#include <SimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SimpleNode:

Public Member Functions
	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
SimpleInteractionGraph *	get_simple_ig_owner ()

SimpleInteractionGraph const *	get_simple_ig_owner () const

void	initialize ()

Private Member Functions
void	setup_for_scoring_for_residue (conformation::ResidueCOP res, basic::datacache::BasicDataCache &residue_data_cache)

void	update_current_one_body_energy ()

void	update_alternate_one_body_energy ()

Constructor & Destructor Documentation

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

References initialize().

core::pack::interaction_graph::SimpleNode::~SimpleNode ( )

overridedefault

Member Function Documentation

Vector const & core::pack::interaction_graph::SimpleNode::alt_sc_centroid ( ) const

References alt_sc_centroid_.

Real core::pack::interaction_graph::SimpleNode::alt_sc_radius ( ) const

References alt_sc_radius_.

Vector const & core::pack::interaction_graph::SimpleNode::bb_centroid ( ) const

References bb_centroid_.

Real core::pack::interaction_graph::SimpleNode::bb_radius ( ) const

References bb_radius_.

void core::pack::interaction_graph::SimpleNode::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.

References alternate_residue_, commit_change_no_res_pointer_update(), and current_residue_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::commit_change_npd().

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

Copy the alternate energies to the current energies for this node and its incident edges.

References alternate_one_body_energy_, current_one_body_energy_, and moved_.

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

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

inlineoverride

platform::Size core::pack::interaction_graph::SimpleNode::count_dynamic_memory ( ) const

inlineoverride

platform::Size core::pack::interaction_graph::SimpleNode::count_static_memory ( ) const

inlineoverride

Vector const & core::pack::interaction_graph::SimpleNode::curr_sc_centroid ( ) const

References curr_sc_centroid_.

Real core::pack::interaction_graph::SimpleNode::curr_sc_radius ( ) const

References curr_sc_radius_.

Real core::pack::interaction_graph::SimpleNode::current_one_body_energy ( ) const

References current_one_body_energy_.

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_alternate ( ) const

return the pointer to the alternate state (might be 0)

References alternate_residue_.

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds(), and core::pack::interaction_graph::SimpleInteractionGraph::get_alternate_for_node().

conformation::Residue const & core::pack::interaction_graph::SimpleNode::get_alternate_ref ( ) const

return the alternate state – must not be 0

References alternate_residue_.

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

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_current ( ) const

return the pointer to the current state (might be 0)

References current_residue_.

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds(), and core::pack::interaction_graph::SimpleInteractionGraph::get_current_for_node().

conformation::Residue const & core::pack::interaction_graph::SimpleNode::get_current_ref ( ) const

return the current state – must not be 0

References current_residue_.

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::calc_curr_hbond_weights(), core::pack::interaction_graph::NPDHBSimpleNode::compute_alt_weights_for_hbonds(), core::pack::interaction_graph::NPDHBSimpleNode::find_curr_hbonds_to_upper_neighbors(), core::pack::interaction_graph::NPDHBSimpleNode::find_hbs_for_nbrs_alt_state_step1(), core::pack::interaction_graph::NPDHBSimpleNode::prepare_for_neighbors_substitution(), and core::pack::interaction_graph::NPDHBSimpleNode::reset_hbs().

SimpleInteractionGraph * core::pack::interaction_graph::SimpleNode::get_simple_ig_owner ( )

inlineprotected

Referenced by setup_for_scoring_for_residue().

SimpleInteractionGraph const * core::pack::interaction_graph::SimpleNode::get_simple_ig_owner ( ) const

inlineprotected

void core::pack::interaction_graph::SimpleNode::initialize ( )

protected

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::initialize(), and SimpleNode().

bool core::pack::interaction_graph::SimpleNode::moved ( ) const

Is this node considering a state substitution?

References moved_.

Real core::pack::interaction_graph::SimpleNode::one_body_energy ( ) const

References alternate_one_body_energy_, current_one_body_energy_, and moved_.

