#include <NPDHBSimpleInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBSimpleNode:

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
NPDHBSimpleNode *	npdhb_cast (utility::graph::Node *) const

NPDHBSimpleNode const *	npdhb_cast (utility::graph::Node const *) const

NPDHBSimpleEdge *	npdhb_cast (utility::graph::Edge *) const

NPDHBSimpleEdge const *	npdhb_cast (utility::graph::Edge const *) const

NPDHBSimpleInteractionGraph const *	npdhb_owner () const

NPDHBSimpleInteractionGraph *	npdhb_owner ()

Protected Member Functions inherited from core::pack::interaction_graph::SimpleNode
SimpleInteractionGraph *	get_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< NPDHBondOP >	curr_hbonds_

utility::vector1< NPDHBondOP >	alt_hbonds_

utility::vector1< Real >	tmp_energies_

utility::vector1< Real >	tmp_weights_

Member Typedef Documentation

typedef SimpleNode core::pack::interaction_graph::NPDHBSimpleNode::parent

Constructor & Destructor Documentation

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

References initialize().

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

overridedefault

Member Function Documentation

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

References alt_atom_hbonds_, alt_hbonds_, curr_atom_hbonds_, and curr_hbonds_.

Referenced by commit_change_no_res_pointer_update(), and commit_change_npd().

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

References core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), curr_atom_hbonds_, curr_hbonds_, core::pack::interaction_graph::SimpleNode::get_current_ref(), tmp_energies_, and tmp_weights_.

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

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

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

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 acknowledge_neighbors_substitution(), 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().

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

References alt_atom_hbonds_, core::pack::interaction_graph::compute_alt_weights_for_npd_hbonds(), core::pack::interaction_graph::SimpleNode::get_alternate(), core::pack::interaction_graph::SimpleNode::get_alternate_ref(), core::pack::interaction_graph::SimpleNode::get_current(), core::pack::interaction_graph::SimpleNode::get_current_ref(), tmp_energies_, and tmp_weights_.

Referenced by find_hbs_for_nbrs_alt_state_step1(), and get_npdhb_deltaE_for_substitution().

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

inlineoverride

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

inlineoverride

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

inlineoverride

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

References core::pack::interaction_graph::create_hbonds_one_way(), curr_atom_hbonds_, curr_hbonds_, core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::pack::interaction_graph::SimpleNode::get_current_ref(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res(), protocols::sic_dock::scores::nbr, core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set(), npdhb_cast(), and npdhb_owner().

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

References alt_atom_hbonds_, alt_hbonds_, compute_alt_weights_for_hbonds(), core::pack::interaction_graph::create_hbonds_one_way(), core::pack::interaction_graph::SimpleNode::get_alternate_ref(), core::pack::interaction_graph::SimpleNode::get_current_ref(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set(), and npdhb_owner().

Referenced by get_npdhb_deltaE_for_substitution().

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

References alt_hbonds_, curr_hbonds_, core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbonding_to_res(), npdhb_owner(), and seqpos_.

Referenced by get_npdhb_deltaE_for_substitution().

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().

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

Compute the change in NPDHBond energy for the given (previously supplied!) rotamer substitution.

References alt_atom_hbonds_, alt_hbonds_, compute_alt_weights_for_hbonds(), core::pack::interaction_graph::create_hbonds_one_way(), curr_hbonds_, find_hbs_for_nbrs_alt_state_step1(), find_hbs_for_nbrs_alt_state_step2(), core::pack::interaction_graph::SimpleNode::get_alternate_ref(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_database(), core::pack::interaction_graph::NPDHBSimpleInteractionGraph::hbond_options(), core::conformation::Residue::natoms(), protocols::sic_dock::scores::nbr, core::pack::interaction_graph::NPDHBSimpleInteractionGraph::npd_hbond_set(), npdhb_cast(), npdhb_owner(), prepare_for_neighbors_substitution(), and seqpos_.

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

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

private

References core::pack::interaction_graph::SimpleNode::initialize().

Referenced by NPDHBSimpleNode().

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

protected

Referenced by commit_change_no_res_pointer_update(), commit_change_npd(), find_curr_hbonds_to_upper_neighbors(), and get_npdhb_deltaE_for_substitution().

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

protected

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

protected

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

protected

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

protected

Referenced by commit_change_no_res_pointer_update(), commit_change_npd(), find_curr_hbonds_to_upper_neighbors(), find_hbs_for_nbrs_alt_state_step1(), find_hbs_for_nbrs_alt_state_step2(), get_npdhb_deltaE_for_substitution(), and reject_change_npd().

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

protected

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

References alt_atom_hbonds_, alt_hbonds_, curr_hbonds_, core::pack::interaction_graph::SimpleNode::get_current_ref(), core::conformation::Residue::natoms(), and seqpos_.

Referenced by get_npdhb_deltaE_for_substitution().

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

inlineoverride

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().

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

References alt_atom_hbonds_, alt_hbonds_, curr_atom_hbonds_, curr_hbonds_, core::pack::interaction_graph::SimpleNode::get_current_ref(), and core::conformation::Residue::natoms().

Member Data Documentation

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

private

Referenced by acknowledge_neighbors_substitution(), commit_change_no_res_pointer_update(), commit_change_npd(), compute_alt_weights_for_hbonds(), find_hbs_for_nbrs_alt_state_step1(), get_npdhb_deltaE_for_substitution(), prepare_for_neighbors_substitution(), and reset_hbs().

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

private

Referenced by acknowledge_neighbors_substitution(), commit_change_no_res_pointer_update(), commit_change_npd(), find_hbs_for_nbrs_alt_state_step1(), find_hbs_for_nbrs_alt_state_step2(), get_npdhb_deltaE_for_substitution(), prepare_for_neighbors_substitution(), reject_change_npd(), and reset_hbs().

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

private

Referenced by acknowledge_neighbors_substitution(), calc_curr_hbond_weights(), commit_change_no_res_pointer_update(), commit_change_npd(), find_curr_hbonds_to_upper_neighbors(), and reset_hbs().

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

private

Referenced by acknowledge_neighbors_substitution(), calc_curr_hbond_weights(), commit_change_no_res_pointer_update(), commit_change_npd(), find_curr_hbonds_to_upper_neighbors(), find_hbs_for_nbrs_alt_state_step2(), get_curr_upper_hbond_energies(), get_npdhb_deltaE_for_substitution(), prepare_for_neighbors_substitution(), and reset_hbs().

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

private

Referenced by find_hbs_for_nbrs_alt_state_step2(), get_curr_upper_hbond_energies(), get_npdhb_deltaE_for_substitution(), and prepare_for_neighbors_substitution().

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

private

Referenced by calc_curr_hbond_weights(), and compute_alt_weights_for_hbonds().

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

private

Referenced by calc_curr_hbond_weights(), and compute_alt_weights_for_hbonds().

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 Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation