated with this iterator.
virtual void retrieve_energy (EnergyMap &) const
 Get the energies for the current disulfide bond from the DisulfideMatchingEnergyContainer associated with this iterator.
virtual void accumulate_energy (EnergyMap &) const
 Add some energies to the totals already in DisulfideMatchingEnergyContainer.
virtual void mark_energy_computed ()
virtual void mark_energy_uncomputed ()
virtual bool energy_computed () const

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 core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

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.

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 core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

ResidueNeighborIterator const & core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator= ( ResidueNeighborIterator const &  rhs) [virtual]

Assignment.

Implements core::scoring::ResidueNeighborIterator.

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.

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 core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

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 core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.

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

Get the higher-numbered residue for this disulfide bond.

Implements core::scoring::ResidueNeighborIterator.

References core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE.


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