Defines the interaction graph that will keep track of changes to the hpatch score. More...

#include <NPDHBondInteractionGraph.hh>

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

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

Public Types inherited from core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
typedef std::vector< BackgroundNode< V, E, G > * >	BackgroundNodeVector

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

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

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

Public Member Functions
	NPDHBondInteractionGraph (int num_nodes)

	~NPDHBondInteractionGraph () override

pose::Pose const &	pose () const

void	set_pose (pose::Pose const &pose)

scoring::ScoreFunction const &	scorefxn () const

void	set_score_function (scoring::ScoreFunction const &scorefxn)

utility::graph::Graph const &	packer_neighbor_graph () const

void	set_packer_neighbor_graph (utility::graph::Graph const &neighbor_graph)

task::PackerTask const &	packer_task () const

void	set_packer_task (task::PackerTask const &task)
	We need a copy of the packer task to figure out which residues are being packed and/or designed. We have to figure the packing options because it determines whether a residue becomes a FirstClass (NPDHBondNode) node or a background node. This method gets called in IGSupport.cc. More...

rotamer_set::RotamerSets const &	rotamer_sets () const

void	set_rotamer_sets (rotamer_set::RotamerSets const &rotsets)

void	initialize (pack_basic::RotamerSetsBase const &rot_sets) override

void	set_num_residues_in_protein (Size num_res)
	tells the graph how many residues there are total in the protein More...

void	set_num_background_residues (Size num_background_residues)
	tells the graph how many residues there are as part of the protein that are not part of the combinatorial optimization process – they are part of the background More...

void	set_residue_as_background_residue (int residue)
	informs the graph that a particular residue is part of the background More...

void	prepare_graph_for_simulated_annealing () override
	Prepares the graph to begin simulated annealing. More...

void	blanket_assign_state_0 () override
	assigns state 0 – the unassigned state – to all (first class) vertices in the graph More...

Real	get_npd_hbond_score ()

void	set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override
	Allows the sim-annealer to specify a deltaE threshold above which, it is no longer necessary to be very accurate. More...

void	consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override
	Returns the (possibly approximate) change in energy induced by switching a particular node from its currently assigned state to some alternate state. More...

core::PackerEnergy	calculate_npd_hbond_deltaE ()

Real	calculate_alt_state_npd_hbond_score ()

core::PackerEnergy	commit_considered_substitution () override
	Commits the substitution that the sim annealer had previously asked the graph to consider. Returns the accurate total energy for the graph. More...

core::PackerEnergy	set_network_state (ObjexxFCL::FArray1_int &node_states) override
	Switch the state assignment of every first class node in the graph. Useful, for instance, if you want to switch to the best network state that you've found so far. More...

core::PackerEnergy	get_energy_current_state_assignment () override
	returns the energy of the entire graph under the current network state assignment. Also sends a bunch of information to standard error. Only seems to be called by the MultiCoolAnnealer. More...

int	get_edge_memory_usage () const override
	Should return a measurement of the memory used by the interaction graph to store the rotamer pair energies. Unimplemented. More...

unsigned int	count_static_memory () const override

unsigned int	count_dynamic_memory () const override

virtual Real	get_energy_sum_for_vertex_group (Size group_id)
	returns the sum of the PD energy and the hpatch energy for all members first class members of a user-defined vertex subset. Unimplemented. More...

void	print_internal_energies_for_current_state_assignment ()

void	print () const override
	useful for debugging More...

int	bg_node_2_resid (Size node_index)
	Provides read access to the bg to resid array. Returns -1 if the index is not in bounds. More...

std::vector< int >	get_network_state () const
	Returns the state on each FCNode, but not necessarily in pose resid order. Only used by the unit tests. More...

void	set_observed_sufficient_boolean_true ()
	Sets the observed_sufficient_npd_hbond_E_to_predict_min_ to true. Only used by the unit tests. More...

