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:

[legend]

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

NPDHBSimpleNode *	get_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

SimpleNode *	get_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

NPDHBSimpleNode *	npdhb_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< NPDHBondOP >	hbonds_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

◆ parent

typedef SimpleInteractionGraph core::pack::interaction_graph::NPDHBSimpleInteractionGraph::parent

Constructor & Destructor Documentation

◆ NPDHBSimpleInteractionGraph()

core::pack::interaction_graph::NPDHBSimpleInteractionGraph::NPDHBSimpleInteractionGraph ( )

◆ ~NPDHBSimpleInteractionGraph()

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

overridedefault

Member Function Documentation

◆ commit_change()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::commit_change ( Size node_id )

overridevirtual

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

◆ consider_substitution()

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().

◆ count_dynamic_memory()

Size core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_dynamic_memory ( ) const

inlineoverride

◆ count_static_memory()

Size core::pack::interaction_graph::NPDHBSimpleInteractionGraph::count_static_memory ( ) const

inlineoverride

◆ create_new_edge()

Edge * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::create_new_edge	(	platform::Size	index1,
		platform::Size	index2
	)

overrideprotected

◆ create_new_node()

Node * core::pack::interaction_graph::NPDHBSimpleInteractionGraph::create_new_node ( platform::Size node_index )

overrideprotected

◆ delete_edge()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::delete_edge ( utility::graph::Edge * edge )

override

◆ get_npdhb_simple_node() [1/2]

NPDHBSimpleNode* core::pack::interaction_graph::NPDHBSimpleInteractionGraph::get_npdhb_simple_node ( Size ind )

inline

Referenced by total_energy().

◆ get_npdhb_simple_node() [2/2]

NPDHBSimpleNode const* core::pack::interaction_graph::NPDHBSimpleInteractionGraph::get_npdhb_simple_node ( Size ind ) const

inline

◆ hbond_database()

scoring::hbonds::HBondDatabase const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database ( ) const

References hbond_database_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), and core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution().

◆ hbond_options()

scoring::hbonds::HBondOptions const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options ( ) const

References hbond_options_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), and core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution().

◆ hbonding_to_res()

utility::vector1< char > & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res ( )

References hbonding_to_res_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), and core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step2().

◆ initialize()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::initialize ( pose::Pose const & pose )

overridevirtual

Initialization where the graph adds its own edges.

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

References hbonding_to_res_, core::pack::interaction_graph::SimpleInteractionGraph::initialize(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), setup_after_edge_addition(), and core::pose::Pose::total_residue().

◆ npd_hb_weight()

Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hb_weight	(	scoring::hbonds::HBEvalType	eval_type,
		bool	intra_res
	)

References core::scoring::hbonds::npd_hb_eval_type_weight(), and core::pack::interaction_graph::SimpleInteractionGraph::scorefunction().

Referenced by core::pack::interaction_graph::create_hbonds_one_way().

◆ npd_hbond_set()

scoring::hbonds::NPDHBondSet const & core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set ( ) const

References npd_hbond_set_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), and core::pack::interaction_graph::NPDHBSimpleNode::get_npdhb_deltaE_for_substitution().

◆ npdhb_cast() [1/2]

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

protected

Referenced by setup_after_edge_addition().

◆ npdhb_cast() [2/2]

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

protected

◆ reject_change()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::reject_change	(	Size	node_id,
		conformation::ResidueCOP	res,
		basic::datacache::BasicDataCache &	residue_data_cache
	)

overridevirtual

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

◆ return_hbond_to_queue()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::return_hbond_to_queue ( NPDHBondOP const & hbond )

References core::scoring::hbond, and hbonds_queue_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::commit_change_no_res_pointer_update(), core::pack::interaction_graph::NPDHBSimpleNode::commit_change_npd(), and core::pack::interaction_graph::NPDHBSimpleNode::reject_change_npd().

