#include <MinimizationGraph.hh>

Inheritance diagram for core::scoring::MinimizationEdge:

Collaboration diagram for core::scoring::MinimizationEdge:

Public Types
typedef graph::Edge	parent

typedef utility::vector1 < TwoBodyEnergyCOP >	TwoBodyEnergies

typedef TwoBodyEnergies::const_iterator	TwoBodyEnergiesIterator

typedef conformation::Residue	Residue

typedef pose::Pose	Pose

Public Types inherited from core::graph::Edge
typedef EdgeListIterator	EdgeListIter

Public Member Functions
	MinimizationEdge (MinimizationGraph *owner, Size n1, Size n2)
	Minimization edge ctor. More...

	MinimizationEdge (MinimizationGraph *owner, MinimizationEdge const &example_edge)

virtual	~MinimizationEdge ()
	virtual dstor; The MinimizationEdge must free the array pool element it holds before it disappears. More...

virtual void	copy_from (parent const *source)
	Copy the data held on the example edge, source. The source edge must be castable to class MinimizationEdge. More...

ResPairMinimizationData const &	res_pair_min_data () const

ResPairMinimizationData &	res_pair_min_data ()

virtual Size	count_static_memory () const
	virtual call to determine the static size of an Edge object dynamic memory use is counted through the recursive count_dynamic_memory() calling path More...

virtual Size	count_dynamic_memory () const
	virtual call to determine the amount of dynamic memory allocated by an edge; this function must recurse to the parent class to determine how much memory the parent class is responsible for. Do not account for the size of the ArrayPool array here; instead, that is accounted for in the MinimizationGraph::count_dynamic_memory method. More...

bool	add_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd1, Residue const &rsd2, Pose const &pose, bool residues_mwrt_eachother)
	Include a particular energy method as part of this edge. It may not show up in the active energy methods should this energy method not define an energy for the residues. More...

bool	any_active_enmeths () const
	It may be possible to determine that an edge does not need to belong to the minimization graph if there are no active two-body energy methods; this is a convenience function that answers quickly if active_2benmths_.begin() == active_2benmeths_.end(). More...

void	setup_for_minimizing (Residue const &rsd1, Residue const &rsd2, pose::Pose const &pose, ScoreFunction const &sfxn, kinematics::MinimizerMapBase const &min_map)

void	setup_for_scoring (Residue const &rsd1, Residue const &rsd2, Pose const &pose, ScoreFunction const &sfxn)
	Initialize the active energy methods for score function evaluation. More...

void	setup_for_derivatives (Residue const &rsd1, Residue const &rsd2, Pose const &pose, ScoreFunction const &sfxn)
	Initialize the active energy methods for derivative evaluation. More...

void	reinitialize_active_energy_methods (Residue const &rsd1, Residue const &rsd2, Pose const &pose, bool res_moving_wrt_eachother)
	Setup the active and inactive energy methods. More...

TwoBodyEnergiesIterator	active_2benmeths_begin () const

TwoBodyEnergiesIterator	active_2benmeths_end () const

TwoBodyEnergiesIterator	active_2benmeths_std_begin () const

TwoBodyEnergiesIterator	active_2benmeths_std_end () const

TwoBodyEnergiesIterator	active_2benmeths_ext_begin () const

TwoBodyEnergiesIterator	active_2benmeths_ext_end () const

TwoBodyEnergiesIterator	sfs_req_2benmeths_begin () const

TwoBodyEnergiesIterator	sfs_req_2benmeths_end () const

TwoBodyEnergiesIterator	sfd_req_2benmeths_begin () const

TwoBodyEnergiesIterator	sfd_req_2benmeths_end () const

Real	weight () const
	The minimization graph will allow the storage of edge weights, should that prove useful for any application (e.g. symmetric minimization) More...

void	weight (Real setting)
	Set the weight for an edge. More...

Public Member Functions inherited from core::graph::Edge
virtual	~Edge ()
	destructor More...

