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

#include <SurfaceInteractionGraph.fwd.hh>

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

Collaboration diagram for core::pack::interaction_graph::SurfaceInteractionGraph< 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
	SurfaceInteractionGraph (int num_nodes)
	Main constructor. More...

virtual	~SurfaceInteractionGraph ()

void	initialize (rotamer_set::RotamerSetsBase const &rot_sets)

virtual void	prepare_for_simulated_annealing ()
	Prepares the graph to begin simulated annealing. More...

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

virtual core::PackerEnergy	set_state_for_node (int node_ind, int new_state)
	Assign new_state to the first class node with index node_ind. More...

virtual core::PackerEnergy	set_network_state (FArray1_int &node_states)
	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. Like after simulated annealing is done with! More...

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

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

virtual core::PackerEnergy	get_energy_current_state_assignment ()
	returns the energy of the entire graph under the current network state assignment. More...

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

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

void	set_num_background_residues (int 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. first class residues, in terms of surface, will be residues that are surface exposed and are varying. background residues will be ones that are surface exposed but not varying since they will contribute to the surface score of the first class residues and whose own surface score will change depending on the first class residues. More...

void	print_internal_energies_for_current_state_assignment ()
	Prints out the one and two-body energies for every node and bgnode in the graph. More...

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

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

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

pose::Pose const &	pose () const

void	set_pose (pose::Pose const &pose)

task::PackerTask const &	packer_task () const

void	set_packer_task (task::PackerTask const &task)
	We need a copy of the packer task for 2 reasons: 1) to figure out what (if any) the weight on the surface score is; and 2) to determine which residues are being packed and/or designed. We have to figure the packing options because it determines whether a residue becomes a FirstClass (SurfaceNode) node or a background node. More...

void	set_surface_score_weight (Real weight)

Real	surface_score_weight ()

rotamer_set::RotamerSets const &	rotamer_sets () const

void	set_rotamer_sets (rotamer_set::RotamerSets const &rotsets)

int	bg_node_2_resid (int 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_surface_E_to_predict_min_ to true. Only used by the unit tests. More...

std::vector< Real >	get_hASA_for_node_and_nbs (int index)
	Sets the observed_sufficient_surface_E_to_predict_min_ to true. Only used by the unit tests. More...

std::vector< Real >	get_alt_state_hASA_for_node_and_nbs (int index)
	Sets the observed_sufficient_surface_E_to_predict_min_ to true. Only used by the unit tests. More...

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...

virtual	~AdditionalBackgroundNodesInteractionGraph ()
	AdditionalBackgroundNodesInteractionGraph destructor. More...

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

int	get_num_background_nodes () const

Protected Member Functions
virtual core::pack::interaction_graph::NodeBase *	create_new_node (int node_index, int num_states)
	factory method pattern for instantiation of SurfaceNode objects, used by InteractionGraphBase class. More...

virtual core::pack::interaction_graph::EdgeBase *	create_new_edge (int index1, int index2)
	factory method pattern for instantiation of SurfaceEdge objects, used by InteractionGraphBase class. More...

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

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

SurfaceNode< V, E, G > *	get_surface_node (int index) const

SurfaceBackgroundNode< V, E, G > *	get_surface_bg_node (int index) const

void	update_internal_energy_totals_surface ()
	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	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_for_simulated_annealing ()
	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	detect_background_residue_and_first_class_residue_neighbors ()
	iterates across all pairs of first- and second-class nodes to determine which should be considered neighbors. Adds a SurfaceBackgroundEdge between any pair that are. More...

void	blanket_reset_alt_state_total_hASAs ()
	Iterates through all Nodes and BGNodes and resets their alt state total hASA to the current state total hASA. More...

	SurfaceInteractionGraph ()

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

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

Static Private Attributes
static const int	COMMIT_LIMIT_BETWEEN_UPDATES = 1024

static const int	SURFACE_EXPOSED_CUTOFF = 20

static const int	BURIED_RESIDUE_NO_HSASA_CUTOFF = 24

Detailed Description

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

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

SurfaceInteractionGraph

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

Definition at line 29 of file SurfaceInteractionGraph.fwd.hh.

Member Typedef Documentation

template<typename V, typename E, typename G>

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

Definition at line 493 of file SurfaceInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

Main constructor.

SurfaceInteractionGraph::SurfaceInteractionGraph

Parameters

num_nodes - [in] - the number of first class nodes in the graph. The number of second class nodes is reported to the graph much later.