◆ set_pose_no_initialize()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_pose_no_initialize ( pose::Pose const & pose )

overridevirtual

Initialize the graph so that all nodes take their current state from the input Pose – this does not add any edges to the graph.

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

References core::scoring::Energies::data(), core::pose::Pose::energies(), hbond_database_, hbond_options_, hbonding_to_res_, core::scoring::EnergiesCacheableDataType::NPD_HBOND_SET, npd_hbond_set_, core::pack::interaction_graph::SimpleInteractionGraph::pose(), core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize(), and core::pose::Pose::total_residue().

◆ set_scorefunction()

void core::pack::interaction_graph::NPDHBSimpleInteractionGraph::set_scorefunction ( scoring::ScoreFunction const & sfxn )

overridevirtual

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

References protocols::mean_field::max(), core::scoring::npd_hbond, core::scoring::npd_hbond_bb_sc, core::scoring::npd_hbond_lr_bb, core::scoring::npd_hbond_sc, core::scoring::npd_hbond_sr_bb, npd_hbond_weight_, core::pack::interaction_graph::SimpleInteractionGraph::set_scorefunction(), and core::scoring::ScoreFunction::weights().

◆ setup_after_edge_addition()

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().

◆ total_energy()

Real core::pack::interaction_graph::NPDHBSimpleInteractionGraph::total_energy ( )

overridevirtual

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

References core::pack::interaction_graph::NPDHBSimpleNode::get_curr_upper_hbond_energies(), get_npdhb_simple_node(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), core::pack::interaction_graph::SimpleInteractionGraph::total_energy(), and core::pose::Pose::total_residue().

◆ unused_hbond()

NPDHBondOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::unused_hbond ( )

References hbonds_queue_.

Referenced by core::pack::interaction_graph::create_hbonds_one_way().

Member Data Documentation

◆ hbond_database_

scoring::hbonds::HBondDatabaseCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database_

private

Referenced by hbond_database(), and set_pose_no_initialize().

◆ hbond_options_

scoring::hbonds::HBondOptionsCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options_

private

Referenced by hbond_options(), and set_pose_no_initialize().

◆ hbonding_to_res_

utility::vector1< char > core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res_

private

Referenced by hbonding_to_res(), initialize(), and set_pose_no_initialize().

◆ hbonds_queue_

std::list< NPDHBondOP > core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonds_queue_

private

Referenced by return_hbond_to_queue(), and unused_hbond().

◆ npd_hbond_set_

scoring::hbonds::NPDHBondSetCOP core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set_

private

Referenced by npd_hbond_set(), and set_pose_no_initialize().

◆ npd_hbond_weight_

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:

src/core/pack/interaction_graph/NPDHBSimpleInteractionGraph.hh
src/core/pack/interaction_graph/NPDHBSimpleInteractionGraph.cc

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Detailed Description

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ NPDHBSimpleInteractionGraph()

◆ ~NPDHBSimpleInteractionGraph()

Member Function Documentation

◆ commit_change()

◆ consider_substitution()

◆ count_dynamic_memory()

◆ count_static_memory()

◆ create_new_edge()

◆ create_new_node()

◆ delete_edge()

◆ get_npdhb_simple_node() [1/2]

◆ get_npdhb_simple_node() [2/2]

◆ hbond_database()

◆ hbond_options()

◆ hbonding_to_res()

◆ initialize()

◆ npd_hb_weight()

◆ npd_hbond_set()

◆ npdhb_cast() [1/2]

◆ npdhb_cast() [2/2]

◆ reject_change()

◆ return_hbond_to_queue()

◆ set_pose_no_initialize()

◆ set_scorefunction()

◆ setup_after_edge_addition()

◆ total_energy()

◆ unused_hbond()

Member Data Documentation

◆ hbond_database_

◆ hbond_options_

◆ hbonding_to_res_

◆ hbonds_queue_

◆ npd_hbond_set_

◆ npd_hbond_weight_