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core::pack::interaction_graph::NPDHBSimpleInteractionGraph Class Reference

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver. More...

#include <NPDHBSimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBSimpleInteractionGraph:
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Public Types

typedef SimpleInteractionGraph parent
 

Public Member Functions

 NPDHBSimpleInteractionGraph ()
 
 ~NPDHBSimpleInteractionGraph () override
 
void set_scorefunction (scoring::ScoreFunction const &sfxn) override
 
void initialize (pose::Pose const &pose) override
 Initialization where the graph adds its own edges. More...
 
void set_pose_no_initialize (pose::Pose const &pose) override
 Initialize the graph so that all nodes take their current state from the input Pose – this does not add any edges to the graph. More...
 
void setup_after_edge_addition () override
 If set_pose_no_initialize was called, then after edges have been added. This function will also do any bookkeeping necessary before the start of simulated annealing. More...
 
void commit_change (Size node_id) override
 
void reject_change (Size node_id, conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache) override
 
scoring::hbonds::HBondDatabase
const & 
hbond_database () const
 
scoring::hbonds::HBondOptions
const & 
hbond_options () const
 
scoring::hbonds::NPDHBondSet
const & 
npd_hbond_set () const
 
Real consider_substitution (Size node_id, conformation::ResidueCOP new_state, basic::datacache::BasicDataCache &residue_data_cache) override
 
Real total_energy () override
 
utility::vector1< char > & hbonding_to_res ()
 
NPDHBondOP unused_hbond ()
 
void return_hbond_to_queue (NPDHBondOP const &hbond)
 
Real npd_hb_weight (scoring::hbonds::HBEvalType eval_type, bool intra_res)
 
Size count_static_memory () const override
 
Size count_dynamic_memory () const override
 
void delete_edge (utility::graph::Edge *) override
 
NPDHBSimpleNodeget_npdhb_simple_node (Size ind)
 
NPDHBSimpleNode const * get_npdhb_simple_node (Size ind) const
 
- Public Member Functions inherited from core::pack::interaction_graph::SimpleInteractionGraph
 SimpleInteractionGraph ()
 
 ~SimpleInteractionGraph () override
 
scoring::ScoreFunction const & scorefunction () const
 
std::list
< scoring::methods::EnergyMethodCOP >
const & 
setup_for_scoring_for_residue_energy_methods ()
 
pose::Pose const & pose () const
 
pose::PoseCOP pose_cop () const
 
virtual void initialize (pose::Pose const &pose, task::PackerTaskCOP task)
 Initialization where the graph creates a packer-neighbor graph from the input packer task so that edges between residues that might become larger than they are in the input Pose (e.g., GLY –> ARG mutation) can be added to the graph. More...
 
Size count_static_memory () const override
 
Size count_dynamic_memory () const override
 
void delete_edge (utility::graph::Edge *) override
 
SimpleNodeget_simple_node (Size ind)
 
SimpleNode const * get_simple_node (Size ind) const
 
conformation::ResidueCOP get_current_for_node (Size id) const
 
conformation::ResidueCOP get_alternate_for_node (Size id) const
 

Protected Member Functions

utility::graph::Node * create_new_node (Size node_index) override
 
utility::graph::Edge * create_new_edge (Size index1, platform::Size index2) override
 
NPDHBSimpleNodenpdhb_cast (utility::graph::Node *)
 
NPDHBSimpleNode const * npdhb_cast (utility::graph::Node const *) const
 
- Protected Member Functions inherited from core::pack::interaction_graph::SimpleInteractionGraph
utility::graph::Node * create_new_node (Size node_index) override
 
utility::graph::Edge * create_new_edge (Size index1, platform::Size index2) override
 