scoring::hbonds::HBondDatabase const &	hbond_database () const

scoring::hbonds::HBondOptions const &	hbond_options () const

scoring::hbonds::NPDHBondSet const &	npd_hbond_set () const

utility::vector1< char > &	hbonding_to_res_vector ()

NPDHBondOP	unused_hbond ()

void	return_hbond_to_queue (NPDHBondOP const &hbond)

Real	npd_hb_weight (scoring::hbonds::HBEvalType eval_type, bool intra_res)

NPDHBondNode< V, E, G > const *	get_npd_hbond_node (int index) const

NPDHBondNode< V, E, G > *	get_npd_hbond_node (int index)

NPDHBondBackgroundNode< V, E, G > const *	get_npd_hbond_bg_node (int index) const

NPDHBondBackgroundNode< V, E, G > *	get_npd_hbond_bg_node (int index)

Public Member Functions inherited from core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
	AdditionalBackgroundNodesInteractionGraph (int num_nodes)
	AdditionalBackgroundNodesInteractionGraph constructor; no default or copy constructors; no operator =. More...

	~AdditionalBackgroundNodesInteractionGraph () override
	AdditionalBackgroundNodesInteractionGraph destructor. More...

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

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

int	get_num_background_nodes () const

Static Public Member Functions
static void	print_npd_hbond_avoidance_stats ()
	reports on the level of success for hpatch score calculation procrastination More...

static void	reset_npd_hbond_avoidance_stats ()
	resets static member variables of NPDHBondIG that measure how worthwhile hpatch calculation procrastination is. More...

Protected Member Functions
NodeBase *	create_new_node (int node_index, int num_states) override
	factory method pattern for instantiation of NPDHBondNode objects, used by InteractionGraphBase class. More...

EdgeBase *	create_new_edge (int index1, int index2) override
	factory method pattern for instantiation of NPDHBondEdge objects, used by InteractionGraphBase class. More...

BackgroundNode< V, E, G > *	create_background_node (int node_index) override
	factory method pattern for instantiation of NPDHBondBackgroundNode objects, used by AdditionalBackgroundNodesInteractionGraph class. More...

BackgroundToFirstClassEdge< V, E, G > *	create_background_edge (int fc_node_index, int bg_node_index) override
	factory method pattern for instantiation of NPDHBondBackgroundEdge objects, used by AdditionalBackgroundNodesInteractionGraph class. More...

void	track_npd_hbond_E_min ()
	Keeps track of the minimum hpatch score seen. Every 100 substitutions, updates the variable npd_hbond_score_min_last_100. More...

void	update_internal_energy_totals_npd_hbond ()
	After every 2^10 commits, the graph traverses its nodes and edges and re-tallies the total energy of the current state assignment. This update prevents the accumulation of numerical drift, increasing accuracy. More...

Protected Member Functions inherited from core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >
void	clean_up_bgtfc_edges_marked_for_deletion ()
	Remove those BackgroundToFirstClassEdges that have marked themselves for deletion. More...

void	drop_background_edge (BackgroundEdgeListIter iter)
	Constant time edge removal. More...

void	set_num_background_nodes (int num_bg_nodes)
	sets the number of background nodes in the graph. Should be called no more than once. Some problem instances do not require background nodes. More...

void	add_background_edge (int first_class_node_index, int bg_node_index)
	adds a BackgroundToFirstClassEdge to the graph and performs the requisite bookkeepking. More...

BackgroundToFirstClassEdge< V, E, G > *	find_background_edge (int first_class_node_index, int bg_node_index) const
	returns a pointer to the background edge, identified by the indices of the first and second class nodes it connects. Returns the null pointer if the edge does not exist. Possibly linear time operation (in the number of BackgroundToFirstClassEdges). More...

int	get_num_bg_edges () const

BackgroundNode< V, E, G > *	get_background_node (int index) const

void	prepare_graph_for_simulated_annealing () override
	invokes prepare_for_simulated_annealing on each of the BackgroundToFirstClassEdges and then invokes prepare_for_simulated_annealing on each of the BackgroundNodes. More...

BackgroundEdgeListConstIter	get_bg_edge_list_begin () const

BackgroundEdgeListConstIter	get_bg_edge_list_end () const

Private Member Functions
void	reset_from_previous_delta_npd_hbond_comp ()

bool	decide_procrastinate_npd_hbond_computations (Real const pd_deltaE, Real const threshold) const

	NPDHBondInteractionGraph ()=delete

	NPDHBondInteractionGraph (NPDHBondInteractionGraph< V, E, G > const &)=delete

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

Private Attributes
pose::PoseOP	pose_

scoring::ScoreFunctionOP	scorefxn_

utility::graph::GraphOP	neighbor_graph_

task::PackerTaskOP	packer_task_

rotamer_set::RotamerSetsOP	rotamer_sets_

scoring::EnergyMap	npd_hbond_score_weights_

Size	num_total_residues_ = 0

Size	num_residues_assigned_as_background_ = 0

utility::vector1< Size >	resid_2_bgenumeration_

utility::vector1< Size >	bgenumeration_2_resid_

bool	prepared_for_simulated_annealing_ = false

bool	observed_sufficient_npd_hbond_E_to_predict_min_ = false

Real	npd_hbond_score_min_last_100_ = 0

Real	npd_hbond_score_min_recent_ = 0

Size	num_substitutions_since_npd_hbond_min_update_ = 0

bool	calculated_npd_hbond_deltaE_ = false

core::PackerEnergy	deltaE_for_substitution_ = 0.0

bool	last_considered_substitution_accepted_ = false

Size	node_considering_alt_state_ = 0

Size	alt_state_being_considered_ = 0

Real	total_energy_current_state_assignment_ = 0

Real	total_energy_alternate_state_assignment_ = 0

Real	npd_hbond_energy_current_state_assignment_ = 0

Real	npd_hbond_energy_alternate_state_assignment_ = 0

int	num_commits_since_last_update_ = 0

float	deltaE_threshold_for_avoiding_npd_hbond_calcs_ = 0.0

scoring::hbonds::HBondDatabaseCOP	hbond_database_

scoring::hbonds::HBondOptionsCOP	hbond_options_

scoring::hbonds::NPDHBondSetCOP	npd_hbond_set_

utility::vector1< char >	hbonding_to_res_

std::list< NPDHBondOP >	hbonds_queue_

Static Private Attributes
static Size	num_state_substitutions_considered_ = 0

static Size	num_npd_hbond_comps_procrastinated_ = 0

static Size	num_npd_hbond_comps_later_made_ = 0

static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 4096

Detailed Description

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

Defines the interaction graph that will keep track of changes to the hpatch score.

In addition to implementing the virtual base class methods, this class additionally defines methods relating to keeping track of data relating to hpatch.

Member Typedef Documentation

◆ parent

template<typename V , typename E , typename G >

typedef AdditionalBackgroundNodesInteractionGraph< V, E, G > core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::parent

Constructor & Destructor Documentation

◆ NPDHBondInteractionGraph() [1/3]

template<typename V , typename E , typename G >

core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::NPDHBondInteractionGraph ( int num_nodes )

Main constructor. Initializes all member variables to 0 and false.

◆ ~NPDHBondInteractionGraph()

template<typename V , typename E , typename G >

core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::~NPDHBondInteractionGraph

override

◆ NPDHBondInteractionGraph() [2/3]

template<typename V , typename E , typename G >

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

privatedelete

◆ NPDHBondInteractionGraph() [3/3]

template<typename V , typename E , typename G >

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

privatedelete

Member Function Documentation

◆ bg_node_2_resid()

template<typename V , typename E , typename G >

int core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::bg_node_2_resid ( Size node_index )

Provides read access to the bg to resid array. Returns -1 if the index is not in bounds.