Definition at line 3172 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceInteractionGraph::~SurfaceInteractionGraph

Definition at line 3190 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

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

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

SurfaceInteractionGraph::bg_node_2_resid

Definition at line 3478 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::blanket_assign_state_0 ( )

virtual

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

SurfaceInteractionGraph::blanket_assign_state_0

Definition at line 3592 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::blanket_reset_alt_state_total_hASAs ( )

private

Iterates through all Nodes and BGNodes and resets their alt state total hASA to the current state total hASA.

SurfaceInteractionGraph::blanket_reset_alt_state_total_hASAs

Detailed:: the Node consider() function is the main entry point from the SIG when the annealer considers a sub. need to make sure that the node's alt_state hASA is the same as the current state before we start incrementing/decrementhing things or otherwise I wind up with total hASAs that are wrong. alt state will be the same as current state on the first time through because of prep for simA call, but not necessarily the case on next substitution coming from annealer. this only sets the alt state hASA on this particular (changing) node. all of the other nodes which were called on to consider a substitution and whose hASAs changed need to reset their alt state hASA also (or, otherwise, it appears as if the substitution was committed). More about this problem can be read in the comments for commit_considered_substitution_surface()

02/23/2009 Updated this function and the functions it calls to do everything in terms of hASA instead of se hp counts.

Definition at line 3731 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::commit_considered_substitution ( )

virtual

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

SurfaceInteractionGraph::commit_considered_substitution

Definition at line 3757 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

virtual

returns the change in energy induced by switching a particular node from its currently assigned state to some alternate state.

SurfaceInteractionGraph::consider_substitution

Detailed:: 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

Definition at line 3689 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

virtual

SurfaceInteractionGraph::count_dynamic_memory

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

Definition at line 3997 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

SurfaceInteractionGraph::count_static_memory

Definition at line 3988 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

protectedvirtual

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

SurfaceInteractionGraph::create_background_edge

Parameters

fc_node_index - [in] - the index of the first class node sc_node_index - [in] - the index of the second class node

Remarks: Returns a pointer to the created SurfaceBackgroundEdge

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

Definition at line 3921 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

protectedvirtual

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

SurfaceInteractionGraph::create_background_node

Parameters

node_index - [in] - the index of the (second class) node

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

Definition at line 3898 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

protectedvirtual

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

SurfaceInteractionGraph::create_new_edge

Parameters

index1 - [in] - the index of the lower-indexed (first class) node index2 - [in] - the index of the higher-indexed (first class) node

Definition at line 3879 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

protectedvirtual

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

SurfaceInteractionGraph::create_new_node

Detailed:: The IGBase class calls this method for all residues that are designable.

Parameters

node_index - [in] - the index of the (first class) node num_states - [in] - the number of states for that node

Definition at line 3858 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::detect_background_residue_and_first_class_residue_neighbors ( )

private

iterates across all pairs of first- and second-class nodes to determine which should be considered neighbors. Adds a SurfaceBackgroundEdge between any pair that are.

SurfaceInteractionGraph::detect_background_residue_and_first_class_residue_neighbors

Definition at line 3553 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

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

SurfaceInteractionGraph::get_alt_state_hASA_for_node_and_nbs

Definition at line 4241 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::get_edge_memory_usage ( ) const

virtual

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

SurfaceInteractionGraph::get_edge_memory_usage

Definition at line 3979 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::get_energy_current_state_assignment ( )

virtual

returns the energy of the entire graph under the current network state assignment.

SurfaceInteractionGraph::get_energy_current_state_assignment

Definition at line 3837 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

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

SurfaceInteractionGraph::get_hASA_for_node_and_nbs

Definition at line 4229 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

std::vector< int > core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::get_network_state ( ) const

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

SurfaceInteractionGraph::get_network_state

Definition at line 4213 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

SurfaceBackgroundNode< V, E, G >* core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::get_surface_bg_node ( int index) const

inlineprotected

Definition at line 566 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

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

inlineprotected

Definition at line 561 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

SurfaceInteractionGraph::initialize()

Detailed:: This initialize() method needs to do two things: 1) it needs to set residues that are not changing as background residues and 2) it needs to save references to the rotamer set or sets so that nodes can later figure out whether a particular rotamer change is a hydrophobic or not.

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 SASAInteractionGraph, it first initializes the PDInteractionGraph (which is the base) and then calls the SASAIG 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 SurfaceInteractionGraph (SIG). 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 SIG init method is called during construction of the SIG, then the init method that's called by the rotsets object causes all the node info that was set in the SIG 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 tasks 1) and 2) above then. It doesn't really matter when the tasks get done as long as it happens before SA starts. This also means that the SIG 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).

prepare_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 SIG init method directly after the IG init method that the RS object calls.

