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

#include <FullatomDisulfideEnergyContainer.hh>

Inheritance diagram for core::scoring::disulfides::FullatomDisulfideEnergyContainer:

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

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

default

core::scoring::disulfides::FullatomDisulfideEnergyContainer::FullatomDisulfideEnergyContainer

(

pose::Pose const &

pose

)

References find_disulfides().

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

overridedefault

Member Function Documentation

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().

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_.

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_.

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_.

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_.

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

overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

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_.

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

overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

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_.

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

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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(), 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().

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().

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().

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().

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().

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::mark_energy_computed

(

Size

disulfide_index

)

References disulfide_info_.

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

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::mark_energy_uncomputed

(

Size

disulfide_index

)

References disulfide_info_.

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

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

overridevirtual

Implements core::scoring::LREnergyContainer.

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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

overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

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

private

References disulfide_partners_.

Referenced by empty().

Size core::scoring::disulfides::FullatomDisulfideEnergyContainer::num_residues

(

)

const

References resid_2_disulfide_index_.

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_.

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().

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

References disulfide_partners_.

bool core::scoring::disulfides::FullatomDisulfideEnergyContainer::residue_forms_disulfide

(

Size

resid

)

const

References empty(), NO_DISULFIDE, and resid_2_disulfide_index_.

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().

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().

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

overridevirtual

Reimplemented from core::scoring::LREnergyContainer.

References NO_DISULFIDE, and resid_2_disulfide_index_.

void core::scoring::disulfides::FullatomDisulfideEnergyContainer::update

(

pose::Pose const &

pose

)

References disulfides_changed(), and find_disulfides().

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().

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_.

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

overridevirtual

Implements core::scoring::LREnergyContainer.

References empty().

Member Data Documentation

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().

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().

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().

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

private

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

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().

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().

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

• src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.hh
• src/core/scoring/disulfides/FullatomDisulfideEnergyContainer.cc