#include <ResidueArrayAnnealingEvaluator.hh>

Inheritance diagram for core::pack::interaction_graph::ResidueArrayAnnealingEvaluator:

Public Member Functions
	ResidueArrayAnnealingEvaluator ()
	Constructor. More...

	~ResidueArrayAnnealingEvaluator () override
	Destructor. More...

	ResidueArrayAnnealingEvaluator (ResidueArrayAnnealingEvaluator const &src)
	Copy constructor. More...

void	initialize (core::scoring::ScoreFunction const &score_function, core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets &rotamer_sets, utility::graph::GraphCOP)

int	get_num_nodes () const override
	Get the number of nodes. More...

int	get_num_states_for_node (int node) const override
	Get the number of states for a specific node. More...

int	get_num_total_states () const override
	Get the total number of states for all nodes. More...

void	prepare_graph_for_simulated_annealing () override
	Utility signal. More...

void	blanket_assign_state_0 () override
	State initialization: set all nodes to state zero. More...

bool	any_vertex_state_unassigned () const override
	Are there any nodes unassigned? More...

core::PackerEnergy	set_state_for_node (int node_ind, int new_state) override
	Explicit state modification: set a particular node to a particular state. More...

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override
	Set states for all nodes across the network. More...

void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override
	Consider setting a particular node to a particular state. More...

core::PackerEnergy	commit_considered_substitution () override
	Set the node that we were considering to the state that we were considering (i.e. commit the change). More...

core::PackerEnergy	get_energy_current_state_assignment () override
	Get the energy fo the current state. More...

void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override
	Set error threshold. More...

virtual bool	has_methods ()
	Do any energy methods have a nonzero weight? More...

void	clean_up_after_packing (core::pose::Pose &pose) override
	Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More...

Public Member Functions inherited from core::pack::interaction_graph::AnnealableGraphBase
	AnnealableGraphBase ()
	Constructor. More...

	AnnealableGraphBase (AnnealableGraphBase const &src)
	Copy constructor. More...

	~AnnealableGraphBase () override
	Destructor. More...

Private Types
typedef std::pair< core::PackerEnergy, core::scoring::annealing::ResidueArrayAnnealableEnergyOP >	WeightedMethodPair

Private Member Functions
core::Real	calculate_weighted_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &current_rotamer_ids, int const substitution_position=0)
	Calculate the energy given the vector of residue owning pointers. More...

void	initialize_symmetry_info (core::pose::Pose const &pose)
	Initialize symmetry information. More...

void	set_consideration (int const node_ind, int const node_resid, int const new_state, utility::vector1< std::pair< int, core::conformation::ResidueCOP > > &unset_info)
	Sets the current consideration. More...

void	unset_consideration (utility::vector1< std::pair< int, core::conformation::ResidueCOP > > const &unset_info)
	Clears the current consideration. More...

void	clear_consideration ()
	Abandon the substitution that was being considered. More...

Private Attributes
std::list< WeightedMethodPair >	weighted_energy_methods_
	List of energy methods and their weights. More...

utility::vector1< core::conformation::ResidueCOP >	source_pose_residues_
	Const-owning pointers to the residues of the source pose. More...

utility::vector1< core::conformation::ResidueCOP >	current_residues_
	Const-owning pointers to the current residues. More...

utility::vector1< core::Size >	current_rotamer_ids_
	holds the current rotamers ids, should always be in sync with current_residues_ More...

core::PackerEnergy	current_energy_
	Current energy. More...

int	considered_node_
	The node being considered for alteration. More...

int	considered_state_
	The state that we're considering changing this node TO. More...

core::PackerEnergy	considered_energy_
	The energy that would result from the considered substitution. More...

utility::vector1< core::pack::rotamer_set::RotamerSetCOP >	per_node_rotamer_sets_
	The rotamer sets for each node (vector of const-owning pointers to RotamerSet objects. More...

bool	is_symmetric_
	Is this a symmetric packing job? More...

bool	has_mirror_symm_
	Is this a symmetric packing job with mirror symmetry? More...

core::Size	num_indep_nodes_
	Number of independent nodes (not symmetry copies). More...

std::map< int, utility::vector1< core::Size > >	dependent_node_map_
	Map of dependent nodes. More...

std::map< int, utility::vector1< core::Size > >	dependent_residue_map_
	Map of dependent residues. More...