	Edge (Graph *owner, platform::Size first_node_ind, platform::Size second_node_ind)
	Main edge constructor. This should only be invoked by create_new_edge, which itself is only called by add_edge. The ONLY way an edge should be added to a graph is through add_edge. NOTE: edges should be only be deleted by a call to the Graph's delete_edge method, and this method absolutely must be implemented by derived Graph classes. More...

platform::Size	get_other_ind (platform::Size node_index) const
	returns the index of the one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node const *	get_other_node (platform::Size node_index) const
	returns a const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

Node *	get_other_node (platform::Size node_index)
	returns a non-const pointer to one node given the index of the other. node_index must be one of the two nodes that this edge is incident upon. More...

platform::Size	get_first_node_ind () const
	returns the index of the lower node More...

platform::Size	get_second_node_ind () const
	returns the index of the upper node More...

void	set_pos_in_owners_list (EdgeListIter edge_iterator)
	called only by class Graph, this function gives the Edge the data it needs to later delete itself from its owner's edge list in constant time. More...

bool	same_edge (platform::Size node1, platform::Size node2) const
	Is this the same edge as another edge (node1,node2)? Note: this graph does not work for multi-graphs. Edges must be unique. More...

bool	is_loop () const
	Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. More...

Public Attributes
	__pad0__:TwoBodyEnergyCOP TwoBodyEnergyCOP

Protected Member Functions
MinimizationGraph const *	get_minimization_owner () const
	Downcasts. More...

MinimizationGraph *	get_minimization_owner ()

MinimizationNode *	get_minimization_node (Size index)

MinimizationNode const *	get_minimization_node (Size index) const

Protected Member Functions inherited from core::graph::Edge
platform::Size	get_node_index (platform::Size index) const
	get the node index for one of the two nodes this edge is incident upon uses c-style index-from-0. More...

Node const *	get_node (platform::Size index) const
	get a const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Node *	get_node (platform::Size index)
	get a non-const * to one node that this edge is incident upon uses c-style index-from-0 for these two nodes More...

Graph const *	get_owner () const
	get a const * to the owning graph More...

Graph *	get_owner ()
	get a non-const * to the owning graph More...

Private Member Functions
void	add_active_enmeth_std (TwoBodyEnergyCOP enmeth)

void	add_active_enmeth_ext (TwoBodyEnergyCOP enmeth)

void	add_sfs_enmeth (TwoBodyEnergyCOP enmeth)

void	add_sfd_enmeth (TwoBodyEnergyCOP enmeth)

bool	classify_twobody_enmeth (TwoBodyEnergyCOP enmeth, Residue const &rsd1, Residue const &rsd2, Pose const &pose, bool res_moving_wrt_eachother)

Private Attributes
ResPairMinimizationData	res_pair_min_data_

TwoBodyEnergies	twobody_enmeths_

TwoBodyEnergies	active_2benmeths_

TwoBodyEnergies	active_2benmeths_std_

TwoBodyEnergies	active_2benmeths_ext_

TwoBodyEnergies	sfs_req_2benmeths_

TwoBodyEnergies	sfd_req_2benmeths_

Real	weight_

Detailed Description

Class MinimizationEdge holds ResPairMinimizationData for a certain pair of interacting residues; this data might be a neighborlist for this residue pair, for example. The data held in this edge will be used in both scoring the residue-pair energies and evaluating atom derivatives during minimization.

Definition at line 212 of file MinimizationGraph.hh.

Member Typedef Documentation

typedef graph::Edge core::scoring::MinimizationEdge::parent

Definition at line 215 of file MinimizationGraph.hh.

typedef pose::Pose core::scoring::MinimizationEdge::Pose

Definition at line 220 of file MinimizationGraph.hh.

typedef conformation::Residue core::scoring::MinimizationEdge::Residue

Definition at line 219 of file MinimizationGraph.hh.

typedef utility::vector1< TwoBodyEnergyCOP > core::scoring::MinimizationEdge::TwoBodyEnergies

Definition at line 217 of file MinimizationGraph.hh.

typedef TwoBodyEnergies::const_iterator core::scoring::MinimizationEdge::TwoBodyEnergiesIterator

Definition at line 218 of file MinimizationGraph.hh.

Constructor & Destructor Documentation

core::scoring::MinimizationEdge::MinimizationEdge	(	MinimizationGraph *	owner,
		Size	n1,
		Size	n2
	)

Minimization edge ctor.

Definition at line 415 of file MinimizationGraph.cc.

Referenced by count_static_memory().

core::scoring::MinimizationEdge::MinimizationEdge	(	MinimizationGraph *	owner,
		MinimizationEdge const &	example_edge
	)

Definition at line 424 of file MinimizationGraph.cc.

References copy_from().

core::scoring::MinimizationEdge::~MinimizationEdge ( )

virtual

virtual dstor; The MinimizationEdge must free the array pool element it holds before it disappears.

Definition at line 437 of file MinimizationGraph.cc.