Older comments: This interaction graph is templated so that it can be used with the original PD or the OTF graphs. If it's an OTF graph, then a reference to the pose object is available with the pose() method. However, I can't rely on having that method for the case when an OTF graph is not used. Thus, take the pose reference in as a parameter and refactor later if necessary.

Newest comments: Don't call the parent classes initialize method because that calls create_new_node for all designable position, making every node in the graph a first class residue (erroneously!). Then after that, some residues are set as background residues so I'm surprised things were even working at all! Unfortunately, the class hierarchy makes setting designable residues that are surface-exposed be the only FirstClassNodes difficult. What has to happen is that non-designable positions will be the BGNodes and molten positions will be FCNodes. Then, each type of node will store a boolean flagging whether it is surface-exposed or not. Then, when a consider sub call is made, the nodes will immediately check the value of the boolean and return 0 immediately if it's not surface-exposed.

07/16/2008- Unfortunately, I can't just replicate all of the functionality of the parent classes initialize method here because it's different for PDIGs and LMIGs. And some of the their corresponding function calls are not defined in both classes so I get compile errors if I try to do it this way. There are a few possible solutions I could use for the problem of schizophrenic node (nodes which are getting assigned as BG and FC nodes). 1) I could just use Andrew's LFs designation that any designable or packable node is a FC node and any node not being packed or designed is a BGNode. This approach is the easiest to implement but since nodes that are only being packed aren't changing in sequence, their surface score shouldn't be changing so it's an inefficiency. 2) I could change the "create_node" call in this class to return either a Node or BGNode depending on what the packer_task has in it. Then the parent templated IG classes would get the right kind of node. But then, I would have to potentially change the AddtlBGNodesIG class method "setNumResiduesAsBackground" because in that call is a for loop which creates background nodes. This would complicate creating new non-PD terms in mini, because it would be specific for this case (surface). 3) Figure out some OO way of handling the distinction between packable and nonpackable residues. The OO-correct way to do this would probably be to subclass AdditionalBackgroundNodesInteractionGraph to something like SurfaceExposedNodesInteractionGraph and then make the SurfaceInteractionGraph inherit that one. Then "FirstClassNodes" would be nodes that are designable and surface-exposed; all other nodes would be "BackgroundNodes".

Since it would require alot of work to write another derived class for probably not that significant (or necessary) performance improvement, I'll just make packable residues be FC nodes also. So continue to call the parent classes initialize() method. Just set residues which are not packable nor designable to BG nodes.

Definition at line 3264 of file SurfaceInteractionGraph.hh.

References core::pack::rotamer_set::RotamerSets::nmoltenres(), and TR_SIG().

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

inline

Definition at line 531 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

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

inline

Definition at line 527 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

virtual

Prepares the graph to begin simulated annealing.

SurfaceInteractionGraph::prepare_for_simulated_annealing

Detailed:: Invokes both base-class prepare_for_simulated_annealing subroutines: InteractionGraphBase first, to prepare the SurfaceNodes and SurfaceEdges. Then the AdditionalBackgroundNodesInteractionGraph, to prepare the SurfaceBackgroundNodes, the SurfaceBackgroundEdges, and to do a little more preparing of the SurfaceNodes.

Remarks: As it is written, it should only be executed once; that will change, however if we make SurfaceInteractionGraph work with ligands (ligands that stay fixed during any single sim annealing process, but that move between anealings.

Definition at line 3506 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

useful for debugging

SurfaceInteractionGraph::print

Definition at line 4060 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::print_internal_energies_for_current_state_assignment ( )

Prints out the one and two-body energies for every node and bgnode in the graph.

SurfaceInteractionGraph::print_internal_energies_for_current_state_assignment

Definition at line 3933 of file SurfaceInteractionGraph.hh.

References core::scoring::surface, and TR_SIG().

template<typename V, typename E, typename G>

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

inline

Definition at line 538 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_errorfull_deltaE_threshold ( Real deltaE)

virtual

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

SurfaceInteractionGraph::set_errorfull_deltaE_threshold

Detailed:: When the annealer asks the graph to consider a state substitution that produces a large collision, the graph may approximate the surface deltaE instead of recalculating it. 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 surface computations and return an accurate total energy for the graph.

Definition at line 3654 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::print_surface_avoidance_stats(), core::pack::interaction_graph::SurfaceNode< V, E, G >::reset_surface_avoidance_stats(), and TR_SIG().

template<typename V , typename E , typename G >

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

virtual

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. Like after simulated annealing is done with!

