Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...

#include <SurfaceInteractionGraph.hh>

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

[legend]

Collaboration diagram for core::pack::interaction_graph::SurfaceNode< V, E, G >:

[legend]

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

Public Types inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >	BackgroundEdgeList

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

typedef std::vector < BackgroundNode< V, E, G > * >	BackgroundNodeVector

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

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

Public Member Functions
	SurfaceNode (G *owner, int node_index, int num_states)
	SurfaceNode constructor. More...

virtual	~SurfaceNode ()
	destructor – no dynamically allocated data, does nothing More...

virtual void	assign_zero_state ()
	Assign the node to state 0 – the "unassigned" state. More...

virtual bool	state_unassigned () const

void	assign_state_surface (int state)
	Assigns the node to one of the states in its state space or to the unassigned state. More...

Real	get_curr_state_surface_energy () const
	returns the surface energy for the node in its current state assignment More...

Real	project_deltaE_for_substitution_surface (int alternate_state, core::PackerEnergy &prev_energy_for_node, float deltaE_thresh_for_avoiding_surface_calcs)
	Returns the (possibly approximate) change in energy induced by changing a node from its current state into some alternate state. More...

Real	get_surface_deltaE_for_neighbors_state_substitution (SurfaceNode< V, E, G > *node_considering_substitution, int changing_nodes_curr_state, int changing_nodes_alt_state)
	returns the change in surface score for this node induced by a state substitution at a neighboring node. More...

Real	commit_considered_substitution_surface ()
	Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering. More...

void	acknowledge_neighbors_substitution_surface ()
	bookkeeping to follow a neighbors state substitution. this method gets called when a SurfaceNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident SurfaceEdges. basically we need to set current state equal to alt state here. (Hopefully alt state is still correct!!) Since there's no way for a SurfaceNode to know what other SurfaceNodes are connected to it except via SurfaceEdges, the calls seem a bit complicated. A SurfaceNode has to call acknowledge_state on each Edge. The Edges have to figure out which Node is changing/not changing and then they call an inform_non_changing node of change method. That method then makes the call to this method on the correct SurfaceNode. The inform_non_changing method can not be removed, because it's used during the substitution evaluations as well. More...

bool	detect_neighborship_with_node (int node_id, bool first_class) const
	Determines if this vertex neighbors the calling node Called by all other nodes, and if true is returned an Edge of some sort is created between the nodes. More...

virtual void	print () const
	useful for debugging - writes information about a node to the tracer More...

virtual void	prepare_for_simulated_annealing ()
	invokes V's prep_for_simA method Also populates a map defining which nodes are neighbors according to the tenA neighbor graph. This map will be checked whenever iterating over all edges defined by the energy graph to see if a Node really needs to be updated for the surface score. More...

virtual unsigned int	getMemoryUsageInBytes () const
	Not implemented, but needs to be! More...

virtual unsigned int	count_static_memory () const
	Returns the amount of static memory used by this Node object. More...

virtual unsigned int	count_dynamic_memory () const
	Returns the amount of dynamic memory used by this Node object. More...

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

conformation::ResidueCOP	get_rotamer (int state) const

int	wt_seqpos_for_node () const

conformation::Residue	wt_residue_for_node () const

Real	get_surface_score_difference () const
	Returns the difference alt state score - current state score. More...

bool	is_surface_exposed () const
	Returns the value of surface_exposed_ which gets set during the SIG initialize() method. More...

void	surface_exposed (bool value)
	setter for the surface_exposed_ bool More...

bool	is_below_buried_residue_no_hsasa_cutoff () const
	Returns the value of is_below_buried_residue_no_hsasa_cutoff_ which gets set during the SIG initialize() method. More...

void	is_below_buried_residue_no_hsasa_cutoff (bool value)
	setter for the is_below_buried_residue_no_hsasa_cutoff_ bool More...

void	reset_alt_state_total_hASA ()
	Sets the alt state total hASA to the current state total hASA. See comments in SIG and commit_considered_substitution_surface for more information about why this method exists. More...

void	initialize_num_neighbors_counting_self () const
	Returns the number of neighbors within the interaction threshold, counting self. More...

int	num_neighbors_counting_self () const
	Returns the value stored in the member variable. More...

void	init_hASA_variables ()

Real	calculate_amount_total_hydrophobic_ASA ()

Real	average_residue_hASA () const
	Returns the amount of hydrophobic ASA this node/residue adds to a patch. More...

Real	average_residue_hASA (chemical::AA residue_type, Size num_nbs) const
	Same function as above, but this one allows you to specify what type and num_nbs. This function is meant to be used only when initializing all of the Nodes/BGNodes because at that point we have to use the wild-type residue type, not the new rotamers residue type (which is what the above function will do). More...

Real	hASA_energy (Real patch_area) const
	Calls a SurfacePotential class method to get the energy for a given patch area. Only nodes with number of nbs less than or equal to SURFACE_EXPOSED_CUTOFF will get a score. All other nodes will have a score of 0.0. More...

void	verify_patch_areas_correct (int node_id, int previous_state, Real previous_state_hASA)
	Checks to make sure that the current state num se hp nbs is correct, by going through all residues in the Pose and brute-force recounting. More...

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

std::vector< Real >	get_hASA_for_node_and_nbs ()
	Returns a vector of Reals containing the hASA of se hp nbs for this node in the first index, and then the hASA for all neighboring nodes and bgnodes. Note: Order is not guaranteed here. Only used by the unit tests. Should not exist in release mode. More...

std::vector< Real >	get_alt_state_hASA_for_node_and_nbs ()
	Returns a vector of Reals containing the hASA of se hp nbs for this node in the first index, and then the hASA for all neighboring nodes and bgnodes. Note: Order is not guaranteed here. Only used by the unit tests. Should not exist in release mode. More...

Real	get_current_hASA ()
	Returns current hASA. Only used by the unit tests. Should not exist in release mode. More...

Real	get_alt_hASA ()
	Returns current hASA. Only used by the unit tests. Should not exist in release mode. More...

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

	FirstClassNode (G *owner, int node_id, int num_states)
	FirstClassNode constructor. More...

BackgroundEdgeListIter	add_background_edge (BackgroundToFirstClassEdge< V, E, G > *edge)
	Adds a BackgroundToFirstClassEdge to the node's list of such edges and returns an iterator to that list position. More...

void	drop_background_edge (BackgroundEdgeListIter edge)
	Removes an edge from the node's BackgroundToFirstClassEdge list. More...

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

static void	reset_surface_avoidance_stats ()
	resets static member variables of SurfaceNode that measure how worthwhile surface score calculation procrastination is. More...

Public Attributes
rotamer_set::RotamerSetCOP	rotamer_set_

utility::vector1 < conformation::ResidueCOP >	rotamers_vector_

Protected Member Functions
SurfaceEdge< V, E, G > *	get_incident_surface_edge (int index) const

SurfaceBackgroundEdge< V, E, G > *	get_edge_to_surface_bg_node (int index) const

SurfaceInteractionGraph< V, E, G > *	get_surface_owner () const

Protected Member Functions inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
int	get_num_edges_to_background_nodes () const

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

int	get_index_of_adjacent_background_node (int index) const

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

bool	get_bg_edge_vector_up_to_date_ () const

void	update_bg_edge_vector ()
	Syncs the background edge vector with the background edge list. More...

Private Member Functions
Real	project_surface_deltaE ()
	returns the change in surface score for this node and all of its neighbors produced by switching from its current state to an alternate state. More...

void	track_surface_E_min ()
	Keeps track of the minimum surface score seen. Every 100 substitutions, updates the variable surface_score_min_last_100. More...

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

	SurfaceNode ()

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

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

Private Attributes
bool	calculated_surface_deltaE_

Real	deltaE_for_substitution_

Real	curr_state_total_hASA_

Real	alt_state_total_hASA_

bool	have_prepared_for_simA_

Real	surface_score_min_last_100_

Real	surface_score_min_recent_

int	num_substitutions_since_surface_min_update_

bool	observed_sufficient_surface_E_to_predict_min_

bool	surface_exposed_

bool	is_below_buried_residue_no_hsasa_cutoff_

std::map< std::pair< int, int > , int >	fc_neighbor_map

std::map< std::pair< int, int > , int >	bg_neighbor_map

int	num_neighbors_counting_self_

Static Private Attributes
static Real	surface_energy_weight_ = 1.0

static const int	MAX_SURFACE_ENERGY = 100

static const int	INTERACTION_RADIUS = 10

static const int	SURFACE_EXPOSED_CUTOFF = 20

static const int	BURIED_RESIDUE_NO_HSASA_CUTOFF = 24

static const int	MAX_PATCH_SURFACE_AREA = 1100

static int	num_state_substitutions_considered_

static int	num_surface_comps_procrastinated_

static int	num_surface_comps_later_made_

Detailed Description

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

Defines a FirstClass node which will keep track of changes in the surface energy. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph.

SurfaceNode

Remarks: No public default constructor makes this class uncopyable.

Definition at line 61 of file SurfaceInteractionGraph.hh.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef FirstClassNode< V, E, G > core::pack::interaction_graph::SurfaceNode< V, E, G >::parent

Definition at line 86 of file SurfaceInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

SurfaceNode constructor.

SurfaceNode< V, E, G >::SurfaceNode

Parameters

owner - [in] - the owning interaction graph node_id - [in] - the index for this node amongst its owners set num_states - [in] - the number of states for this node

Definition at line 641 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_owner(), core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_energy_weight_, and core::pack::interaction_graph::TR_NODE().

template<typename V , typename E , typename G >

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

virtual

destructor – no dynamically allocated data, does nothing

SurfaceNode< V, E, G >::~SurfaceNode

Definition at line 673 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::acknowledge_neighbors_substitution_surface ( )

bookkeeping to follow a neighbors state substitution. this method gets called when a SurfaceNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident SurfaceEdges. basically we need to set current state equal to alt state here. (Hopefully alt state is still correct!!) Since there's no way for a SurfaceNode to know what other SurfaceNodes are connected to it except via SurfaceEdges, the calls seem a bit complicated. A SurfaceNode has to call acknowledge_state on each Edge. The Edges have to figure out which Node is changing/not changing and then they call an inform_non_changing node of change method. That method then makes the call to this method on the correct SurfaceNode. The inform_non_changing method can not be removed, because it's used during the substitution evaluations as well.

SurfaceNode::acknowledge_neighbors_substitution_surface

Definition at line 858 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::assign_state_surface ( int state)

Assigns the node to one of the states in its state space or to the unassigned state.

SurfaceNode::assign_state_surface

Detailed:: Piggy backs on the standard project_deltaE/commit_considered_substitution protocol. Slightly inefficient; however, this code is executed once per simulated annealing run. Not worth optimizing. (apl)

Definition at line 896 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::assign_zero_state ( )

virtual

Assign the node to state 0 – the "unassigned" state.

SurfaceNode::assign_zero_state

Detailed:: A node in state 0 produces no surface score. Its neighbors have to adjust their scores appropriately. This method iterates over all the edges emanating from this node and tells them to acknowledge that they've been zeroed out.

Definition at line 817 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::average_residue_hASA ( ) const

Returns the amount of hydrophobic ASA this node/residue adds to a patch.

SurfaceNode::average_residue_hASA

Detailed:: This method is oblivious to whether a given residue should contribute to the patch area. This function just does the lookup for the hASA (using the SurfacePotential class). Calls to this function should be surrounded by is-this- a-surface-exposed-hydrophobic checks.

Definition at line 2108 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::average_residue_hASA	(	chemical::AA	residue_type,
		Size	num_nbs
	)		const

Same function as above, but this one allows you to specify what type and num_nbs. This function is meant to be used only when initializing all of the Nodes/BGNodes because at that point we have to use the wild-type residue type, not the new rotamers residue type (which is what the above function will do).

SurfaceNode::average_residue_hASA

Definition at line 2121 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfacePotential::average_residue_hASA(), and core::pack::interaction_graph::SurfacePotential::get_instance().

