core::scoring::PolymerBondedEnergyContainer Class Reference

#include <PolymerBondedEnergyContainer.hh>

Inheritance diagram for core::scoring::PolymerBondedEnergyContainer:

Public Member Functions
	~PolymerBondedEnergyContainer () override
	Destructor. More...
LREnergyContainerOP	clone () const override
	PolymerBondedEnergyContainer (core::pose::Pose const &pose, utility::vector1< ScoreType > const &score_type_in)
	Pose constructor. More...
bool	empty () const override
bool	any_neighbors_for_residue (int) const override
bool	any_upper_neighbors_for_residue (int) const override
Size	size () const
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	is_valid (core::pose::Pose const &pose) const
	Is this PolymerBondedEnergyContainer properly set up for the pose? More...
utility::vector1< ScoreType > const &	score_types () const
bool	get_computed (core::Size res1, core::Size res2) const
void	set_computed (core::Size res1, core::Size res2, bool val)
core::Real	get_energy (core::Size res1, core::Size res2, core::Size scoreterm) const
void	set_energy (core::Size res1, core::Size res2, core::Size scoreterm, core::Real E)
Public Member Functions inherited from core::scoring::LREnergyContainer
	~LREnergyContainer () override
virtual void	set_num_nodes (Size)

Private Member Functions
void	initialize_peptide_bonded_pair_indices (core::pose::Pose const &pose)
	Given a pose, set up a list of pairs of residues. More...

Private Attributes
Size	size_
	number of chemical connections in the pose More...
std::multimap< core::Size, core::Size >	chemical_edges_
	A map of all chemical edges in the pose. More...
std::set< std::pair< core::Size, core::Size > >	chemical_edge_set_
utility::vector1< ScoreType >	score_types_
	The vector of score types that this PolymerBondedEnergyContainer will be used to calculate. More...
std::map< std::pair< core::Size, core::Size >, utility::vector1< core::Real > >	tables_
	energy tables. maps each edge to a vector (one for each type) More...
std::map< std::pair< core::Size, core::Size >, bool >	computed_
	computed tables. maps each edge to a bool More...

Friends
std::ostream &	operator<< (std::ostream &os, PolymerBondedEnergyContainer const &t)
	Operator to allow object to be summarized. More...

Constructor & Destructor Documentation

~PolymerBondedEnergyContainer()

core::scoring::PolymerBondedEnergyContainer::~PolymerBondedEnergyContainer ( )

overridedefault

Destructor.

PolymerBondedEnergyContainer()

core::scoring::PolymerBondedEnergyContainer::PolymerBondedEnergyContainer	(	core::pose::Pose const &	pose,
		utility::vector1< ScoreType > const &	score_type_in
	)

Pose constructor.

Initializes PolymerBondedEnergyContainer from a pose, facilitating calculations involving non-canonical connections (e.g. terminal peptide bonds).

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::pose::Pose::annotated_sequence(), initialize_peptide_bonded_pair_indices(), and core::scoring::TR().

Member Function Documentation

any_neighbors_for_residue()

bool core::scoring::PolymerBondedEnergyContainer::any_neighbors_for_residue ( int  ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

any_upper_neighbors_for_residue()

bool core::scoring::PolymerBondedEnergyContainer::any_upper_neighbors_for_residue ( int  ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

clone()

LREnergyContainerOP core::scoring::PolymerBondedEnergyContainer::clone ( ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

const_neighbor_iterator_begin()

ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_begin ( int  resid ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

References chemical_edges_, and protocols::sic_dock::range().

const_neighbor_iterator_end()

ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_end ( int  resid ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

Referenced by const_upper_neighbor_iterator_end().

const_upper_neighbor_iterator_begin()

ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_begin ( int  resid ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

References chemical_edges_, and protocols::sic_dock::range().

const_upper_neighbor_iterator_end()

ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_end ( int  resid ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

References const_neighbor_iterator_end().

empty()

bool core::scoring::PolymerBondedEnergyContainer::empty ( ) const

overridevirtual

Implements core::scoring::LREnergyContainer.

References size_.

get_computed()

bool core::scoring::PolymerBondedEnergyContainer::get_computed ( core::Size  res1, core::Size  res2  ) const

inline

References computed_, protocols::mean_field::max(), and protocols::mean_field::min().

Referenced by core::scoring::PolymerBondedNeighborIterator::energy_computed(), and core::scoring::PolymerBondedNeighborConstIterator::energy_computed().

get_energy()

core::Real core::scoring::PolymerBondedEnergyContainer::get_energy ( core::Size  res1, core::Size  res2, core::Size  scoreterm  ) const

inline

References protocols::mean_field::max(), protocols::mean_field::min(), and tables_.

Referenced by core::scoring::PolymerBondedNeighborIterator::accumulate_energy(), core::scoring::PolymerBondedNeighborConstIterator::accumulate_energy(), core::scoring::PolymerBondedNeighborIterator::retrieve_energy(), and core::scoring::PolymerBondedNeighborConstIterator::retrieve_energy().

initialize_peptide_bonded_pair_indices()

void core::scoring::PolymerBondedEnergyContainer::initialize_peptide_bonded_pair_indices ( core::pose::Pose const &  pose )

private

Given a pose, set up a list of pairs of residues.

Given a pose, set up a list of pairs of peptide-bonded residues.

The first index is the lower residue (the residue contributing the carboxyl/UPPER_CONNECT) and the second is the upper residue (the residue contributing the amide/LOWER_CONNECT).