Member Function Documentation

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_begin ( ) const

Definition at line 600 of file MinimizationGraph.cc.

References active_2benmeths_.

Referenced by core::scoring::eval_atom_derivatives_for_minedge().

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_end ( ) const

Definition at line 605 of file MinimizationGraph.cc.

References active_2benmeths_.

Referenced by core::scoring::eval_atom_derivatives_for_minedge().

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_ext_begin ( ) const

Definition at line 621 of file MinimizationGraph.cc.

References active_2benmeths_ext_.

Referenced by core::scoring::eval_res_pair_energy_for_minedge(), and core::scoring::eval_weighted_res_pair_energy_for_minedge().

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_ext_end ( ) const

Definition at line 626 of file MinimizationGraph.cc.

References active_2benmeths_ext_.

Referenced by core::scoring::eval_res_pair_energy_for_minedge(), and core::scoring::eval_weighted_res_pair_energy_for_minedge().

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_std_begin ( ) const

Definition at line 610 of file MinimizationGraph.cc.

References active_2benmeths_std_.

Referenced by core::scoring::eval_res_pair_energy_for_minedge(), and core::scoring::eval_weighted_res_pair_energy_for_minedge().

MinimizationEdge::TwoBodyEnergiesIterator core::scoring::MinimizationEdge::active_2benmeths_std_end ( ) const

Definition at line 615 of file MinimizationGraph.cc.

References active_2benmeths_std_.

Referenced by core::scoring::eval_res_pair_energy_for_minedge(), and core::scoring::eval_weighted_res_pair_energy_for_minedge().

void core::scoring::MinimizationEdge::add_active_enmeth_ext ( TwoBodyEnergyCOP enmeth)

private

Definition at line 568 of file MinimizationGraph.cc.

References active_2benmeths_, and active_2benmeths_ext_.

Referenced by classify_twobody_enmeth().

void core::scoring::MinimizationEdge::add_active_enmeth_std ( TwoBodyEnergyCOP enmeth)

private

Definition at line 567 of file MinimizationGraph.cc.

References active_2benmeths_, and active_2benmeths_std_.

Referenced by classify_twobody_enmeth().

void core::scoring::MinimizationEdge::add_sfd_enmeth ( TwoBodyEnergyCOP enmeth)

private

Definition at line 570 of file MinimizationGraph.cc.

References sfd_req_2benmeths_.

Referenced by classify_twobody_enmeth().

void core::scoring::MinimizationEdge::add_sfs_enmeth ( TwoBodyEnergyCOP enmeth)

private

Definition at line 569 of file MinimizationGraph.cc.

References sfs_req_2benmeths_.

Referenced by classify_twobody_enmeth().

bool core::scoring::MinimizationEdge::add_twobody_enmeth	(	TwoBodyEnergyCOP	enmeth,
		Residue const &	rsd1,
		Residue const &	rsd2,
		pose::Pose const &	pose,
		bool	residues_mwrt_eachother
	)

Include a particular energy method as part of this edge. It may not show up in the active energy methods should this energy method not define an energy for the residues.

Definition at line 482 of file MinimizationGraph.cc.

References classify_twobody_enmeth(), and twobody_enmeths_.

Referenced by core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(), and core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge().

bool core::scoring::MinimizationEdge::any_active_enmeths ( ) const

inline

It may be possible to determine that an edge does not need to belong to the minimization graph if there are no active two-body energy methods; this is a convenience function that answers quickly if active_2benmths_.begin() == active_2benmeths_.end().

Definition at line 245 of file MinimizationGraph.hh.

References active_2benmeths_.

Referenced by core::scoring::symmetry::SymmetricScoreFunction::setup_for_minimizing(), and core::scoring::ScoreFunction::setup_for_minimizing().

bool core::scoring::MinimizationEdge::classify_twobody_enmeth	(	TwoBodyEnergyCOP	enmeth,
		Residue const &	rsd1,
		Residue const &	rsd2,
		pose::Pose const &	pose,
		bool	res_moving_wrt_eachother
	)

private

Definition at line 572 of file MinimizationGraph.cc.

References add_active_enmeth_ext(), add_active_enmeth_std(), add_sfd_enmeth(), and add_sfs_enmeth().

Referenced by add_twobody_enmeth(), and reinitialize_active_energy_methods().

void core::scoring::MinimizationEdge::copy_from ( parent const * source)

virtual

Copy the data held on the example edge, source. The source edge must be castable to class MinimizationEdge.

copies data from MinimizationEdge const * source;

called from the copy ctor and operator= methods defined in the Graph base class

Reimplemented from core::graph::Edge.