Member Typedef Documentation

◆ WeightedMethodPair

typedef std::pair< core::PackerEnergy, core::scoring::annealing::ResidueArrayAnnealableEnergyOP > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::WeightedMethodPair

private

Constructor & Destructor Documentation

◆ ResidueArrayAnnealingEvaluator() [1/2]

core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::ResidueArrayAnnealingEvaluator ( )

Constructor.

References considered_energy_, and current_energy_.

◆ ~ResidueArrayAnnealingEvaluator()

core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::~ResidueArrayAnnealingEvaluator ( )

overridedefault

Destructor.

◆ ResidueArrayAnnealingEvaluator() [2/2]

core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::ResidueArrayAnnealingEvaluator ( ResidueArrayAnnealingEvaluator const & src )

Copy constructor.

References considered_energy_, and current_energy_.

Member Function Documentation

◆ any_vertex_state_unassigned()

bool core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::any_vertex_state_unassigned ( ) const

overridevirtual

Are there any nodes unassigned?

Implements core::pack::interaction_graph::AnnealableGraphBase.

References current_residues_, get_num_nodes(), per_node_rotamer_sets_, and source_pose_residues_.

◆ blanket_assign_state_0()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::blanket_assign_state_0 ( )

overridevirtual

State initialization: set all nodes to state zero.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References calculate_weighted_energy(), clear_consideration(), current_energy_, current_residues_, current_rotamer_ids_, and source_pose_residues_.

Referenced by initialize().

◆ calculate_weighted_energy()

core::Real core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::calculate_weighted_energy	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::Size > const &	current_rotamer_ids,
		int const	substitution_position = `0`
	)

private

Calculate the energy given the vector of residue owning pointers.

Parameters

[in]	resvect	1-vector of const-owning pointers to Residue objects representing current state
[in]	vector	of rotamer state assignments per resid (same dimension as first parameter)

References weighted_energy_methods_.

Referenced by blanket_assign_state_0(), consider_substitution(), set_network_state(), and set_state_for_node().

◆ clean_up_after_packing()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::clean_up_after_packing ( core::pose::Pose & pose )

overridevirtual

Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing.

This version calls the clean_up_residuearrayannealableenergy_after_packing() function in the associated energy methods.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Reimplemented from core::pack::interaction_graph::AnnealableGraphBase.

References weighted_energy_methods_.

◆ clear_consideration()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::clear_consideration ( )

private

Abandon the substitution that was being considered.

References considered_energy_, considered_node_, considered_state_, and current_energy_.

Referenced by blanket_assign_state_0(), set_network_state(), and set_state_for_node().

◆ commit_considered_substitution()

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::commit_considered_substitution ( )

overridevirtual

Set the node that we were considering to the state that we were considering (i.e. commit the change).

Implements core::pack::interaction_graph::AnnealableGraphBase.

References considered_energy_, considered_node_, considered_state_, current_energy_, per_node_rotamer_sets_, set_consideration(), and weighted_energy_methods_.

◆ consider_substitution()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

overridevirtual

Consider setting a particular node to a particular state.

Parameters

[in]	node_ind	Index of the node to be potentially modified.
[in]	new_state	Index of the state that we might set this node to.
[out]	delta_energy	The change in energy that would result from the substitution, returned by this function.
[out]	prev_energy_for_node	The previous energy for this node, prior to the substitution, returned by this function.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References calculate_weighted_energy(), considered_energy_, considered_node_, considered_state_, current_energy_, current_residues_, current_rotamer_ids_, per_node_rotamer_sets_, set_consideration(), and unset_consideration().

◆ get_energy_current_state_assignment()

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::get_energy_current_state_assignment ( )

overridevirtual

Get the energy fo the current state.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References current_energy_.

◆ get_num_nodes()

int core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::get_num_nodes ( ) const

overridevirtual

Get the number of nodes.

This lies a little bit. It only returns the number of independent nodes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References num_indep_nodes_.

Referenced by any_vertex_state_unassigned(), and set_network_state().

◆ get_num_states_for_node()

int core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::get_num_states_for_node ( int n ) const

overridevirtual

Get the number of states for a specific node.

Parameters

[in] node Index of the node.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References per_node_rotamer_sets_.

◆ get_num_total_states()

int core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::get_num_total_states ( ) const

overridevirtual

Get the total number of states for all nodes.

This lies a little bit. It only returns the total number of states for the independent nodes.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References num_indep_nodes_, and per_node_rotamer_sets_.

◆ has_methods()

virtual bool core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::has_methods ( )

inlinevirtual

Do any energy methods have a nonzero weight?