Note

fpd: this now includes all chemical edges

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

The first index is the lower residue (the residue contributing the carboxyl/UPPER_CONNECT) and the second is the upper residue (the residue contributing the amide/LOWER_CONNECT).

Note

Since the PolymerBondedEnergyContainer is also apparently used for RNA, I'm going to base this on UPPER_CONNECT/LOWER_CONNECT, not on any peptide-specific geometry.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References chemical_edge_set_, chemical_edges_, computed_, core::conformation::Residue::connected_residue_at_resconn(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::n_possible_residue_connections(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), score_types_, size_, core::pose::symmetry::symmetry_info(), tables_, and core::pose::Pose::total_residue().

Referenced by PolymerBondedEnergyContainer().

is_valid()

bool core::scoring::PolymerBondedEnergyContainer::is_valid

(

core::pose::Pose const &

pose

)

const

Is this PolymerBondedEnergyContainer properly set up for the pose?

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References chemical_edges_, core::conformation::Residue::connected_residue_at_resconn(), core::pose::symmetry::is_symmetric(), core::conformation::Residue::n_possible_residue_connections(), protocols::sic_dock::range(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), core::pose::Pose::size(), size_, and core::pose::symmetry::symmetry_info().

neighbor_iterator_begin()

ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::neighbor_iterator_begin ( int  resid )

overridevirtual

Implements core::scoring::LREnergyContainer.

References chemical_edges_, and protocols::sic_dock::range().

neighbor_iterator_end()

ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::neighbor_iterator_end ( int  resid )

overridevirtual

Implements core::scoring::LREnergyContainer.

Referenced by upper_neighbor_iterator_end().

score_types()

utility::vector1< ScoreType > const& core::scoring::PolymerBondedEnergyContainer::score_types ( ) const

inline

References score_types_.

Referenced by core::scoring::PolymerBondedNeighborIterator::accumulate_energy(), core::scoring::PolymerBondedNeighborConstIterator::accumulate_energy(), core::scoring::PolymerBondedNeighborIterator::retrieve_energy(), core::scoring::PolymerBondedNeighborConstIterator::retrieve_energy(), and core::scoring::PolymerBondedNeighborIterator::save_energy().

set_computed()

void core::scoring::PolymerBondedEnergyContainer::set_computed ( core::Size  res1, core::Size  res2, bool  val  )

inline

References computed_, protocols::mean_field::max(), protocols::mean_field::min(), and protocols::hybridization::val.

Referenced by core::scoring::PolymerBondedNeighborIterator::mark_energy_computed(), and core::scoring::PolymerBondedNeighborIterator::mark_energy_uncomputed().

set_energy()

void core::scoring::PolymerBondedEnergyContainer::set_energy ( core::Size  res1, core::Size  res2, core::Size  scoreterm, core::Real  E  )

inline

References protocols::comparative_modeling::features::E, protocols::mean_field::max(), protocols::mean_field::min(), and tables_.

Referenced by core::scoring::PolymerBondedNeighborIterator::save_energy().

size()

Size core::scoring::PolymerBondedEnergyContainer::size

(

)

const

References size_.

upper_neighbor_iterator_begin()

ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::upper_neighbor_iterator_begin ( int  resid )

overridevirtual

Implements core::scoring::LREnergyContainer.

References chemical_edges_, and protocols::sic_dock::range().

upper_neighbor_iterator_end()

ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::upper_neighbor_iterator_end ( int  resid )

overridevirtual

Implements core::scoring::LREnergyContainer.

References neighbor_iterator_end().

Friends And Related Function Documentation

operator<<

std::ostream& operator<< ( std::ostream &  os, PolymerBondedEnergyContainer const &  t  )

friend

Operator to allow object to be summarized.

Author

Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Member Data Documentation

chemical_edge_set_

std::set< std::pair< core::Size, core::Size > > core::scoring::PolymerBondedEnergyContainer::chemical_edge_set_

private

Referenced by initialize_peptide_bonded_pair_indices().

chemical_edges_

std::multimap< core::Size, core::Size > core::scoring::PolymerBondedEnergyContainer::chemical_edges_

private

A map of all chemical edges in the pose.

Referenced by const_neighbor_iterator_begin(), const_upper_neighbor_iterator_begin(), initialize_peptide_bonded_pair_indices(), is_valid(), neighbor_iterator_begin(), and upper_neighbor_iterator_begin().

computed_

std::map< std::pair<core::Size, core::Size> , bool > core::scoring::PolymerBondedEnergyContainer::computed_

private

computed tables. maps each edge to a bool

Referenced by get_computed(), initialize_peptide_bonded_pair_indices(), and set_computed().

score_types_

utility::vector1< ScoreType > core::scoring::PolymerBondedEnergyContainer::score_types_

private

The vector of score types that this PolymerBondedEnergyContainer will be used to calculate.

Referenced by initialize_peptide_bonded_pair_indices(), and score_types().

size_

Size core::scoring::PolymerBondedEnergyContainer::size_

private

number of chemical connections in the pose

Referenced by empty(), initialize_peptide_bonded_pair_indices(), is_valid(), and size().

tables_

std::map< std::pair<core::Size, core::Size> , utility::vector1< core::Real > > core::scoring::PolymerBondedEnergyContainer::tables_

private

energy tables. maps each edge to a vector (one for each type)

Referenced by get_energy(), initialize_peptide_bonded_pair_indices(), and set_energy().

---

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

• src/core/scoring/PolymerBondedEnergyContainer.hh
• src/core/scoring/PolymerBondedEnergyContainer.cc