Definition at line 444 of file MinimizationGraph.cc.

References active_2benmeths_, active_2benmeths_ext_, active_2benmeths_std_, res_pair_min_data_, sfd_req_2benmeths_, sfs_req_2benmeths_, twobody_enmeths_, and weight_.

Referenced by MinimizationEdge().

Size core::scoring::MinimizationEdge::count_dynamic_memory ( ) const

virtual

virtual call to determine the amount of dynamic memory allocated by an edge; this function must recurse to the parent class to determine how much memory the parent class is responsible for. Do not account for the size of the ArrayPool array here; instead, that is accounted for in the MinimizationGraph::count_dynamic_memory method.

Reimplemented from core::graph::Edge.

Definition at line 474 of file MinimizationGraph.cc.

References core::graph::Edge::count_dynamic_memory().

Size core::scoring::MinimizationEdge::count_static_memory ( ) const

virtual

virtual call to determine the static size of an Edge object dynamic memory use is counted through the recursive count_dynamic_memory() calling path

Reimplemented from core::graph::Edge.

Definition at line 464 of file MinimizationGraph.cc.

References MinimizationEdge().

MinimizationNode* core::scoring::MinimizationEdge::get_minimization_node ( Size index)

inlineprotected

Definition at line 317 of file MinimizationGraph.hh.

References core::graph::Edge::get_node().

Referenced by setup_for_derivatives(), setup_for_minimizing(), and setup_for_scoring().

MinimizationNode const* core::scoring::MinimizationEdge::get_minimization_node ( Size index) const

inlineprotected

Definition at line 323 of file MinimizationGraph.hh.

References core::graph::Edge::get_node().

MinimizationGraph const * core::scoring::MinimizationEdge::get_minimization_owner ( ) const

inlineprotected

Downcasts.

Definition at line 417 of file MinimizationGraph.hh.

References core::graph::Edge::get_owner().

MinimizationGraph * core::scoring::MinimizationEdge::get_minimization_owner ( )

inlineprotected

Definition at line 423 of file MinimizationGraph.hh.

References core::graph::Edge::get_owner().

void core::scoring::MinimizationEdge::reinitialize_active_energy_methods	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Pose const &	pose,
		bool	res_moving_wrt_eachother
	)

Setup the active and inactive energy methods.

Definition at line 548 of file MinimizationGraph.cc.

References active_2benmeths_, active_2benmeths_ext_, active_2benmeths_std_, classify_twobody_enmeth(), sfd_req_2benmeths_, sfs_req_2benmeths_, and twobody_enmeths_.

Referenced by core::pack::reinitialize_mingraph_neighborhood_for_residue(), and core::pack::RTMin::rtmin().

ResPairMinimizationData const& core::scoring::MinimizationEdge::res_pair_min_data ( ) const

inline

Definition at line 231 of file MinimizationGraph.hh.

References res_pair_min_data_.

Referenced by core::scoring::eval_atom_derivatives_for_minedge(), core::scoring::eval_res_pair_energy_for_minedge(), and core::scoring::eval_weighted_res_pair_energy_for_minedge().

ResPairMinimizationData& core::scoring::MinimizationEdge::res_pair_min_data ( )

inline

Definition at line 232 of file MinimizationGraph.hh.

References res_pair_min_data_.

void core::scoring::MinimizationEdge::setup_for_derivatives	(	Residue const &	rsd1,
		Residue const &	rsd2,
		Pose const &	pose,
		ScoreFunction const &	sfxn
	)

Initialize the active energy methods for derivative evaluation.

Definition at line 530 of file MinimizationGraph.cc.

References get_minimization_node(), res_pair_min_data_, sfd_req_2benmeths_begin(), and sfd_req_2benmeths_end().

Referenced by core::pack::scmin::CartSCMinMultifunc::dfunc(), core::pack::scmin::SCMinMultifunc::dfunc(), core::scoring::symmetry::SymmetricScoreFunction::setup_for_derivatives(), and core::scoring::ScoreFunction::setup_for_derivatives().

void core::scoring::MinimizationEdge::setup_for_minimizing	(	Residue const &	rsd1,
		Residue const &	rsd2,
		pose::Pose const &	pose,
		ScoreFunction const &	sfxn,
		kinematics::MinimizerMapBase const &	min_map
	)