References weighted_energy_methods_.

◆ initialize()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize	(	core::scoring::ScoreFunction const &	score_function,
		core::pose::Pose &	pose,
		core::pack::rotamer_set::RotamerSets &	rotamer_sets,
		utility::graph::GraphCOP
	)

References blanket_assign_state_0(), foreach_, core::conformation::Residue::get_self_ptr(), core::scoring::ScoreFunction::get_weight(), initialize_symmetry_info(), core::pack::rotamer_set::RotamerSets::nmoltenres(), num_indep_nodes_, per_node_rotamer_sets_, core::pose::Pose::residue(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue(), core::pose::Pose::size(), source_pose_residues_, core::pack::rotamer_set::RotamerSets::total_residue(), weighted_energy_methods_, core::scoring::ScoreFunction::ws_methods_begin(), and core::scoring::ScoreFunction::ws_methods_end().

◆ initialize_symmetry_info()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::initialize_symmetry_info ( core::pose::Pose const & pose )

private

Initialize symmetry information.

Called by initialize().

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References core::pose::Pose::conformation_ptr(), dependent_node_map_, dependent_residue_map_, has_mirror_symm_, is_symmetric_, num_indep_nodes_, per_node_rotamer_sets_, core::pose::Pose::residue(), and core::pack::interaction_graph::TR().

Referenced by initialize().

◆ prepare_graph_for_simulated_annealing()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::prepare_graph_for_simulated_annealing ( )

overridevirtual

Utility signal.

Implements core::pack::interaction_graph::AnnealableGraphBase.

◆ set_consideration()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::set_consideration	(	int const	node_ind,
		int const	node_resid,
		int const	new_state,
		utility::vector1< std::pair< int, core::conformation::ResidueCOP > > &	unset_information
	)

private

Sets the current consideration.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References current_residues_, current_rotamer_ids_, dependent_node_map_, dependent_residue_map_, is_symmetric_, and per_node_rotamer_sets_.

Referenced by commit_considered_substitution(), and consider_substitution().

◆ set_errorfull_deltaE_threshold()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::set_errorfull_deltaE_threshold ( core::PackerEnergy deltaE )

overridevirtual

Set error threshold.

Parameters

[in] deltaE Error threshold value to set.

Implements core::pack::interaction_graph::AnnealableGraphBase.

◆ set_network_state()

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::set_network_state ( ObjexxFCL::FArray1_int & node_states )

overridevirtual

Set states for all nodes across the network.

Parameters

[in] node_states Fortran-style 1-array of state indices for all nodes in the network.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References calculate_weighted_energy(), clear_consideration(), current_energy_, current_residues_, current_rotamer_ids_, dependent_node_map_, dependent_residue_map_, get_num_nodes(), is_symmetric_, and per_node_rotamer_sets_.

◆ set_state_for_node()

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::set_state_for_node	(	int	node_ind,
		int	new_state
	)

overridevirtual

Explicit state modification: set a particular node to a particular state.

Parameters

[in]	node_ind	Index of the node to modify.
[in]	new_state	Index of the state that we're setting this node TO.

Implements core::pack::interaction_graph::AnnealableGraphBase.

References calculate_weighted_energy(), clear_consideration(), current_energy_, current_residues_, current_rotamer_ids_, dependent_node_map_, dependent_residue_map_, is_symmetric_, and per_node_rotamer_sets_.

◆ unset_consideration()

void core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::unset_consideration ( utility::vector1< std::pair< int, core::conformation::ResidueCOP > > const & unset_info )

private

Clears the current consideration.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu)

References current_residues_.

Referenced by consider_substitution().

Member Data Documentation

◆ considered_energy_

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::considered_energy_

private

The energy that would result from the considered substitution.

Referenced by clear_consideration(), commit_considered_substitution(), consider_substitution(), and ResidueArrayAnnealingEvaluator().

◆ considered_node_

int core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::considered_node_

private

The node being considered for alteration.

Referenced by clear_consideration(), commit_considered_substitution(), and consider_substitution().

◆ considered_state_

int core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::considered_state_

private

The state that we're considering changing this node TO.

Referenced by clear_consideration(), commit_considered_substitution(), and consider_substitution().

◆ current_energy_

core::PackerEnergy core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::current_energy_

private

Current energy.

Referenced by blanket_assign_state_0(), clear_consideration(), commit_considered_substitution(), consider_substitution(), get_energy_current_state_assignment(), ResidueArrayAnnealingEvaluator(), set_network_state(), and set_state_for_node().