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::calculate_amount_total_hydrophobic_ASA ( )

SurfaceNode::calculate_amount_total_hydrophobic_ASA

Detailed:: Iterates over all the edges emanating from a residues context graph and determines how many surface-exposed total neighbors that residue has including itself. Uses the context graph in the Pose object because this function is only used for initialization. After being calculated once, incrementing and decrementing can be used instead of reiterating over all edges.

Bug source. This function is not just used once during initialization.

As of 8/1/08, changing this function to iterate over all residues in the pose to determine the number of se nbs instead of using the tenA neighbor graph. This change is so that different interaction thresholds can be used. For example, say I want to find all patches within 8A, not 10A. Can't use the 10A to initialize with or certain correctness checks fail in the Node methods.

Big change: Making this method be part of Node/BGNodes. It's just too difficult to keep this method as part of the SIG. And I can't immediately think of a good reason to keep it in the SIG. It's more a functionality which the nodes should handle.

02/20/09, Changing the method to return the total amount of hydrophobic accessibile surface area instead of the number of hydrophobic neighbors. But most of the code remains the same. We want to sum up the average residue hASA for all of the surface-exposed neighbors within 10A.

Definition at line 2023 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::commit_considered_substitution_surface ( )

Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering.

SurfaceNode::commit_considered_substitution_surface

Detailed:: If the node had procrastinated the surface deltaE computation because it thought the sim-annealer unlikely to accept the substitition, then the node must now do the work it procrastinated.

There's a potential situation with considers() and commits() that needs to be checked for here. It's possible that a consider() call is made which causes a set of Nodes to update their alt state counts correspondingly. Since the consider() only gets processed by (or actually the call only goes out to) Nodes which are neighbor graph neighbors, only those Nodes will have their counts updated. Assume that the first consider() is really bad and no commit goes out. If we then consider() another sub, the alt state counts at the previous consider()'s set of nodes are incorrect. If get_deltaE is called by this consider() on some of those nodes, some of them will have their alt states reset. But when the commit goes out to ALL Nodes that are neighbors (NOT just the neighbor graph neighbors) it's possible that some of the Nodes will save the wrong alt state count. One way I think this can be avoided to is check at this node, if the alt state count is different from current, whether the node that originally changed is a neighbor graph neighbor of this node. If it is, that means the counts changed because of that node. If it's not, then this Node must have been one of the ones that fell out of sync. Oooooh, I just thought of another way. When the SIG consider() method is called, I could have a reset alt state counts method that will deal with Nodes that are out of sync. That's more elegant than yet another if statement here!

Definition at line 1372 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

virtual

Returns the amount of dynamic memory used by this Node object.

SurfaceNode::count_dynamic_memory

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

Definition at line 1734 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

Returns the amount of static memory used by this Node object.

SurfaceNode::count_static_memory

Definition at line 1723 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

private

SurfaceNode< V, E, G >::decide_procrastinate_surface_computations()

Detailed:: Makes the decision whether or not to procrastinate calculating the surface 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 surface deltaE also comes back better (dE < 0), then return false. Finally, if the difference between the deltaE for the PD terms and the (guessed) surface deltaE is greater than the threshold, return true so we do procrastinate. So basically if the energy (especially the PD energy) gets worse, procrastinate. Otherwise, don't.

Definition at line 1156 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node	(	int	node_index,
		bool	first_class
	)		const

Determines if this vertex neighbors the calling node Called by all other nodes, and if true is returned an Edge of some sort is created between the nodes.

SurfaceNode::detect_neighborship_with_node

Detailed:: To determine whether the passed in fc node is neighbors with this one, we need to iterate through the list of neighbors in the tenA neighbor graph (a ContextGraph) that's stored in the Pose Energies object. Assumes that the Pose has already been scored by some ScoreFunction. The tenA neighbor graph is cool if we want to look at an interaction distance of 10A. But what if we want to only find patches of exposed hydrophobics within an 8A sphere. Then we can't use the tenA neighbor. Instead use an expensive distance measurement between the centroids of the wild-type residues to determine "are they neighbors".

The only problem with making this method generic for fc nodes or bg nodes is that when an index is passed in, it's not possible to really tell if it's a fc node index or bg node index. Rather than making two separate methods for detecting neighborship, add a second parameter to this function which specificies if the node being checked is fc or not. That way we can get the pose residue object correct.