◆ blanket_assign_state_0()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::blanket_assign_state_0

override

assigns state 0 – the unassigned state – to all (first class) vertices in the graph

This is the 3rd entry point into the NPDHBIG. It is called by the Annealer just before simulated annealing and rotamer substitutions begin to init the graph to unassigned values everywhere.

◆ calculate_alt_state_npd_hbond_score()

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::calculate_alt_state_npd_hbond_score ( )

◆ calculate_npd_hbond_deltaE()

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::calculate_npd_hbond_deltaE

Goes through the entire process of calculating the hpatch deltaE for a substitution.

◆ commit_considered_substitution()

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::commit_considered_substitution

override

Commits the substitution that the sim annealer had previously asked the graph to consider. Returns the accurate total energy for the graph.

◆ consider_substitution()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::consider_substitution	(	int	node_ind,
		int	new_state,
		core::PackerEnergy &	delta_energy,
		core::PackerEnergy &	prev_energy_for_node
	)

override

Returns the (possibly approximate) change in energy induced by switching a particular node from its currently assigned state to some alternate state.

First, queries the NPDHBondNode for the pairwise-decomposable (PD) energy. If the PD difference implies a collision, then the NPDHBondIG pretends as if the state substitution causes the best improvement possible in hpatch score, and returns the PD difference + pretend hpatch difference. It will procrastinate computing the actual hpatch score difference until the guiding SimAnnealer decides to commit the substitution. If the SimAnnealer rejects the substitution, then the work to compute the hpatch score is never done. If it is unclear that the SimAnnealer will reject the substitution based on the PD difference, then the Graph goes ahead and computes the change in hpatch score accurately.

This function is the 4th major entry point from the Annealer into the NPDHBIG.

Also returns the sum of the two body energies for the node in its current state; the sim-annealer accepts state substitutions at higher chance if the original state was also at a poor energy.

Parameters

node_ind - [in] - the index of the (first class) node new_state - [in] - the alternate state that the node should consider delta_energy - [out] - the change in energy induced on the entire graph by substituting a node's current state with the alternate. This energy may be inaccurate if it exceeds a threshold set by the sim-annealer. prev_energy_for_node - [out] - the sum of the pair-wise decomposable portion of the energy function for the node's currently assigned state

◆ count_dynamic_memory()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::count_dynamic_memory

override

◆ count_static_memory()

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::count_static_memory

override

◆ create_background_edge()

template<typename V , typename E , typename G >

BackgroundToFirstClassEdge< V, E, G > * core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::create_background_edge	(	int	fc_node_index,
		int	bg_node_index
	)

overrideprotectedvirtual

factory method pattern for instantiation of NPDHBondBackgroundEdge objects, used by AdditionalBackgroundNodesInteractionGraph class.

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

◆ create_background_node()

template<typename V , typename E , typename G >

BackgroundNode< V, E, G > * core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::create_background_node ( int node_index )

overrideprotectedvirtual

factory method pattern for instantiation of NPDHBondBackgroundNode objects, used by AdditionalBackgroundNodesInteractionGraph class.

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

◆ create_new_edge()

template<typename V , typename E , typename G >

EdgeBase * core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::create_new_edge	(	int	index1,
		int	index2
	)

overrideprotected

factory method pattern for instantiation of NPDHBondEdge objects, used by InteractionGraphBase class.

◆ create_new_node()

template<typename V , typename E , typename G >

NodeBase * core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::create_new_node	(	int	node_index,
		int	num_states
	)

overrideprotected

factory method pattern for instantiation of NPDHBondNode objects, used by InteractionGraphBase class.

◆ decide_procrastinate_npd_hbond_computations()

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::decide_procrastinate_npd_hbond_computations	(	Real const	pd_deltaE,
		Real const	threshold
	)		const

private

Makes the decision whether or not to procrastinate calculating the NPD-hbond score. Basically, if the PD energy got better (dE < 0) then return false so we don't procrastinate the calculation (because the alternate state probably will be accepted?). If the best guess for the hpatch deltaE also comes back better (dE < 0), then return false. Finally, if the difference between the deltaE for the PD terms and the (guessed) npd-hbond deltaE is greater than the threshold, return true so we do procrastinate. So basically if the PD energy gets much worse, procrastinate. Otherwise, don't.

◆ get_edge_memory_usage()

template<typename V , typename E , typename G >

int core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_edge_memory_usage

override

Should return a measurement of the memory used by the interaction graph to store the rotamer pair energies. Unimplemented.

◆ get_energy_current_state_assignment()

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_energy_current_state_assignment

override

returns the energy of the entire graph under the current network state assignment. Also sends a bunch of information to standard error. Only seems to be called by the MultiCoolAnnealer.

◆ get_energy_sum_for_vertex_group()

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_energy_sum_for_vertex_group ( Size group_id )

virtual

returns the sum of the PD energy and the hpatch energy for all members first class members of a user-defined vertex subset. Unimplemented.

◆ get_network_state()

template<typename V , typename E , typename G >

std::vector< int > core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_network_state

Returns the state on each FCNode, but not necessarily in pose resid order. Only used by the unit tests.

◆ get_npd_hbond_bg_node() [1/2]

template<typename V , typename E , typename G >

NPDHBondBackgroundNode< V, E, G >* core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_bg_node ( int index )

inline

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_background_node().

◆ get_npd_hbond_bg_node() [2/2]

template<typename V , typename E , typename G >

NPDHBondBackgroundNode< V, E, G > const* core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_bg_node ( int index ) const

inline

References core::pack::interaction_graph::AdditionalBackgroundNodesInteractionGraph< V, E, G >::get_background_node().

◆ get_npd_hbond_node() [1/2]

template<typename V , typename E , typename G >

NPDHBondNode< V, E, G >* core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_node ( int index )

inline

◆ get_npd_hbond_node() [2/2]

template<typename V , typename E , typename G >

NPDHBondNode< V, E, G > const* core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_node ( int index ) const

inline

◆ get_npd_hbond_score()

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::get_npd_hbond_score ( )

◆ hbond_database()

template<typename V , typename E , typename G >

scoring::hbonds::HBondDatabase const & core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::hbond_database

Referenced by core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), and core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

◆ hbond_options()

template<typename V , typename E , typename G >

scoring::hbonds::HBondOptions const & core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::hbond_options

Referenced by core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), and core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

◆ hbonding_to_res_vector()

template<typename V , typename E , typename G >

utility::vector1< char > & core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::hbonding_to_res_vector

◆ initialize()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::initialize ( pack_basic::RotamerSetsBase const & rot_sets_base )

override

This function is the 1st major entry point (well, after the constructor) into the NPDHBIG. It needs to set residues that are not changing as background residues

Oldest comments: In ++, there's a file InteractionGraphSupport.cc which is an analog of the InteractionGraphFactory in mini. In ++, the InteractionGraphSupport file instantiates and initializes, depending on the command line switches, the right interaction graph. For the NPDHBondInteractionGraph, it first initializes the PDInteractionGraph (which is the base) and then calls the NPDHBondIG initialize method.

The thing is that this initialize method can't be called when the graph is constructed in the InteractionGraphFactory. The reason is that the PDInteractionGraph base initialize() method is NOT called until later in the pack rotamers process. (Actually it's called from within rotsets->compute_energies().) Only after the rotsets->compute energies returns can I stick in an initialize() method call for the NPDHBondInteractionGraph (NPDHBIG). But then that's too late because the rotsets object has already computed some energies. Perhaps that's ok though. The rotsets object only calculates the PD energy terms - it doesn't do anything with non-PD terms.

If a NPDHBIG init method is called during construction of the NPDHBIG, then the init method that's called by the rotsets object causes all the node info that was set in the NPDHBIG init method to be lost because the rotsets init method recreates all the nodes in the interaction graph when it runs. (That was a fun behaviour to figure out.)