◆ current_residues_

utility::vector1< core::conformation::ResidueCOP > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::current_residues_

private

Const-owning pointers to the current residues.

Referenced by any_vertex_state_unassigned(), blanket_assign_state_0(), consider_substitution(), set_consideration(), set_network_state(), set_state_for_node(), and unset_consideration().

◆ current_rotamer_ids_

utility::vector1< core::Size > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::current_rotamer_ids_

private

holds the current rotamers ids, should always be in sync with current_residues_

Referenced by blanket_assign_state_0(), consider_substitution(), set_consideration(), set_network_state(), and set_state_for_node().

◆ dependent_node_map_

std::map< int, utility::vector1< core::Size > > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::dependent_node_map_

private

Map of dependent nodes.

Maps controlling node index -> vector of dependent node indices.

Referenced by initialize_symmetry_info(), set_consideration(), set_network_state(), and set_state_for_node().

◆ dependent_residue_map_

std::map< int, utility::vector1< core::Size > > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::dependent_residue_map_

private

Map of dependent residues.

Maps controlling node index -> vector of dependent residue indices.

Referenced by initialize_symmetry_info(), set_consideration(), set_network_state(), and set_state_for_node().

◆ has_mirror_symm_

bool core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::has_mirror_symm_

private

Is this a symmetric packing job with mirror symmetry?

Referenced by initialize_symmetry_info().

◆ is_symmetric_

bool core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::is_symmetric_

private

Is this a symmetric packing job?

Referenced by initialize_symmetry_info(), set_consideration(), set_network_state(), and set_state_for_node().

◆ num_indep_nodes_

core::Size core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::num_indep_nodes_

private

Number of independent nodes (not symmetry copies).

Referenced by get_num_nodes(), get_num_total_states(), initialize(), and initialize_symmetry_info().

◆ per_node_rotamer_sets_

utility::vector1< core::pack::rotamer_set::RotamerSetCOP > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::per_node_rotamer_sets_

private

The rotamer sets for each node (vector of const-owning pointers to RotamerSet objects.

Referenced by any_vertex_state_unassigned(), commit_considered_substitution(), consider_substitution(), get_num_states_for_node(), get_num_total_states(), initialize(), initialize_symmetry_info(), set_consideration(), set_network_state(), and set_state_for_node().

◆ source_pose_residues_

utility::vector1< core::conformation::ResidueCOP > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::source_pose_residues_

private

Const-owning pointers to the residues of the source pose.

Referenced by any_vertex_state_unassigned(), blanket_assign_state_0(), and initialize().

◆ weighted_energy_methods_

std::list< WeightedMethodPair > core::pack::interaction_graph::ResidueArrayAnnealingEvaluator::weighted_energy_methods_

private

List of energy methods and their weights.

Referenced by calculate_weighted_energy(), clean_up_after_packing(), commit_considered_substitution(), has_methods(), and initialize().

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

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

Public Member Functions

Private Types

Private Member Functions

Private Attributes

Member Typedef Documentation

◆ WeightedMethodPair

Constructor & Destructor Documentation

◆ ResidueArrayAnnealingEvaluator() [1/2]

◆ ~ResidueArrayAnnealingEvaluator()

◆ ResidueArrayAnnealingEvaluator() [2/2]

Member Function Documentation

◆ any_vertex_state_unassigned()

◆ blanket_assign_state_0()

◆ calculate_weighted_energy()

◆ clean_up_after_packing()

◆ clear_consideration()

◆ commit_considered_substitution()

◆ consider_substitution()

◆ get_energy_current_state_assignment()

◆ get_num_nodes()

◆ get_num_states_for_node()

◆ get_num_total_states()

◆ has_methods()

◆ initialize()

◆ initialize_symmetry_info()

◆ prepare_graph_for_simulated_annealing()

◆ set_consideration()

◆ set_errorfull_deltaE_threshold()

◆ set_network_state()

◆ set_state_for_node()

◆ unset_consideration()

Member Data Documentation

◆ considered_energy_

◆ considered_node_

◆ considered_state_

◆ current_energy_

◆ current_residues_

◆ current_rotamer_ids_

◆ dependent_node_map_

◆ dependent_residue_map_

◆ has_mirror_symm_

◆ is_symmetric_

◆ num_indep_nodes_

◆ per_node_rotamer_sets_

◆ source_pose_residues_

◆ weighted_energy_methods_