Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...

#include <HPatchInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >:

[legend]

Public Types
typedef BackgroundNode< V, E, G >	parent

Public Types inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeListIter

typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeList

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeVector

typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >::iterator	BackgroundEdgeVectorIter

typedef std::vector < FirstClassNode< V, E, G > * >	FirstClassNodeVector

Public Member Functions
	HPatchBackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
	main constructor. No default constructor, copy constructor or assignment operator More...

	~HPatchBackgroundNode () override

void	set_rotamer (conformation::ResidueOP const &rotamer)
	inits the RotamerOP held by a background node. called in the HPatchIG::initialize method. More...

conformation::ResidueCOP	get_rotamer () const
	returns a const reference to the ResidueOP object held by this background Node. needed by the initialize_bg_bg_overlap call in this class so that one BGNode can get at the residue/rotamer information on another BGNode instance. More...

void	set_rotamer_dots (RotamerDots const &bg_rd)
	inits the RotamerDots object held by a background node. called in the HPatchIG::initialize method. More...

bool	detect_overlap (HPatchNode< V, E, G > *node) const
	returns true if this background residue overlaps with any atom on any rotamer of a HPatchNode. More...

void	prepare_for_simulated_annealing () override
	detects self overlap and asks its incident HPatchBackgroundEdges to compute and cache the overlaps of this residue with all states on the neighboring HPatchNode. More...

void	initialize_bg_bg_overlap (HPatchBackgroundNode< V, E, G > &other)
	stores the sphere overlap for a pair of background nodes More...

Real	update_state_for_substitution (HPatchNode< V, E, G > *fc_node_changing, RotamerDotsCache const &nodes_curr_overlap_with_bg_res, RotamerDotsCache const &nodes_alt_overlap_with_bg_res)
	returns the change in sasa induced by a HPatchNode undergoing a state substitution. The overlap between the HPatchNode and this HPatchBackgroundNode has been precomputed and stored in the HPatchBackgroundEdge that connects them. There is little work to do in this subroutine. More...

void	reset_alt_state_dots ()
	Sets the alt state dots to the current state dots. See comments in HIG and commit_considered_substitution for more information about why this method exists. More...

void	acknowledge_substitution ()
	bookkeeping to reflect a HPatchNode's state substitution. uses the RotamerDots class method operator=. More...

Real	get_current_sasa () const
	returns the total SASA under the current state assignment More...

Real	get_current_sasa (Size atom_index) const
	Returns the current state SASA for the passed in atom index. More...

Real	get_alternate_sasa () const
	returns the total SASA under the alternate state assignment More...

Real	get_alternate_sasa (Size atom_index) const
	Returns the alternate state SASA for the passed in atom index. More...

utility::vector1 < utility::vector1< bool > > const &	get_atom_atom_self_overlaps () const
	Returns a const reference to the atom x atom pair vector of vectors of bools that specifies which atoms are overlapping. More...

utility::vector1< Size > const &	get_hphobes () const

Size	n_hphobes () const

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override
	Returns an int representing the amount of memory in bytes used by this node. More...

void	print () const override
	used only for debugging More...

RotamerDots const &	get_current_state_rotamer_dots ()
	Returns current state. Only used by the unit tests. More...

RotamerDots const &	get_alt_state_rotamer_dots ()
	Returns current state. Only used by the unit tests. More...

InvRotamerDots const &	curr_state_inv_dots () const

InvRotamerDots const &	alt_state_inv_dots () const

utility::vector1< Size > const &	curr_state_exp_hphobes () const

utility::vector1< Size > const &	alt_state_exp_hphobes () const

Size	n_curr_state_exp_hphobes () const

Size	n_alt_state_exp_hphobes () const

Public Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
virtual	~BackgroundNode ()
	BackgroundNode destructor. More...

	BackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
	BackgroundNode constructor - no default or copy constructors; no operator =. More...

BackgroundEdgeListIter	add_edge (BackgroundToFirstClassEdge< V, E, G > *edge_ptr)
	Adds a BackgroundToFirstClassEdge to the edge list for this node. Returns an iterator to the new list element. More...

void	drop_edge (BackgroundEdgeListIter edge)
	removes an edge from the nodes edge list in constant time More...

BackgroundToFirstClassEdge< V, E, G > *	find_edge (int fc_node_index)
	Linear time edge lookup function. More...

Protected Member Functions
HPatchBackgroundEdge< V, E, G > *	get_hpatch_bg_edge (int index)

HPatchInteractionGraph< V, E, G > *	get_hpatch_owner () const

Protected Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G >
void	update_edge_vector ()
	Syncs the edge vector with the edge list. More...

int	get_node_index () const

int	get_num_incident_edges () const

BackgroundToFirstClassEdge< V, E, G > *	get_incident_edge (int index) const

int	get_index_of_adjacent_first_class_node (int index) const

FirstClassNode< V, E, G > *	get_adjacent_first_class_node (int index) const

bool	get_edge_vector_up_to_date () const

AdditionalBackgroundNodesInteractionGraph < V, E, G > *	get_owner () const

Private Member Functions
void	update_alt_state_exphphobes ()
	Updates the vector alt_state_exp_hphobes_ with the atom id (??) of the exposed hydrophobic atoms in this residue. More...

void	initialize_self_overlap ()
	initializes the self overlap for its RotamerDots object More...

void	initialize_atom_atom_overlaps ()
	initializes the atom-atom overlap vector stored by this background node. called once during prep_for_simA. More...

	HPatchBackgroundNode ()

	HPatchBackgroundNode (HPatchBackgroundNode< V, E, G > const &)

HPatchBackgroundNode< V, E, G > &	operator= (HPatchBackgroundNode< V, E, G > const &)

Private Attributes
conformation::ResidueOP	rotamer_

utility::vector1< Size >	hphobe_ats_

Size	n_hphobes_

bool	prepared_for_simA_

RotamerDots	current_state_rotamer_dots_

RotamerDots	alt_state_rotamer_dots_

InvRotamerDots	curr_state_inv_dots_

InvRotamerDots	alt_state_inv_dots_

utility::vector1< Size >	curr_state_exp_hphobes_

utility::vector1< Size >	alt_state_exp_hphobes_

bool	alt_state_dots_matches_current_state_dots_

utility::vector1 < utility::vector1< bool > >	self_atom_atom_overlaps_

Detailed Description

template<typename V, typename E, typename G>
class core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >

Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef BackgroundNode< V, E, G > core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::HPatchBackgroundNode	(	AdditionalBackgroundNodesInteractionGraph< V, E, G > *	owner,
		int	node_index
	)

main constructor. No default constructor, copy constructor or assignment operator

template<typename V , typename E , typename G >

core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::~HPatchBackgroundNode ( )

override

template<typename V, typename E, typename G>

core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::HPatchBackgroundNode ( )

private

template<typename V, typename E, typename G>

core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::HPatchBackgroundNode ( HPatchBackgroundNode< V, E, G > const & )

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::acknowledge_substitution ( )

bookkeeping to reflect a HPatchNode's state substitution. uses the RotamerDots class method operator=.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_exp_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_exp_hphobes_.

template<typename V, typename E, typename G>

InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_inv_dots ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_inv_dots_, core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_rotamer_dots_, core::pack::interaction_graph::RotamerDots::rotamer(), and core::pack::interaction_graph::InvRotamerDots::rotamer().

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_dynamic_memory ( ) const

overridevirtual

Returns an int representing the amount of memory in bytes used by this node.

Remarks: ronj lists consume more memory because they maintain pointers to the previous and next nodes ronj current calculation uses 4 * # elements in list * sizeof(pointer), but I think this is wrong ronj isn't it only 3 * # elements in list * sizeof(pointer)?

Parameters

total_memory - [out] - the amount of memory used by this node

Reimplemented from core::pack::interaction_graph::BackgroundNode< V, E, G >.

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_static_memory ( ) const

overridevirtual

Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_exp_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_exp_hphobes_.

template<typename V, typename E, typename G>

InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_rotamer_dots_, core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots_, core::pack::interaction_graph::RotamerDots::rotamer(), and core::pack::interaction_graph::InvRotamerDots::rotamer().

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::detect_overlap ( HPatchNode< V, E, G > * node ) const

returns true if this background residue overlaps with any atom on any rotamer of a HPatchNode.

Uses the HPatchNode function detect_any_overlap_with_rotamer. It calls the function on the passed in HPatchNode with the RotamerDots object this BGNode keeps in current_state_rotamer_dots_.

References core::pack::interaction_graph::HPatchNode< V, E, G >::detect_any_overlap_with_rotamer().

template<typename V , typename E , typename G >

RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alt_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alternate_sasa ( ) const

returns the total SASA under the alternate state assignment

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alternate_sasa ( Size atom_index ) const

Returns the alternate state SASA for the passed in atom index.

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_atom_atom_self_overlaps ( ) const

Returns a const reference to the atom x atom pair vector of vectors of bools that specifies which atoms are overlapping.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_sasa ( ) const

returns the total SASA under the current state assignment

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_sasa ( Size atom_index ) const

Returns the current state SASA for the passed in atom index.

template<typename V , typename E , typename G >

RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

template<typename V, typename E, typename G>

HPatchBackgroundEdge< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_bg_edge ( int index )

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_incident_edge().

template<typename V, typename E, typename G>

HPatchInteractionGraph< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_owner ( ) const

inlineprotected

References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_owner().

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::hphobe_ats_.

template<typename V , typename E , typename G >

conformation::ResidueCOP core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_rotamer ( ) const

returns a const reference to the ResidueOP object held by this background Node. needed by the initialize_bg_bg_overlap call in this class so that one BGNode can get at the residue/rotamer information on another BGNode instance.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_atom_atom_overlaps ( )

private

initializes the atom-atom overlap vector stored by this background node. called once during prep_for_simA.

References core::kinematics::tree::distance_squared(), and core::scoring::sasa::get_legrand_atomic_overlap().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_bg_bg_overlap ( HPatchBackgroundNode< V, E, G > & other )

stores the sphere overlap for a pair of background nodes

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::current_state_rotamer_dots_.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_self_overlap ( )

private

initializes the self overlap for its RotamerDots object

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_alt_state_exp_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_exp_hphobes_.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_curr_state_exp_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_exp_hphobes_.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_hphobes ( ) const

inline

References core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_hphobes_.

template<typename V, typename E, typename G>

HPatchBackgroundNode< V, E, G >& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::operator= ( HPatchBackgroundNode< V, E, G > const & )

private

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::prepare_for_simulated_annealing ( )

overridevirtual

detects self overlap and asks its incident HPatchBackgroundEdges to compute and cache the overlaps of this residue with all states on the neighboring HPatchNode.

if we've already gone through this method once, then don't update the parent classes edge vectors. but we do need to reinitialize the self overlap on the BGNode as well as the overlap caused by all other bg nodes.

Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::print ( ) const

overridevirtual

used only for debugging

Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.

References core::pack::interaction_graph::TR_BGNODE().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::reset_alt_state_dots ( )

Sets the alt state dots to the current state dots. See comments in HIG and commit_considered_substitution for more information about why this method exists.

References core::pack::interaction_graph::TR_BGNODE().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer ( conformation::ResidueOP const & rotamer )

inits the RotamerOP held by a background node. called in the HPatchIG::initialize method.

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::element(), and core::chemical::ResidueType::nheavyatoms().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer_dots ( RotamerDots const & bg_rd )

inits the RotamerDots object held by a background node. called in the HPatchIG::initialize method.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::update_alt_state_exphphobes ( )

private

Updates the vector alt_state_exp_hphobes_ with the atom id (??) of the exposed hydrophobic atoms in this residue.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::update_state_for_substitution	(	HPatchNode< V, E, G > *	fc_node_changing,
		RotamerDotsCache const &	nodes_curr_overlap_with_bg_res,
		RotamerDotsCache const &	nodes_alt_overlap_with_bg_res
	)

returns the change in sasa induced by a HPatchNode undergoing a state substitution. The overlap between the HPatchNode and this HPatchBackgroundNode has been precomputed and stored in the HPatchBackgroundEdge that connects them. There is little work to do in this subroutine.

References core::pack::interaction_graph::TR_BGNODE(), and core::pack::interaction_graph::HPatchNode< V, E, G >::wt_seqpos_for_node().