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core::scoring::disulfides::FullatomDisulfideEnergyContainer Class Reference

#include <FullatomDisulfideEnergyContainer.hh>

Inheritance diagram for core::scoring::disulfides::FullatomDisulfideEnergyContainer:
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Public Member Functions

 FullatomDisulfideEnergyContainer ()
 
 FullatomDisulfideEnergyContainer (pose::Pose const &)
 
void update (pose::Pose const &)
 
virtual ~FullatomDisulfideEnergyContainer ()
 
virtual bool empty () const
 
virtual LREnergyContainerOP clone () const
 
virtual void set_num_nodes (Size)
 
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
 
Size num_residues () const
 
- Public Member Functions inherited from core::scoring::LREnergyContainer
virtual ~LREnergyContainer ()
 

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
< FullatomDisulfideEnergyComponents,
bool > > 		disulfide_info_
 

Detailed Description

Definition at line 150 of file FullatomDisulfideEnergyContainer.hh.

Constructor & Destructor Documentation

core::scoring::disulfides::FullatomDisulfideEnergyContainer::FullatomDisulfideEnergyContainer ( )

Definition at line 308 of file FullatomDisulfideEnergyContainer.cc.

Referenced by clone().

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

Definition at line 318 of file FullatomDisulfideEnergyContainer.cc.

References find_disulfides().

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

Definition at line 329 of file FullatomDisulfideEnergyContainer.cc.

Member Function Documentation

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

Definition at line 523 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

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

Implements core::scoring::LREnergyContainer.

Definition at line 333 of file FullatomDisulfideEnergyContainer.cc.

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

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

Implements core::scoring::LREnergyContainer.

Definition at line 353 of file FullatomDisulfideEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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

Implements core::scoring::LREnergyContainer.

Definition at line 365 of file FullatomDisulfideEnergyContainer.cc.

References empty().

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

Implements core::scoring::LREnergyContainer.

Definition at line 372 of file FullatomDisulfideEnergyContainer.cc.

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

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

Implements core::scoring::LREnergyContainer.

Definition at line 386 of file FullatomDisulfideEnergyContainer.cc.

References empty().

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

Definition at line 498 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

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

Definition at line 432 of file FullatomDisulfideEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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

Definition at line 604 of file FullatomDisulfideEnergyContainer.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(), core::pose::symmetry::is_symmetric(), 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::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by update().

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

Implements core::scoring::LREnergyContainer.

Definition at line 312 of file FullatomDisulfideEnergyContainer.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(), neighbor_iterator_begin(), neighbor_iterator_end(), residue_forms_disulfide(), and upper_neighbor_iterator_end().

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

Definition at line 541 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_.

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

Definition at line 548 of file FullatomDisulfideEnergyContainer.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_, core::chemical::ResidueType::has_atom_name(), core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::n_residue_connections(), NO_DISULFIDE, core::chemical::ResConnID::resid(), resid_2_disulfide_index_, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::pose::Pose::residue_type(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::conformation::Residue::type().

Referenced by FullatomDisulfideEnergyContainer(), and update().

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

Definition at line 478 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_partners_.

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

Definition at line 466 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_.

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

Definition at line 472 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_.

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

Implements core::scoring::LREnergyContainer.

Definition at line 393 of file FullatomDisulfideEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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

Implements core::scoring::LREnergyContainer.

Definition at line 405 of file FullatomDisulfideEnergyContainer.cc.

References empty().

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

Definition at line 634 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_partners_.

Referenced by empty().

Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::num_residues ( ) const

Definition at line 639 of file FullatomDisulfideEnergyContainer.cc.

References resid_2_disulfide_index_.

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

Definition at line 511 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

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

Definition at line 448 of file FullatomDisulfideEnergyContainer.cc.

References resid_2_disulfide_index_.

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

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

Definition at line 488 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_partners_.

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

Definition at line 441 of file FullatomDisulfideEnergyContainer.cc.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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

Definition at line 532 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

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

Definition at line 456 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::set_num_nodes ( Size  newsize)
virtual

Reimplemented from core::scoring::LREnergyContainer.

Definition at line 347 of file FullatomDisulfideEnergyContainer.cc.

References NO_DISULFIDE, and resid_2_disulfide_index_.

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

Definition at line 324 of file FullatomDisulfideEnergyContainer.cc.

References disulfides_changed(), and find_disulfides().

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

Definition at line 483 of file FullatomDisulfideEnergyContainer.cc.

References disulfide_partners_.

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

Implements core::scoring::LREnergyContainer.

Definition at line 412 of file FullatomDisulfideEnergyContainer.cc.

References NO_DISULFIDE, other_neighbor_id(), and resid_2_disulfide_index_.

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

Implements core::scoring::LREnergyContainer.

Definition at line 425 of file FullatomDisulfideEnergyContainer.cc.

References empty().

Member Data Documentation

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

Definition at line 249 of file FullatomDisulfideEnergyContainer.hh.

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

utility::vector1< std::pair< FullatomDisulfideEnergyComponents, bool > > core::scoring::disulfides::FullatomDisulfideEnergyContainer::disulfide_info_
private

Definition at line 250 of file FullatomDisulfideEnergyContainer.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::FullatomDisulfideEnergyContainer::disulfide_partners_
private

Definition at line 248 of file FullatomDisulfideEnergyContainer.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::FullatomDisulfideEnergyContainer::disulfide_residue_types_
private

Definition at line 247 of file FullatomDisulfideEnergyContainer.hh.

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

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

Disulfide Energy Container Class Implementation.

Definition at line 152 of file FullatomDisulfideEnergyContainer.hh.

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

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

Definition at line 246 of file FullatomDisulfideEnergyContainer.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(), num_residues(), other_neighbor_atom_indices(), other_neighbor_id(), residue_forms_disulfide(), set_num_nodes(), and upper_neighbor_iterator_begin().

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