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core::scoring::disulfides::DisulfideMatchingEnergyContainer Class Reference

#include <DisulfideMatchingEnergyContainer.hh>

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Public Member Functions

 DisulfideMatchingEnergyContainer ()
 
 DisulfideMatchingEnergyContainer (pose::Pose const &)
 
void update (pose::Pose const &)
 
virtual ~DisulfideMatchingEnergyContainer ()
 
virtual bool empty () const
 
virtual LREnergyContainerOP clone () const
 
virtual
ResidueNeighborConstIteratorOP 		const_neighbor_iterator_begin (int resid) const
 
virtual
ResidueNeighborConstIteratorOP 		const_neighbor_iterator_end (int resid) const
 
virtual
ResidueNeighborConstIteratorOP 		const_upper_neighbor_iterator_begin (int resid) const
 
virtual
ResidueNeighborConstIteratorOP 		const_upper_neighbor_iterator_end (int resid) const
 
virtual ResidueNeighborIteratorOP neighbor_iterator_begin (int resid)
 
virtual ResidueNeighborIteratorOP neighbor_iterator_end (int resid)
 
virtual ResidueNeighborIteratorOP upper_neighbor_iterator_begin (int resid)
 
virtual ResidueNeighborIteratorOP upper_neighbor_iterator_end (int resid)
 
bool disulfide_bonded (Size res1id, Size res2id) const
 
bool residue_forms_disulfide (Size resid) const
 
Size other_neighbor_id (Size resid) const
 
DisulfideAtomIndices const & disulfide_atom_indices (Size resid) const
 
DisulfideAtomIndices const & other_neighbor_atom_indices (Size resid) const
 
void save_energy (Size disulfide_index, EnergyMap const &emap)
 
void mark_energy_computed (Size disulfide_index)
 
void mark_energy_uncomputed (Size disulfide_index)
 
Size lower_neighbor_id (Size disulfide_index) const
 
Size upper_neighbor_id (Size disulfide_index) const
 
Size other_neighbor_id (Size disulfide_index, Size resid) const
 
void accumulate_energy (Size disulfide_index, EnergyMap &emap) const
 
void retrieve_energy (Size disulfide_index, EnergyMap &emap) const
 
bool energy_computed (Size disulfide_index) const
 
- Public Member Functions inherited from core::scoring::LREnergyContainer
virtual ~LREnergyContainer ()
 
virtual void set_num_nodes (Size)
 

Static Public Attributes

static Size const NO_DISULFIDE
 Disulfide Energy Container Class Implementation. More...
 

Private Member Functions

void find_disulfides (pose::Pose const &pose)
 
bool disulfides_changed (pose::Pose const &pose)
 
Size num_disulfides () const
 

Private Attributes

utility::vector1< Size > resid_2_disulfide_index_
 
utility::vector1
< chemical::ResidueTypeCOP > 		disulfide_residue_types_
 
utility::vector1< std::pair
< Size, Size > > 		disulfide_partners_
 
utility::vector1< std::pair
< DisulfideAtomIndices,
DisulfideAtomIndices > > 		disulfide_atom_indices_
 
utility::vector1< std::pair
< DisulfideMatchingEnergyComponents,
bool > > 		disulfide_info_
 

Detailed Description

Definition at line 160 of file DisulfideMatchingEnergyContainer.hh.

Constructor & Destructor Documentation

core::scoring::disulfides::DisulfideMatchingEnergyContainer::DisulfideMatchingEnergyContainer ( )

Definition at line 320 of file DisulfideMatchingEnergyContainer.cc.

Referenced by clone().

core::scoring::disulfides::DisulfideMatchingEnergyContainer::DisulfideMatchingEnergyContainer ( pose::Pose const &  pose)

Definition at line 330 of file DisulfideMatchingEnergyContainer.cc.

References find_disulfides().

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

Definition at line 341 of file DisulfideMatchingEnergyContainer.cc.

Member Function Documentation

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::accumulate_energy ( Size  disulfide_index,
EnergyMap &  emap 
) const

Definition at line 525 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_, core::scoring::dslfc_rot, core::scoring::dslfc_RT, and core::scoring::dslfc_trans.

LREnergyContainerOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::clone ( ) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 345 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_atom_indices_, disulfide_info_, disulfide_partners_, disulfide_residue_types_, DisulfideMatchingEnergyContainer(), empty(), and resid_2_disulfide_index_.

ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_neighbor_iterator_begin ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 359 of file DisulfideMatchingEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_neighbor_iterator_end ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 371 of file DisulfideMatchingEnergyContainer.cc.

References empty().

ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_upper_neighbor_iterator_begin ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 378 of file DisulfideMatchingEnergyContainer.cc.

References empty(), NO_DISULFIDE, other_neighbor_id(), and resid_2_disulfide_index_.

ResidueNeighborConstIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::const_upper_neighbor_iterator_end ( int  resid) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 391 of file DisulfideMatchingEnergyContainer.cc.

References empty().

DisulfideAtomIndices const & core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_atom_indices ( Size  resid) const

Definition at line 500 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_bonded ( Size  res1id,
Size  res2id 
) const

Definition at line 436 of file DisulfideMatchingEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfides_changed ( pose::Pose const &  pose)
private

Definition at line 615 of file DisulfideMatchingEnergyContainer.cc.

References core::conformation::Residue::aa(), core::chemical::aa_cys, core::conformation::Residue::atom_index(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, disulfide_residue_types_, core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::has_variant_type(), NO_DISULFIDE, other_neighbor_id(), core::chemical::ResConnID::resid(), resid_2_disulfide_index_, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by update().

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::empty ( ) const
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 324 of file DisulfideMatchingEnergyContainer.cc.

References num_disulfides().

Referenced by clone(), const_neighbor_iterator_begin(), const_neighbor_iterator_end(), const_upper_neighbor_iterator_begin(), const_upper_neighbor_iterator_end(), disulfide_bonded(), find_disulfides(), neighbor_iterator_begin(), neighbor_iterator_end(), residue_forms_disulfide(), and upper_neighbor_iterator_end().

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::energy_computed ( Size  disulfide_index) const

Definition at line 539 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::find_disulfides ( pose::Pose const &  pose)
private

Definition at line 546 of file DisulfideMatchingEnergyContainer.cc.

References core::conformation::Residue::aa(), core::chemical::aa_cys, core::conformation::Residue::atom_index(), core::chemical::ResidueConnection::atomno(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, disulfide_atom_indices_, disulfide_info_, disulfide_partners_, disulfide_residue_types_, empty(), core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::n_residue_connections(), core::chemical::ResidueTypeSet::name(), NO_DISULFIDE, num_disulfides(), core::chemical::ResConnID::resid(), resid_2_disulfide_index_, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::pose::Pose::residue_type(), core::chemical::ResidueType::residue_type_set(), core::pose::Pose::total_residue(), core::scoring::disulfides::TR(), and core::conformation::Residue::type().

Referenced by DisulfideMatchingEnergyContainer(), and update().

Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::lower_neighbor_id ( Size  disulfide_index) const

Definition at line 480 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_partners_.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::mark_energy_computed ( Size  disulfide_index)

Definition at line 468 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::mark_energy_uncomputed ( Size  disulfide_index)

Definition at line 474 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_.

ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::neighbor_iterator_begin ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 398 of file DisulfideMatchingEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::neighbor_iterator_end ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 410 of file DisulfideMatchingEnergyContainer.cc.

References empty().

Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::num_disulfides ( ) const
private

Definition at line 641 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_partners_.

Referenced by empty(), and find_disulfides().

DisulfideAtomIndices const & core::scoring::disulfides::DisulfideMatchingEnergyContainer::other_neighbor_atom_indices ( Size  resid) const

Definition at line 513 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::other_neighbor_id ( Size  resid) const

Definition at line 452 of file DisulfideMatchingEnergyContainer.cc.

References resid_2_disulfide_index_.

Referenced by const_upper_neighbor_iterator_begin(), disulfides_changed(), and upper_neighbor_iterator_begin().

Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::other_neighbor_id ( Size  disulfide_index,
Size  resid 
) const

Definition at line 490 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_partners_.

bool core::scoring::disulfides::DisulfideMatchingEnergyContainer::residue_forms_disulfide ( Size  resid) const

Definition at line 445 of file DisulfideMatchingEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::retrieve_energy ( Size  disulfide_index,
EnergyMap &  emap 
) const

Definition at line 532 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_, core::scoring::dslfc_rot, core::scoring::dslfc_RT, and core::scoring::dslfc_trans.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::save_energy ( Size  disulfide_index,
EnergyMap const &  emap 
)

Definition at line 460 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_info_, core::scoring::dslfc_rot, core::scoring::dslfc_RT, and core::scoring::dslfc_trans.

void core::scoring::disulfides::DisulfideMatchingEnergyContainer::update ( pose::Pose const &  pose)

Definition at line 336 of file DisulfideMatchingEnergyContainer.cc.

References disulfides_changed(), and find_disulfides().

Size core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_id ( Size  disulfide_index) const

Definition at line 485 of file DisulfideMatchingEnergyContainer.cc.

References disulfide_partners_.

ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_iterator_begin ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 417 of file DisulfideMatchingEnergyContainer.cc.

References NO_DISULFIDE, other_neighbor_id(), and resid_2_disulfide_index_.

ResidueNeighborIteratorOP core::scoring::disulfides::DisulfideMatchingEnergyContainer::upper_neighbor_iterator_end ( int  resid)
virtual

Implements core::scoring::LREnergyContainer.

Definition at line 429 of file DisulfideMatchingEnergyContainer.cc.

References empty().

Member Data Documentation

utility::vector1< std::pair< DisulfideAtomIndices, DisulfideAtomIndices > > core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_atom_indices_
private

Definition at line 252 of file DisulfideMatchingEnergyContainer.hh.

Referenced by clone(), disulfide_atom_indices(), find_disulfides(), and other_neighbor_atom_indices().

utility::vector1< std::pair< DisulfideMatchingEnergyComponents, bool > > core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_info_
private

Definition at line 253 of file DisulfideMatchingEnergyContainer.hh.

Referenced by accumulate_energy(), clone(), energy_computed(), find_disulfides(), mark_energy_computed(), mark_energy_uncomputed(), retrieve_energy(), and save_energy().

utility::vector1< std::pair< Size, Size > > core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_partners_
private

Definition at line 251 of file DisulfideMatchingEnergyContainer.hh.

Referenced by clone(), disulfide_atom_indices(), find_disulfides(), lower_neighbor_id(), num_disulfides(), other_neighbor_atom_indices(), other_neighbor_id(), and upper_neighbor_id().

utility::vector1< chemical::ResidueTypeCOP > core::scoring::disulfides::DisulfideMatchingEnergyContainer::disulfide_residue_types_
private

Definition at line 250 of file DisulfideMatchingEnergyContainer.hh.

Referenced by clone(), disulfides_changed(), and find_disulfides().

Size const core::scoring::disulfides::DisulfideMatchingEnergyContainer::NO_DISULFIDE
static

Disulfide Energy Container Class Implementation.

Definition at line 162 of file DisulfideMatchingEnergyContainer.hh.

Referenced by core::scoring::disulfides::DisulfideMatchingNeighborIterator::accumulate_energy(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::accumulate_energy(), const_neighbor_iterator_begin(), const_upper_neighbor_iterator_begin(), disulfide_atom_indices(), disulfide_bonded(), disulfides_changed(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::energy_computed(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::energy_computed(), find_disulfides(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::lower_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::lower_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_computed(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::mark_energy_uncomputed(), neighbor_iterator_begin(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::operator++(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::operator++(), other_neighbor_atom_indices(), residue_forms_disulfide(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::retrieve_energy(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::retrieve_energy(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::save_energy(), core::scoring::disulfides::DisulfideMatchingNeighborIterator::upper_neighbor_id(), core::scoring::disulfides::DisulfideMatchingNeighborConstIterator::upper_neighbor_id(), and upper_neighbor_iterator_begin().

utility::vector1< Size > core::scoring::disulfides::DisulfideMatchingEnergyContainer::resid_2_disulfide_index_
private

Definition at line 249 of file DisulfideMatchingEnergyContainer.hh.

Referenced by clone(), const_neighbor_iterator_begin(), const_upper_neighbor_iterator_begin(), disulfide_atom_indices(), disulfide_bonded(), disulfides_changed(), find_disulfides(), neighbor_iterator_begin(), other_neighbor_atom_indices(), other_neighbor_id(), residue_forms_disulfide(), and upper_neighbor_iterator_begin().

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