So the solution I'm going for is to call this init method in the prepare for simulated annealing method of this class. That gets called just before SA starts, so it will do the task above then. It doesn't really matter when the task gets done as long as it happens before SA starts. This also means that the NPDHBIG will now have to keep a reference to the Pose, the Task, and the RotamerSets objects since it needs all of these things to do tasks 1) and 2). (For the port of this NPDHBondIG, we might not need the task and rotamer sets objects.)

prepare_graph_for_simulated_annealing gets called by the FixbbSA::run() method. Before this method, the rotamersets object has called compute_energies() (the whole process being started in pack_rotamers) which calls initialize() on the IG. I need to place the NPDHBIG init method directly after the IG init method that the RS object calls.

References core::pack::rotamer_set::RotamerSets::nmoltenres().

◆ npd_hb_weight()

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::npd_hb_weight	(	scoring::hbonds::HBEvalType	eval_type,
		bool	intra_res
	)

References core::scoring::hbonds::npd_hb_eval_type_weight().

Referenced by core::pack::interaction_graph::create_hbonds_one_way().

◆ npd_hbond_set()

template<typename V , typename E , typename G >

scoring::hbonds::NPDHBondSet const & core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::npd_hbond_set

Referenced by core::pack::interaction_graph::NPDHBondEdge< V, E, G >::consider_alternate_state_step1(), and core::pack::interaction_graph::NPDHBondBackgroundEdge< V, E, G >::consider_alternate_state_step1().

◆ operator=()

template<typename V , typename E , typename G >

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

privatedelete

◆ packer_neighbor_graph()

template<typename V , typename E , typename G >

utility::graph::Graph const& core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::packer_neighbor_graph ( ) const

inline

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::neighbor_graph_.

◆ packer_task()

template<typename V , typename E , typename G >

task::PackerTask const& core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::packer_task ( ) const

inline

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::packer_task_.

◆ pose()

template<typename V , typename E , typename G >

pose::Pose const& core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::pose ( ) const

inline

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::pose_.

◆ prepare_graph_for_simulated_annealing()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::prepare_graph_for_simulated_annealing

override

Prepares the graph to begin simulated annealing.

Invokes both base-class prepare_graph_for_simulated_annealing subroutines: InteractionGraphBase first, to prepare the NPDHBondNodes and NPDHBondEdges. Then the AdditionalBackgroundNodesInteractionGraph, to prepare the NPDHBondBackgroundNodes, the NPDHBondBackgroundEdges, and to do a little more preparing of the NPDHBondNodes. Also computes background/background overlap. This is the 2nd major entry point into the NPDHBIG.

◆ print()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::print

override

useful for debugging

◆ print_internal_energies_for_current_state_assignment()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::print_internal_energies_for_current_state_assignment

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

◆ print_npd_hbond_avoidance_stats()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::print_npd_hbond_avoidance_stats

static

reports on the level of success for hpatch score calculation procrastination

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

◆ reset_from_previous_delta_npd_hbond_comp()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::reset_from_previous_delta_npd_hbond_comp

private

◆ reset_npd_hbond_avoidance_stats()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::reset_npd_hbond_avoidance_stats

static

resets static member variables of NPDHBondIG that measure how worthwhile hpatch calculation procrastination is.

Referenced by core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_errorfull_deltaE_threshold().

◆ return_hbond_to_queue()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::return_hbond_to_queue ( NPDHBondOP const & hbond )

References core::scoring::hbond.

◆ rotamer_sets()

template<typename V , typename E , typename G >

rotamer_set::RotamerSets const& core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::rotamer_sets ( ) const

inline

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::rotamer_sets_.

◆ scorefxn()

template<typename V , typename E , typename G >

scoring::ScoreFunction const& core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::scorefxn ( ) const

inline

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::scorefxn_.