This method basically makes the decision for whether to create a SurfaceEdge or SurfaceBackgroundEdge between two Nodes. It really is what defines how much of the surface we design for.

Definition at line 749 of file SurfaceInteractionGraph.hh.

References core::kinematics::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::detect_neighborship().

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::get_alt_hASA ( )

Returns current hASA. Only used by the unit tests. Should not exist in release mode.

SurfaceNode::get_alt_hASA

Definition at line 4195 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

std::vector< Real > core::pack::interaction_graph::SurfaceNode< V, E, G >::get_alt_state_hASA_for_node_and_nbs ( )

Returns a vector of Reals containing the hASA of se hp nbs for this node in the first index, and then the hASA for all neighboring nodes and bgnodes. Note: Order is not guaranteed here. Only used by the unit tests. Should not exist in release mode.

SurfaceNode::get_alt_state_hASA_for_node_and_nbs

Definition at line 4161 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::get_curr_state_surface_energy ( ) const

returns the surface energy for the node in its current state assignment

SurfaceNode::get_curr_state_surface_energy()

Definition at line 922 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::get_current_hASA ( )

Returns current hASA. Only used by the unit tests. Should not exist in release mode.

SurfaceNode::get_current_hASA

Definition at line 4140 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceBackgroundEdge< V, E, G >* core::pack::interaction_graph::SurfaceNode< V, E, G >::get_edge_to_surface_bg_node ( int index) const

inlineprotected

Definition at line 169 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::FirstClassNode< V, E, G >::get_edge_to_bg_node().

template<typename V , typename E , typename G >

std::vector< Real > core::pack::interaction_graph::SurfaceNode< V, E, G >::get_hASA_for_node_and_nbs ( )

Returns a vector of Reals containing the hASA of se hp nbs for this node in the first index, and then the hASA for all neighboring nodes and bgnodes. Note: Order is not guaranteed here. Only used by the unit tests. Should not exist in release mode.

SurfaceNode::get_hASA_for_node_and_nbs

Definition at line 4107 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceEdge< V, E, G >* core::pack::interaction_graph::SurfaceNode< V, E, G >::get_incident_surface_edge ( int index) const

inlineprotected

Definition at line 164 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

SurfaceNode::get_rotamer

Need to save a reference to the rotamer_set so that we can determine what a particular state change will do to the score

Definition at line 1838 of file SurfaceInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution().

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution	(	SurfaceNode< V, E, G > *	node_considering_substitution,
		int	changing_nodes_curr_state,
		int	changing_nodes_alt_state
	)

returns the change in surface score for this node induced by a state substitution at a neighboring node.

SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution

Detailed:: So a neighboring first class node that is changing is invoking (via the SurfaceEdge that connects them) this method so that this node can update its counts and then return a change in surface score for this node. This method needs to check if the alt_state that the connected node is considering is going to change the counts here and then perform the lookup for the change in score.

is the rotamer id (state) the same for every node? no. need to either do the work in the edge class method or pass a reference to the node. oooooh, we can use the SIG to get the node changing, too!!! NO! Can't. The SIG get_surface_node( index ) method is protected. Lame. Since I need a way to check the rotamer vector for the changing node (to see what the changing states are) I have to make this method take a raw pointer to the node changing. The alternative would be to do all the state checking in the edge class method, but I feel like this sort of state checking should be done by a Node, not an Edge. Further, this frees the Edge class from having to keep any of the data that the Nodes contains (i.e. the counts of neighbors). The edges just pass along the message (from the changing node) to the other Node, not doing any kind of Node-specific behaviour.

the current state of this node may be unassigned (0). if so, we need to initialize the hASA properly. as of 7/22, the current amount of hydrophobic surface area should be init'd after prep for simA runs. alt state also. if ( parent::get_current_state() == 0 ) curr_state_total_hASA_ = get_surface_owner()->calculate_amount_total_hydrophobic_ASA;

07/24/08 problem situation it's probable that a sub that was considered before wasn't committed, so the alt state count at this node needs to go back to what the current state count is. the problem that may crop up with the reset here is that on a previous consider call, a set of nodes will update their counts. if commit is not called, and a second consider is called, then this node will have its alt state count reset but what about all the other nodes in the previous set. how will their counts get reset to the current state count? perhaps a check in the commit method can be added. nope, a new method has been added to Nodes and BGNodes to handle this case. alt_state_total_hASA_ = curr_state_total_hASA_;

02/20/09 Changed all variable names above to reflect hASA instead of counts.

Definition at line 1238 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::get_rotamer(), core::pack::interaction_graph::SurfaceNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff(), core::pack::interaction_graph::SurfaceNode< V, E, G >::num_neighbors_counting_self(), core::pack::interaction_graph::TR_NODE(), and core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_residue_for_node().

template<typename V, typename E, typename G>

SurfaceInteractionGraph< V, E, G >* core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_owner ( ) const

inlineprotected

Definition at line 174 of file SurfaceInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::SurfaceNode(), core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_residue_for_node(), and core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_seqpos_for_node().

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_score_difference ( ) const

Returns the difference alt state score - current state score.

SurfaceNode::get_surface_score_difference

Detailed:: This method requires that the variables current_state_ and alternate_state_ hold the correct values. An assert guard checks to make sure an out-of-bounds exception won't occur.

Definition at line 1309 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

unsigned int core::pack::interaction_graph::SurfaceNode< V, E, G >::getMemoryUsageInBytes ( ) const

virtual

Not implemented, but needs to be!

SurfaceNode::getMemoryUsageInBytes

Definition at line 1751 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::hASA_energy ( Real patch_area) const

Calls a SurfacePotential class method to get the energy for a given patch area. Only nodes with number of nbs less than or equal to SURFACE_EXPOSED_CUTOFF will get a score. All other nodes will have a score of 0.0.

SurfaceNode::hASA_energy()

Definition at line 2136 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfacePotential::get_instance(), and core::pack::interaction_graph::SurfacePotential::hASA_patch_energy().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::init_hASA_variables ( )

SurfaceNode::init_hASA_variables

Definition at line 1992 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::initialize_num_neighbors_counting_self ( ) const

Returns the number of neighbors within the interaction threshold, counting self.

SurfaceNode::initialize_num_neighbors_counting_self Detailed: A member variable stores the value so that this method only has to run once and lookups can be performed thereafter. The reason we need to know the number of neighbors is that determining whether a residue is surface exposed depends on how many neighbors it has. For most applications, we have been using the approximation that residues with fewer than 16 neighbors in a 10A radius are surface-exposed. The original method of doing this was done with the tenA nb graph. Then I switched to using cB-cB distances and using the INTERACTION_RADIUS to define neighbors. I'm reverting back to using the tenA neighbor graph. The number of neighbors variable is only used to determine whether a residue is surface exposed or not. It's not like the detect neighborship between Node objects method that effectively defines how much of the surface gets looked at per substitution. Thus, using the tenA nb graph here is ok.

Definition at line 1933 of file SurfaceInteractionGraph.hh.

References core::graph::Graph::get_node(), core::graph::Node::num_neighbors_counting_self(), and core::pack::interaction_graph::TR_NODE().

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff ( ) const

Returns the value of is_below_buried_residue_no_hsasa_cutoff_ which gets set during the SIG initialize() method.

SurfaceNode::is_below_buried_residue_no_hsasa_cutoff

Definition at line 1875 of file SurfaceInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff ( bool value)

setter for the is_below_buried_residue_no_hsasa_cutoff_ bool

SurfaceNode::is_below_buried_residue_no_hsasa_cutoff

Definition at line 1886 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::is_surface_exposed ( ) const

Returns the value of surface_exposed_ which gets set during the SIG initialize() method.

SurfaceNode::is_surface_exposed

Definition at line 1852 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_neighbors_counting_self ( ) const

Returns the value stored in the member variable.

SurfaceNode::num_neighbors_counting_self

Definition at line 1978 of file SurfaceInteractionGraph.hh.

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution().

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

virtual

invokes V's prep_for_simA method Also populates a map defining which nodes are neighbors according to the tenA neighbor graph. This map will be checked whenever iterating over all edges defined by the energy graph to see if a Node really needs to be updated for the surface score.

SurfaceNode::prepare_for_simulated_annealing

Definition at line 686 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

useful for debugging - writes information about a node to the tracer

SurfaceNode::print

Definition at line 1687 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::print_surface_avoidance_stats ( )

static

reports on the level of success for surface score calculation procrastination

SurfaceNode::print_surface_avoidance_stats

Definition at line 1763 of file SurfaceInteractionGraph.hh.

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

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::project_deltaE_for_substitution_surface	(	int	alternate_state,
		core::PackerEnergy &	prev_PDenergies_for_node,
		float	deltaE_thresh_for_avoiding_surface_calcs
	)

Returns the (possibly approximate) change in energy induced by changing a node from its current state into some alternate state.

SurfaceNode::project_deltaE_for_substitution_surface

Detailed:: Iterates across the edges first to determine the sum of the pairwise decomposable (PD) energy. If the PD difference implies a collision, then the SurfaceNode pretends as if the state substitution causes the best improvement possible in surface score for it and its neighbors, returns the PD difference + pretend surface difference. It will procrastinate computing the actual surface score difference until the guiding SimAnnealer decides to commit the substitution. If the SimAnnealer rejects the substitution, then the work to compute the surface score is never done. If it is unclear that the SimAnnealer will reject the substitution based on the PD difference, then the vertex computes the change in surface score that it induces on its neighbors. The surface score calculation really isn't that intensive but it doesn't make sense to calculate it needlessly. (apl)

Bug source: Incident edges to a node are edges which have some energy on them based on the score function used (meaning they connect to nodes that interact with this node). This set of nodes is larger than the set of nodes that the tenA neighbor graph in the Pose considers neighbors for this node. Thus, when calculating the true number of se hp neighbors, some nodes are updated when they shouldn't be leading to incorrect counts. Possible solutions include 1) keeping some type of data structure (e.g. a map) which specifies which residues are neighbors (in the tenA neighbor graph sort of way) and whenever iterating over incident edges checking to make sure nodes are really neighbors before doing any updating of the counts; 2) forget about which nodes are truly neighbors (as determined by the tenA neighbor graph) and just use whatever the energy function thinks neighbors should be. I don't like this approach though, because I want to have the freedom to adjust what kind of radius I use for residue neighbors for future versions of the surface energy term. Not just assume that the energy function picks neighors correctly.

Where should the neighbor cache be kept? If I keep it on the Node, then the lookups would have to occur in the Node methods that change the counts. If I keep it on the Edges though, I can check for neighborship when iterating over edges and not ever even go into the Node methods. Keep it on the Nodes. That's where it makes sense to keep it.

Parameters

alternate_state - [in] - the alternate state that the node must consider prev_PDenergies_for_node - [out] - the sum of the PD energies (one-and two-body) for the node in its current state deltaE_thresh_for_avoiding_surface_calcs - [in] - the minimum deltaE for which the SimAnnealer will accept slopyness in the deltaE projections

Definition at line 983 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::project_surface_deltaE ( )

private

returns the change in surface score for this node and all of its neighbors produced by switching from its current state to an alternate state.

SurfaceNode< V, E, G >::project_surface_deltaE()

Definition at line 1022 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::reset_alt_state_total_hASA ( )

Sets the alt state total hASA to the current state total hASA. See comments in SIG and commit_considered_substitution_surface for more information about why this method exists.

SurfaceNode::reset_alt_state_total_hASA

Definition at line 1899 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::reset_surface_avoidance_stats ( )

static

resets static member variables of SurfaceNode that measure how worthwhile surface score calculation procrastination is.

SurfaceNode::reset_surface_avoidance_stats

Definition at line 1792 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::set_observed_sufficient_boolean_true ( )

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

SurfaceNode::set_observed_sufficient_boolean_true

Definition at line 4087 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::set_rotamers ( rotamer_set::RotamerSetCOP rotamers)

SurfaceNode::set_rotamers

Need to save a reference to the rotamer_set so that we can determine what a particular state change will do to the score

Definition at line 1806 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

virtual bool core::pack::interaction_graph::SurfaceNode< V, E, G >::state_unassigned ( ) const

inlinevirtual

Definition at line 93 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_exposed ( bool value)

setter for the surface_exposed_ bool

SurfaceNode::surface_exposed

Definition at line 1863 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::track_surface_E_min ( )

private

Keeps track of the minimum surface score seen. Every 100 substitutions, updates the variable surface_score_min_last_100.

SurfaceNode< V, E, G >::track_surface_E_min

Definition at line 1656 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceNode< V, E, G >::verify_patch_areas_correct	(	int	node_id,
		int	previous_state,
		Real	previous_state_hASA
	)

Checks to make sure that the current state num se hp nbs is correct, by going through all residues in the Pose and brute-force recounting.

SurfaceNode< V, E, G >::verify_patch_areas_correct

Definition at line 1425 of file SurfaceInteractionGraph.hh.

References core::kinematics::distance(), core::conformation::Residue::nbr_atom(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), core::pack::interaction_graph::TR_NODE(), and core::conformation::Residue::xyz().

template<typename V, typename E, typename G>

conformation::Residue core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_residue_for_node ( ) const

inline

Definition at line 130 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_owner().

Referenced by core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_deltaE_for_neighbors_state_substitution(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution().

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_seqpos_for_node ( ) const

inline

Definition at line 126 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::get_surface_owner().

Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution().

Member Data Documentation

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::alt_state_total_hASA_

private

Definition at line 188 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

std::map< std::pair<int, int >, int > core::pack::interaction_graph::SurfaceNode< V, E, G >::bg_neighbor_map

private

Definition at line 200 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceNode< V, E, G >::BURIED_RESIDUE_NO_HSASA_CUTOFF = 24

staticprivate

Definition at line 208 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::calculated_surface_deltaE_

private

Definition at line 184 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::curr_state_total_hASA_

private

Definition at line 187 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::deltaE_for_substitution_

private

Definition at line 185 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

std::map< std::pair<int, int >, int > core::pack::interaction_graph::SurfaceNode< V, E, G >::fc_neighbor_map

private

Definition at line 199 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::have_prepared_for_simA_

private

Definition at line 190 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceNode< V, E, G >::INTERACTION_RADIUS = 10

staticprivate

Definition at line 206 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff_

private

Definition at line 198 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceNode< V, E, G >::MAX_PATCH_SURFACE_AREA = 1100

staticprivate

Definition at line 209 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceNode< V, E, G >::MAX_SURFACE_ENERGY = 100

staticprivate

Definition at line 205 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_neighbors_counting_self_

mutableprivate

Definition at line 202 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_state_substitutions_considered_

staticprivate

Definition at line 211 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_substitutions_since_surface_min_update_

private

Definition at line 194 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_surface_comps_later_made_

staticprivate

Definition at line 213 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceNode< V, E, G >::num_surface_comps_procrastinated_

staticprivate

Definition at line 212 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::observed_sufficient_surface_E_to_predict_min_

private

Definition at line 195 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

rotamer_set::RotamerSetCOP core::pack::interaction_graph::SurfaceNode< V, E, G >::rotamer_set_

Definition at line 122 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

utility::vector1< conformation::ResidueCOP > core::pack::interaction_graph::SurfaceNode< V, E, G >::rotamers_vector_

Definition at line 123 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_energy_weight_ = 1.0

staticprivate

Definition at line 204 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_exposed_

private

Definition at line 197 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceNode< V, E, G >::SURFACE_EXPOSED_CUTOFF = 20

staticprivate

Definition at line 207 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_score_min_last_100_

private

Definition at line 192 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceNode< V, E, G >::surface_score_min_recent_

private

Definition at line 193 of file SurfaceInteractionGraph.hh.

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

src/core/pack/interaction_graph/SurfaceInteractionGraph.hh

Public Types

Public Member Functions

Static Public Member Functions

Public Attributes

Protected Member Functions

Private Member Functions

Private Attributes

Static Private Attributes

Detailed Description

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

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation

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