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core::scoring::PolymerBondedEnergyContainer Class Reference

#include <PolymerBondedEnergyContainer.hh>

Inheritance diagram for core::scoring::PolymerBondedEnergyContainer:
Inheritance graph
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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< ScoreTypescore_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

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

Destructor.

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

bool core::scoring::PolymerBondedEnergyContainer::any_neighbors_for_residue ( int  ) const
overridevirtual
bool core::scoring::PolymerBondedEnergyContainer::any_upper_neighbors_for_residue ( int  ) const
overridevirtual
LREnergyContainerOP core::scoring::PolymerBondedEnergyContainer::clone ( ) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_begin ( int  resid) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_neighbor_iterator_end ( int  resid) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_begin ( int  resid) const
overridevirtual
ResidueNeighborConstIteratorOP core::scoring::PolymerBondedEnergyContainer::const_upper_neighbor_iterator_end ( int  resid) const
overridevirtual
bool core::scoring::PolymerBondedEnergyContainer::empty ( ) const
overridevirtual

Implements core::scoring::LREnergyContainer.

References size_.

bool core::scoring::PolymerBondedEnergyContainer::get_computed ( core::Size  res1,
core::Size  res2 
) const
inline
core::Real core::scoring::PolymerBondedEnergyContainer::get_energy ( core::Size  res1,
core::Size  res2,
core::Size  scoreterm 
) const
inline
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().

bool core::scoring::PolymerBondedEnergyContainer::is_valid ( core::pose::Pose const &  pose) const
ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::neighbor_iterator_begin ( int  resid)
overridevirtual
ResidueNeighborIteratorOP core::scoring::PolymerBondedEnergyContainer::neighbor_iterator_end ( int  resid)
overridevirtual
utility::vector1< ScoreType > const& core::scoring::PolymerBondedEnergyContainer::score_types ( ) const
inline
void core::scoring::PolymerBondedEnergyContainer::set_computed ( core::Size  res1,
core::Size  res2,
bool  val 
)
inline
void core::scoring::PolymerBondedEnergyContainer::set_energy ( core::Size  res1,
core::Size  res2,
core::Size  scoreterm,
core::Real  E 
)
inline
Size core::scoring::PolymerBondedEnergyContainer::size ( ) const

References size_.

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

Friends And Related Function Documentation

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

std::set< std::pair< core::Size, core::Size > > core::scoring::PolymerBondedEnergyContainer::chemical_edge_set_
private
std::multimap< core::Size, core::Size > core::scoring::PolymerBondedEnergyContainer::chemical_edges_
private
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().

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 core::scoring::PolymerBondedEnergyContainer::size_
private

number of chemical connections in the pose

Referenced by empty(), initialize_peptide_bonded_pair_indices(), is_valid(), core::scoring::operator<<(), and size().

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: