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Public Member Functions | Static Public Attributes | Private Member Functions | Private Attributes | List of all members
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 &)
 
 ~FullatomDisulfideEnergyContainer () override
 
bool empty () const override
 
LREnergyContainerOP clone () const override
 
void set_num_nodes (Size) override
 
bool any_neighbors_for_residue (int resid) const override
 
bool any_upper_neighbors_for_residue (int resid) const override
 
ResidueNeighborConstIteratorOP const_neighbor_iterator_begin (int resid) const override
 
ResidueNeighborConstIteratorOP const_neighbor_iterator_end (int resid) const override
 
ResidueNeighborConstIteratorOP const_upper_neighbor_iterator_begin (int resid) const override
 
ResidueNeighborConstIteratorOP const_upper_neighbor_iterator_end (int resid) const override
 
ResidueNeighborIteratorOP neighbor_iterator_begin (int resid) override
 
ResidueNeighborIteratorOP neighbor_iterator_end (int resid) override
 
ResidueNeighborIteratorOP upper_neighbor_iterator_begin (int resid) override
 
ResidueNeighborIteratorOP upper_neighbor_iterator_end (int resid) override
 
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
 ~LREnergyContainer () override
 

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_
 

Constructor & Destructor Documentation

◆ FullatomDisulfideEnergyContainer() [1/2]

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

◆ FullatomDisulfideEnergyContainer() [2/2]

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

References find_disulfides().

◆ ~FullatomDisulfideEnergyContainer()

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

Member Function Documentation

◆ accumulate_energy()

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

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::accumulate_energy(), and core::scoring::disulfides::DisulfResNeighbConstIterator::accumulate_energy().

◆ any_neighbors_for_residue()

bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::any_neighbors_for_residue ( int  resid) const
overridevirtual

Implements core::scoring::LREnergyContainer.

References NO_DISULFIDE, and resid_2_disulfide_index_.

◆ any_upper_neighbors_for_residue()

bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::any_upper_neighbors_for_residue ( int  resid) const
overridevirtual

Implements core::scoring::LREnergyContainer.

References disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

◆ clone()

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

Implements core::scoring::LREnergyContainer.

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

◆ const_neighbor_iterator_begin()

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

Implements core::scoring::LREnergyContainer.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

◆ const_neighbor_iterator_end()

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

Implements core::scoring::LREnergyContainer.

References empty().

◆ const_upper_neighbor_iterator_begin()

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

Implements core::scoring::LREnergyContainer.

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

◆ const_upper_neighbor_iterator_end()

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

Implements core::scoring::LREnergyContainer.

References empty().

◆ disulfide_atom_indices()

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

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

◆ disulfide_bonded()

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

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

◆ disulfides_changed()

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

References core::conformation::Residue::atom_index(), core::conformation::Residue::connect_map(), core::chemical::DISULFIDE, disulfide_residue_types_, core::chemical::ResidueTypeBase::get_disulfide_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::Pose::size(), core::pose::symmetry::symmetry_info(), and core::conformation::Residue::type().

Referenced by update().

◆ empty()

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

Implements core::scoring::LREnergyContainer.

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().

◆ energy_computed()

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

References disulfide_info_.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::energy_computed(), and core::scoring::disulfides::DisulfResNeighbConstIterator::energy_computed().

◆ find_disulfides()

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

References 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::ResidueTypeBase::get_disulfide_atom_name(), core::chemical::ResidueType::has(), core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), core::chemical::ResidueType::n_possible_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::Pose::residue_type_ptr(), core::pose::Pose::size(), core::pose::symmetry::symmetry_info(), and core::conformation::Residue::type().

Referenced by FullatomDisulfideEnergyContainer(), and update().

◆ lower_neighbor_id()

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

References disulfide_partners_.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::lower_neighbor_id(), and core::scoring::disulfides::DisulfResNeighbConstIterator::lower_neighbor_id().

◆ mark_energy_computed()

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

References disulfide_info_.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::mark_energy_computed().

◆ mark_energy_uncomputed()

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

References disulfide_info_.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::mark_energy_uncomputed().

◆ neighbor_iterator_begin()

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

Implements core::scoring::LREnergyContainer.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

◆ neighbor_iterator_end()

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

Implements core::scoring::LREnergyContainer.

References empty().

◆ num_disulfides()

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

References disulfide_partners_.

Referenced by empty().

◆ num_residues()

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

References resid_2_disulfide_index_.

◆ other_neighbor_atom_indices()

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

References disulfide_atom_indices_, disulfide_partners_, NO_DISULFIDE, and resid_2_disulfide_index_.

◆ other_neighbor_id() [1/2]

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

References disulfide_partners_.

◆ other_neighbor_id() [2/2]

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

References resid_2_disulfide_index_.

Referenced by const_upper_neighbor_iterator_begin(), disulfides_changed(), core::scoring::disulfides::DisulfResNeighbIterator::neighbor_id(), core::scoring::disulfides::DisulfResNeighbConstIterator::neighbor_id(), and upper_neighbor_iterator_begin().

◆ residue_forms_disulfide()

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

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

◆ retrieve_energy()

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

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::retrieve_energy(), and core::scoring::disulfides::DisulfResNeighbConstIterator::retrieve_energy().

◆ save_energy()

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

References disulfide_info_, core::scoring::dslf_ca_dih, core::scoring::dslf_cbs_ds, core::scoring::dslf_cs_ang, core::scoring::dslf_fa13, core::scoring::dslf_ss_dih, and core::scoring::dslf_ss_dst.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::save_energy().

◆ set_num_nodes()

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

Reimplemented from core::scoring::LREnergyContainer.

References NO_DISULFIDE, and resid_2_disulfide_index_.

◆ update()

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

References disulfides_changed(), and find_disulfides().

◆ upper_neighbor_id()

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

References disulfide_partners_.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::upper_neighbor_id(), and core::scoring::disulfides::DisulfResNeighbConstIterator::upper_neighbor_id().

◆ upper_neighbor_iterator_begin()

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

Implements core::scoring::LREnergyContainer.

References NO_DISULFIDE, other_neighbor_id(), and resid_2_disulfide_index_.

◆ upper_neighbor_iterator_end()

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

Implements core::scoring::LREnergyContainer.

References empty().

Member Data Documentation

◆ disulfide_atom_indices_

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

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

◆ disulfide_info_

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

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

◆ disulfide_partners_

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

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

◆ disulfide_residue_types_

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

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

◆ NO_DISULFIDE

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

Disulfide Energy Container Class Implementation.

Referenced by core::scoring::disulfides::DisulfResNeighbIterator::accumulate_energy(), core::scoring::disulfides::DisulfResNeighbConstIterator::accumulate_energy(), any_neighbors_for_residue(), any_upper_neighbors_for_residue(), 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().

◆ resid_2_disulfide_index_

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

Referenced by any_neighbors_for_residue(), any_upper_neighbors_for_residue(), 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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