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core::pack::interaction_graph::NPDHBSimpleNode Class Reference

#include <NPDHBSimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBSimpleNode:
Inheritance graph
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Public Types

typedef SimpleNode parent
 

Public Member Functions

 NPDHBSimpleNode (utility::graph::Graph *owner, Size resnum)
 
 ~NPDHBSimpleNode () override
 
void copy_from (utility::graph::Node const *) override
 
void print () const override
 
platform::Size count_static_memory () const override
 
platform::Size count_dynamic_memory () const override
 
void commit_change_npd ()
 Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges. More...
 
void commit_change_no_res_pointer_update ()
 Copy the alternate energies to the current energies for this node and its incident edges. More...
 
void reject_change_npd (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation. More...
 
Real get_curr_upper_hbond_energies ()
 Compute the total energy for the current state assignment. More...
 
Real get_npdhb_deltaE_for_substitution ()
 Compute the change in NPDHBond energy for the given (previously supplied!) rotamer substitution. More...
 
void prepare_for_neighbors_substitution (NPDHBSimpleNode *changing_nbr)
 
void find_hbs_for_nbrs_alt_state_step1 (NPDHBSimpleNode *changing_nbr)
 
Real find_hbs_for_nbrs_alt_state_step2 (NPDHBSimpleNode *changing_nbr)
 
void acknowledge_neighbors_substitution ()
 
void compute_alt_weights_for_hbonds (bool curr_state)
 
void reset_hbs ()
 
void find_curr_hbonds_to_upper_neighbors ()
 
void calc_curr_hbond_weights ()
 
- Public Member Functions inherited from core::pack::interaction_graph::SimpleNode
 SimpleNode (utility::graph::Graph *owner, Size resnum)
 
 ~SimpleNode () override
 
void copy_from (utility::graph::Node const *) override
 
void print () const override
 
platform::Size count_static_memory () const override
 
platform::Size count_dynamic_memory () const override
 
Real one_body_energy () const
 
Real proposed_one_body_energy () const
 
Real current_one_body_energy () const
 
bool moved () const
 Is this node considering a state substitution? More...
 
void commit_change ()
 Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges. More...
 
void commit_change_no_res_pointer_update ()
 Copy the alternate energies to the current energies for this node and its incident edges. More...
 
void reject_change (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation. More...
 
void set_current (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies. More...
 
void set_alternate (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies. More...
 
void set_current_no_E_update (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Passive mode behavior: set the current residue pointer without updating the current one body or two body energies. More...
 
void set_alternate_no_E_update (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)
 Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies. More...
 
void update_energies_after_passive_change ()
 
conformation::ResidueCOP get_current () const
 return the pointer to the current state (might be 0) More...
 
conformation::ResidueCOP get_alternate () const
 return the pointer to the alternate state (might be 0) More...
 
conformation::Residue const & get_current_ref () const
 return the current state – must not be 0 More...
 
conformation::Residue const & get_alternate_ref () const
 return the alternate state – must not be 0 More...
 
Vector const & bb_centroid () const
 
Real bb_radius () const
 
Vector const & curr_sc_centroid () const
 
Real curr_sc_radius () const
 
Vector const & alt_sc_centroid () const
 
Real alt_sc_radius () const
 

Protected Member Functions

NPDHBSimpleNodenpdhb_cast (utility::graph::Node *) const
 
NPDHBSimpleNode const * npdhb_cast (utility::graph::Node const *) const
 
NPDHBSimpleEdgenpdhb_cast (utility::graph::Edge *) const
 
NPDHBSimpleEdge const * npdhb_cast (utility::graph::Edge const *) const
 
NPDHBSimpleInteractionGraph const * npdhb_owner () const
 
NPDHBSimpleInteractionGraphnpdhb_owner ()
 
- Protected Member Functions inherited from core::pack::interaction_graph::SimpleNode
SimpleInteractionGraphget_simple_ig_owner ()
 
SimpleInteractionGraph const * get_simple_ig_owner () const
 
void initialize ()
 

Private Member Functions

void initialize ()
 

Private Attributes

Size seqpos_
 
utility::vector1< utility::vector1< NPDHBondOP > > curr_atom_hbonds_
 
utility::vector1< utility::vector1< NPDHBondOP > > alt_atom_hbonds_
 
utility::vector1< NPDHBondOPcurr_hbonds_
 
utility::vector1< NPDHBondOPalt_hbonds_
 
utility::vector1< Realtmp_energies_
 
utility::vector1< Realtmp_weights_
 

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ NPDHBSimpleNode()

core::pack::interaction_graph::NPDHBSimpleNode::NPDHBSimpleNode ( utility::graph::Graph owner,
Size  resnum 
)

References initialize().

◆ ~NPDHBSimpleNode()

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

Member Function Documentation

◆ acknowledge_neighbors_substitution()

void core::pack::interaction_graph::NPDHBSimpleNode::acknowledge_neighbors_substitution ( )

◆ calc_curr_hbond_weights()

void core::pack::interaction_graph::NPDHBSimpleNode::calc_curr_hbond_weights ( )

◆ commit_change_no_res_pointer_update()

void core::pack::interaction_graph::NPDHBSimpleNode::commit_change_no_res_pointer_update ( )

◆ commit_change_npd()

void core::pack::interaction_graph::NPDHBSimpleNode::commit_change_npd ( )

Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges.

References alt_atom_hbonds_, alt_hbonds_, core::pack::interaction_graph::SimpleNode::commit_change(), curr_atom_hbonds_, curr_hbonds_, protocols::sic_dock::scores::nbr, npdhb_cast(), npdhb_owner(), and core::pack::interaction_graph::NPDHBSimpleInteractionGraph::return_hbond_to_queue().

◆ compute_alt_weights_for_hbonds()

void core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds ( bool  curr_state)

◆ copy_from()

void core::pack::interaction_graph::NPDHBSimpleNode::copy_from ( utility::graph::Node const *  )
inlineoverride

◆ count_dynamic_memory()

platform::Size core::pack::interaction_graph::NPDHBSimpleNode::count_dynamic_memory ( ) const
inlineoverride

◆ count_static_memory()

platform::Size core::pack::interaction_graph::NPDHBSimpleNode::count_static_memory ( ) const
inlineoverride

◆ find_curr_hbonds_to_upper_neighbors()

void core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors ( )

◆ find_hbs_for_nbrs_alt_state_step1()

void core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1 ( NPDHBSimpleNode changing_nbr)

◆ find_hbs_for_nbrs_alt_state_step2()

Real core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step2 ( NPDHBSimpleNode changing_nbr)

◆ get_curr_upper_hbond_energies()

Real core::pack::interaction_graph::NPDHBSimpleNode::get_curr_upper_hbond_energies ( )

Compute the total energy for the current state assignment.

References curr_hbonds_, and seqpos_.

Referenced by core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy().

◆ get_npdhb_deltaE_for_substitution()

Real core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution ( )

◆ initialize()

void core::pack::interaction_graph::NPDHBSimpleNode::initialize ( )
private

◆ npdhb_cast() [1/4]

NPDHBSimpleEdge * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_cast ( utility::graph::Edge edge) const
protected

◆ npdhb_cast() [2/4]

NPDHBSimpleEdge const * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_cast ( utility::graph::Edge const *  edge) const
protected

◆ npdhb_cast() [3/4]

NPDHBSimpleNode * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_cast ( utility::graph::Node node) const
protected

◆ npdhb_cast() [4/4]

NPDHBSimpleNode const * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_cast ( utility::graph::Node const *  node) const
protected

◆ npdhb_owner() [1/2]

NPDHBSimpleInteractionGraph * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_owner ( )
protected

◆ npdhb_owner() [2/2]

NPDHBSimpleInteractionGraph const * core::pack::interaction_graph::NPDHBSimpleNode::npdhb_owner ( ) const
protected

◆ prepare_for_neighbors_substitution()

void core::pack::interaction_graph::NPDHBSimpleNode::prepare_for_neighbors_substitution ( NPDHBSimpleNode changing_nbr)

◆ print()

void core::pack::interaction_graph::NPDHBSimpleNode::print ( ) const
inlineoverride

◆ reject_change_npd()

void core::pack::interaction_graph::NPDHBSimpleNode::reject_change_npd ( conformation::ResidueCOP  res,
basic::datacache::BasicDataCache &  residue_data_cache 
)

Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation.

References alt_hbonds_, npdhb_owner(), core::pack::interaction_graph::SimpleNode::reject_change(), and core::pack::interaction_graph::NPDHBSimpleInteractionGraph::return_hbond_to_queue().

◆ reset_hbs()

void core::pack::interaction_graph::NPDHBSimpleNode::reset_hbs ( )

Member Data Documentation

◆ alt_atom_hbonds_

utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBSimpleNode::alt_atom_hbonds_
private

◆ alt_hbonds_

utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBSimpleNode::alt_hbonds_
private

◆ curr_atom_hbonds_

utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBSimpleNode::curr_atom_hbonds_
private

◆ curr_hbonds_

utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBSimpleNode::curr_hbonds_
private

◆ seqpos_

Size core::pack::interaction_graph::NPDHBSimpleNode::seqpos_
private

◆ tmp_energies_

utility::vector1< Real > core::pack::interaction_graph::NPDHBSimpleNode::tmp_energies_
private

◆ tmp_weights_

utility::vector1< Real > core::pack::interaction_graph::NPDHBSimpleNode::tmp_weights_
private

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