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

void core::pack::interaction_graph::SimpleNode::print ( ) const

inlineoverride

Real core::pack::interaction_graph::SimpleNode::proposed_one_body_energy ( ) const

References alternate_one_body_energy_.

Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph().

void core::pack::interaction_graph::SimpleNode::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.

References moved_, and setup_for_scoring_for_residue().

Referenced by core::pack::interaction_graph::NPDHBSimpleNode::reject_change_npd().

void core::pack::interaction_graph::SimpleNode::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.

References alt_sc_centroid_, alt_sc_radius_, alternate_residue_, core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), moved_, setup_for_scoring_for_residue(), core::pack::interaction_graph::TR(), and update_alternate_one_body_energy().

void core::pack::interaction_graph::SimpleNode::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.

References alternate_residue_, moved_, and setup_for_scoring_for_residue().

void core::pack::interaction_graph::SimpleNode::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.

References bb_centroid_, bb_radius_, core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), curr_sc_centroid_, curr_sc_radius_, current_residue_, moved_, setup_for_scoring_for_residue(), and update_current_one_body_energy().

void core::pack::interaction_graph::SimpleNode::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.

References current_residue_, and setup_for_scoring_for_residue().

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

private

References get_simple_ig_owner().

Referenced by reject_change(), set_alternate(), set_alternate_no_E_update(), set_current(), and set_current_no_E_update().

void core::pack::interaction_graph::SimpleNode::update_alternate_one_body_energy ( )

private

References alternate_one_body_energy_, and alternate_residue_.

Referenced by set_alternate(), and update_energies_after_passive_change().

void core::pack::interaction_graph::SimpleNode::update_current_one_body_energy ( )

private

References current_one_body_energy_, and current_residue_.

Referenced by set_current().

void core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change ( )

References update_alternate_one_body_energy().

Member Data Documentation

Vector core::pack::interaction_graph::SimpleNode::alt_sc_centroid_

private

Referenced by alt_sc_centroid(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alt_sc_radius_

private

Referenced by alt_sc_radius(), and set_alternate().

Real core::pack::interaction_graph::SimpleNode::alternate_one_body_energy_

private

Referenced by commit_change_no_res_pointer_update(), one_body_energy(), proposed_one_body_energy(), and update_alternate_one_body_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::alternate_residue_

private

Referenced by commit_change(), get_alternate(), get_alternate_ref(), set_alternate(), set_alternate_no_E_update(), and update_alternate_one_body_energy().

Vector core::pack::interaction_graph::SimpleNode::bb_centroid_

private

Referenced by bb_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::bb_radius_

private

Referenced by bb_radius(), and set_current().

Vector core::pack::interaction_graph::SimpleNode::curr_sc_centroid_

private

Referenced by curr_sc_centroid(), and set_current().

Real core::pack::interaction_graph::SimpleNode::curr_sc_radius_

private

Referenced by curr_sc_radius(), and set_current().

Real core::pack::interaction_graph::SimpleNode::current_one_body_energy_

private

Referenced by commit_change_no_res_pointer_update(), current_one_body_energy(), one_body_energy(), and update_current_one_body_energy().

conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::current_residue_

private

Referenced by commit_change(), get_current(), get_current_ref(), set_current(), set_current_no_E_update(), and update_current_one_body_energy().

bool core::pack::interaction_graph::SimpleNode::moved_

private

Referenced by commit_change_no_res_pointer_update(), moved(), one_body_energy(), reject_change(), set_alternate(), set_alternate_no_E_update(), and set_current().

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

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

Private Attributes
bool	moved_

Real	current_one_body_energy_

Real	alternate_one_body_energy_

conformation::ResidueCOP	current_residue_

conformation::ResidueCOP	alternate_residue_

Vector	bb_centroid_

Real	bb_radius_

Vector	curr_sc_centroid_

Real	curr_sc_radius_

Vector	alt_sc_centroid_

Real	alt_sc_radius_

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation