#include <MinimizationGraph.hh>

Inheritance diagram for core::scoring::MinimizationEdge:

Public Types
typedef utility::graph::Edge	parent

typedef utility::vector1 < TwoBodyEnergyCOP >	TwoBodyEnergies

typedef TwoBodyEnergies::const_iterator	TwoBodyEnergiesIterator

typedef conformation::Residue	Residue

typedef pose::Pose	Pose

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

	MinimizationEdge (MinimizationGraph *owner, MinimizationEdge const &example_edge)

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

void	copy_from (parent const *source) override
	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 ()

Size	count_static_memory () const override
	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...

Size	count_dynamic_memory () const override
	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...

void	activate_dof_deriv_two_body_method (TwoBodyEnergyCOP enmeth, pose::Pose const &pose)
	Activate a particular two body energy method as part of this edge. Sometimes energy methods defining DOF derivatives have to be evaluated even when the residues defining the interaction are not moving with respect to each other (causing the energy method to be activated when given to the edge in the add_twobody_enmeth function above) because the DOFs that define the interaction spill into a third residue and that third residue's coordinates are changing, causing the DOF to change. 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...

Real	dweight () const

void	dweight (Real setting)

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

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)

void	_activate_2benmeth (TwoBodyEnergyCOP enmeth)

void	_check_sfs_and_sfd_for_2benmeth (TwoBodyEnergyCOP enmeth, Pose const &pose)

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_

Real	dweight_

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.

Member Typedef Documentation

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

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

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

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

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

Constructor & Destructor Documentation

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

Minimization edge ctor.

Referenced by count_static_memory().

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

References copy_from().

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

overridedefault

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

Member Function Documentation

void core::scoring::MinimizationEdge::_activate_2benmeth ( TwoBodyEnergyCOP enmeth )

private

References add_active_enmeth_ext(), and add_active_enmeth_std().

Referenced by activate_dof_deriv_two_body_method(), and classify_twobody_enmeth().

void core::scoring::MinimizationEdge::_check_sfs_and_sfd_for_2benmeth	(	TwoBodyEnergyCOP	enmeth,
		Pose const &	pose
	)

private

References add_sfd_enmeth(), and add_sfs_enmeth().

Referenced by activate_dof_deriv_two_body_method(), and classify_twobody_enmeth().

void core::scoring::MinimizationEdge::activate_dof_deriv_two_body_method	(	TwoBodyEnergyCOP	enmeth,
		pose::Pose const &	pose
	)

Activate a particular two body energy method as part of this edge. Sometimes energy methods defining DOF derivatives have to be evaluated even when the residues defining the interaction are not moving with respect to each other (causing the energy method to be activated when given to the edge in the add_twobody_enmeth function above) because the DOFs that define the interaction spill into a third residue and that third residue's coordinates are changing, causing the DOF to change.

References _activate_2benmeth(), _check_sfs_and_sfd_for_2benmeth(), and active_2benmeths_.

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

References active_2benmeths_.

Referenced by core::scoring::eval_atom_derivatives_for_minedge(), and core::scoring::eval_weighted_atom_derivatives_for_minedge().

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

References active_2benmeths_.

Referenced by core::scoring::eval_atom_derivatives_for_minedge(), and core::scoring::eval_weighted_atom_derivatives_for_minedge().

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

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

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

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

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

References active_2benmeths_, and active_2benmeths_ext_.

Referenced by _activate_2benmeth().

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

private

References active_2benmeths_, and active_2benmeths_std_.

Referenced by _activate_2benmeth().

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

private

References sfd_req_2benmeths_.

Referenced by _check_sfs_and_sfd_for_2benmeth().

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

private

References sfs_req_2benmeths_.

Referenced by _check_sfs_and_sfd_for_2benmeth().

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.

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().

References active_2benmeths_.

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

References _activate_2benmeth(), and _check_sfs_and_sfd_for_2benmeth().

Referenced by add_twobody_enmeth(), and reinitialize_active_energy_methods().

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

override

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

References active_2benmeths_, active_2benmeths_ext_, active_2benmeths_std_, dweight_, 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

override

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.

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

override

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

References MinimizationEdge().

Real core::scoring::MinimizationEdge::dweight ( ) const

inline

References dweight_.

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

void core::scoring::MinimizationEdge::dweight ( Real setting )

inline

References dweight_.

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

inlineprotected

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

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

inlineprotected

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

inlineprotected

Downcasts.

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

inlineprotected

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.

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

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

inline

References res_pair_min_data_.

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

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

inline

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.

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

Referenced by core::scoring::ScoreFunction::asym_setup_for_derivatives(), core::pack::scmin::SCMinMultifunc::dfunc(), core::pack::scmin::CartSCMinMultifunc::dfunc(), and core::scoring::ScoreFunction::sym_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
	)