◆ set_errorfull_deltaE_threshold()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_errorfull_deltaE_threshold ( core::PackerEnergy deltaE )

override

Allows the sim-annealer to specify a deltaE threshold above which, it is no longer necessary to be very accurate.

When the annealer asks the graph to consider a state substitution that produces a large collision, the graph may approximate the hpatch deltaE instead of performing expensive sphere overlap computations. The deltaE returned by consider_substitution() will be inaccurate, but if the annealer is unlikely to accept the substitution, then time can be saved. The graph guarantees that if the annealer does commit that substitution that it will go back and perform the hpatch computations and return an accurate total energy for the graph.

References core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::reset_npd_hbond_avoidance_stats().

◆ set_network_state()

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_network_state ( ObjexxFCL::FArray1_int & node_states )

override

Switch the state assignment of every first class node in the graph. Useful, for instance, if you want to switch to the best network state that you've found so far.

This function is the last major entry point from the Annealer into the NPDHBIG.

◆ set_num_background_residues()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_num_background_residues ( Size num_background_residues )

tells the graph how many residues there are as part of the protein that are not part of the combinatorial optimization process – they are part of the background

The other half of switching between enumeration schemes for the background residues is knowing how many background residues there are.

◆ set_num_residues_in_protein()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_num_residues_in_protein ( Size num_res )

tells the graph how many residues there are total in the protein

The graph maintains its own enumeration for the background residues; but asks that anyone wanting to refer to them use their original resid. The graph has to switch back and forth between enumeration schemes and must know how many residues there are total to do that efficiently.

◆ set_observed_sufficient_boolean_true()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_observed_sufficient_boolean_true

Sets the observed_sufficient_npd_hbond_E_to_predict_min_ to true. Only used by the unit tests.

◆ set_packer_neighbor_graph()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_packer_neighbor_graph ( utility::graph::Graph const & neighbor_graph )

◆ set_packer_task()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_packer_task ( task::PackerTask const & task )

We need a copy of the packer task to figure out which residues are being packed and/or designed. We have to figure the packing options because it determines whether a residue becomes a FirstClass (NPDHBondNode) node or a background node. This method gets called in IGSupport.cc.

References core::pack::task::PackerTask::clone().

◆ set_pose()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_pose ( pose::Pose const & pose )

All throughout this class, I refer back to the original pose sequence. To be able to do that, I need to have a handle to the pose in this class. That's what this method provides. In IGFactory.cc, this method gets called with the pose object that's being packed/designed.

◆ set_residue_as_background_residue()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_residue_as_background_residue ( int residue )

informs the graph that a particular residue is part of the background

◆ set_rotamer_sets()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_rotamer_sets ( rotamer_set::RotamerSets const & rotsets )

◆ set_score_function()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::set_score_function ( scoring::ScoreFunction const & sfxn )

All throughout this class, I refer back to the original pose sequence. To be able to do that, I need to have a handle to the pose in this class. That's what this method provides. In IGFactory.cc, this method gets called with the pose object that's being packed/designed.

References core::scoring::ScoreFunction::clone(), and core::scoring::EnergiesCacheableDataType::NPD_HBOND_SET.

◆ track_npd_hbond_E_min()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::track_npd_hbond_E_min

protected

Keeps track of the minimum hpatch score seen. Every 100 substitutions, updates the variable npd_hbond_score_min_last_100.

◆ unused_hbond()

template<typename V , typename E , typename G >

NPDHBondOP core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::unused_hbond

Referenced by core::pack::interaction_graph::create_hbonds_one_way().

◆ update_internal_energy_totals_npd_hbond()

template<typename V , typename E , typename G >

void core::pack::interaction_graph::NPDHBondInteractionGraph< V, E, G >::update_internal_energy_totals_npd_hbond

protected

After every 2^10 commits, the graph traverses its nodes and edges and re-tallies the total energy of the current state assignment. This update prevents the accumulation of numerical drift, increasing accuracy.