Private Attributes

scoring::hbonds::HBondDatabaseCOP hbond_database_
 
scoring::hbonds::HBondOptionsCOP hbond_options_
 
scoring::hbonds::NPDHBondSetCOP npd_hbond_set_
 
Real npd_hbond_weight_
 
utility::vector1< char > hbonding_to_res_
 
std::list< NPDHBondOPhbonds_queue_
 

Detailed Description

A simple graph class for calculating pairwise decomposable energies as sidechains are moving on a fixed backbone. This class is responsible for calculating energy changes, but is passive about how the sidechains are changing. There are two main ways to drive the graph: one where the graph ACTIVELY takes charge of updating pointers to the sidechains, where, each external change of one pointer triggers an update to the energies; and a second, where the graph is PASSIVE wrt the pointers, and they must be maintained by an external driver.

Member Typedef Documentation

Constructor & Destructor Documentation

core::pack::interaction_graph::NPDHBSimpleInteractionGraph::NPDHBSimpleInteractionGraph ( )
core::pack::interaction_graph::NPDHBSimpleInteractionGraph::~NPDHBSimpleInteractionGraph ( )
overridedefault

Member Function Documentation

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::commit_change ( Size  node_id)
overridevirtual
Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::consider_substitution ( Size  node_id,
conformation::ResidueCOP  new_state,
basic::datacache::BasicDataCache &  residue_data_cache 
)
overridevirtual

Note, this function returns (currE - altE) which represents the negative of the change in energy for the substition

Reimplemented from core::pack::interaction_graph::SimpleInteractionGraph.

References core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution(), and core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution().

Size core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_dynamic_memory ( ) const
inlineoverride
Size core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_static_memory ( ) const
inlineoverride
Edge * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::create_new_edge ( platform::Size  index1,
platform::Size  index2 
)
overrideprotected
Node * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::create_new_node ( platform::Size  node_index)
overrideprotected
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::delete_edge ( utility::graph::Edge *  edge)
override
NPDHBSimpleNode* core::pack::interaction_graph::NPDHBSimpleInteractionGraph::get_npdhb_simple_node ( Size  ind)
inline

Referenced by total_energy().

NPDHBSimpleNode const* core::pack::interaction_graph::NPDHBSimpleInteractionGraph::get_npdhb_simple_node ( Size  ind) const
inline
scoring::hbonds::HBondDatabase const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database ( ) const
scoring::hbonds::HBondOptions const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options ( ) const
utility::vector1< char > & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res ( )
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::initialize ( pose::Pose const &  pose)
overridevirtual
Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hb_weight ( scoring::hbonds::HBEvalType  eval_type,
bool  intra_res 
)
scoring::hbonds::NPDHBondSet const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set ( ) const
NPDHBSimpleNode * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npdhb_cast ( utility::graph::Node *  node)
protected
NPDHBSimpleNode const * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npdhb_cast ( utility::graph::Node const *  node) const
protected
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::reject_change ( Size  node_id,
conformation::ResidueCOP  res,
basic::datacache::BasicDataCache &  residue_data_cache 
)
overridevirtual
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::return_hbond_to_queue ( NPDHBondOP const &  hbond)
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize ( pose::Pose const &  pose)
overridevirtual
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction ( scoring::ScoreFunction const &  sfxn)
overridevirtual
void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::setup_after_edge_addition ( )
overridevirtual

If set_pose_no_initialize was called, then after edges have been added. This function will also do any bookkeeping necessary before the start of simulated annealing.

Reimplemented from core::pack::interaction_graph::SimpleInteractionGraph.

References npdhb_cast().

Referenced by initialize().

Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy ( )
overridevirtual
NPDHBondOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::unused_hbond ( )

Member Data Documentation

scoring::hbonds::HBondDatabaseCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database_
private
scoring::hbonds::HBondOptionsCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options_
private
utility::vector1< char > core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res_
private
std::list< NPDHBondOP > core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonds_queue_
private
scoring::hbonds::NPDHBondSetCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set_
private
Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_weight_
private

Referenced by set_scorefunction().


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