SurfaceInteractionGraph::set_network_state

Remarks: Considered removing the use of FArrays here, but unfortunately it's what the Annealers use and I'm not qualified to be refactoring the annealers.

Parameters

node_states - [in] - the array of states, one for each vertex in the graph

Definition at line 3792 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_num_background_residues ( int 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

SurfaceInteractionGraph::set_num_background_residues

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

Parameters

num_background_residues - [in] - the number of background residues in the protein.

Definition at line 3423 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_num_residues_in_protein ( int num_res)

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

SurfaceInteractionGraph::set_num_residues_in_protein

Detailed:: 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.

How does this method handle cofactors, ligands that get included in pose().total_residue()? It definitely allocates space in the array for them, and those residues will apparently be made into first-class nodes. But when it comes time to do the packing, they don't matter because they're not hydrophobic - they're not even amino acids - so they don't get updated.

Parameters

num_res - [in] - the total number of residues

Definition at line 3398 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< 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.

SurfaceInteractionGraph::set_observed_sufficient_boolean_true

Definition at line 4253 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

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

We need a copy of the packer task for 2 reasons: 1) to figure out what (if any) the weight on the surface score is; and 2) to determine which residues are being packed and/or designed. We have to figure the packing options because it determines whether a residue becomes a FirstClass (SurfaceNode) node or a background node.

SurfaceInteractionGraph::set_packer_task

Definition at line 4037 of file SurfaceInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

SurfaceInteractionGraph::set_pose

Definition at line 4012 of file SurfaceInteractionGraph.hh.

References protocols::comparative_modeling::features::G, and TR_SIG().

template<typename V , typename E , typename G >

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

informs the graph that a particular residue is part of the background. first class residues, in terms of surface, will be residues that are surface exposed and are varying. background residues will be ones that are surface exposed but not varying since they will contribute to the surface score of the first class residues and whose own surface score will change depending on the first class residues.

SurfaceInteractionGraph::set_residue_as_background_residue

Parameters

residue - [in] - the residue identifier

Definition at line 3453 of file SurfaceInteractionGraph.hh.

References TR_SIG().

template<typename V , typename E , typename G >

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

SurfaceInteractionGraph::set_rotamer_sets

Definition at line 4047 of file SurfaceInteractionGraph.hh.

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_state_for_node	(	int	node_ind,
		int	new_state
	)

virtual

Assign new_state to the first class node with index node_ind.

SurfaceInteractionGraph::set_state_for_node

Parameters

node_ind - [in] - the index of the (first class) node new_state - [in] - the new state assigned to the node

Definition at line 3820 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::set_surface_score_weight ( Real weight)

inline

Definition at line 534 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::surface_score_weight_.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::surface_score_weight ( )

inline

Definition at line 535 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::surface_score_weight_.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::update_internal_energy_totals_surface ( )

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.

SurfaceInteractionGraph::update_internal_energy_totals_surface

Definition at line 3613 of file SurfaceInteractionGraph.hh.

References core::pack::interaction_graph::SurfaceNode< V, E, G >::print_surface_avoidance_stats(), and TR_SIG().

Member Data Documentation

template<typename V, typename E, typename G>

utility::vector1< int > core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::bgenumeration_2_resid_

private

Definition at line 580 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

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

staticprivate

Definition at line 591 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

const int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::COMMIT_LIMIT_BETWEEN_UPDATES = 1024

staticprivate

Definition at line 589 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::deltaE_threshold_for_avoiding_surface_calcs_

private

Definition at line 586 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::node_considering_alt_state_

private

Definition at line 585 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::num_commits_since_last_update_

private

Definition at line 582 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::num_residues_assigned_as_background_

private

Definition at line 577 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

int core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::num_total_residues_

private

Definition at line 576 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

task::PackerTaskOP core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::packer_task_

private

Definition at line 594 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

pose::PoseOP core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::pose_

private

Definition at line 593 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::prepared_for_simulated_annealing_

private

Definition at line 587 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

utility::vector1< int > core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::resid_2_bgenumeration_

private

Definition at line 579 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

rotamer_set::RotamerSetsOP core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::rotamer_sets_

private

Definition at line 595 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

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

staticprivate

Definition at line 590 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

core::Real core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::surface_score_weight_

private

Definition at line 596 of file SurfaceInteractionGraph.hh.

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

template<typename V, typename E, typename G>

core::PackerEnergy core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::total_energy_alternate_state_assignment_

private

Definition at line 584 of file SurfaceInteractionGraph.hh.

template<typename V, typename E, typename G>

core::PackerEnergy core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::total_energy_current_state_assignment_

private

Definition at line 583 of file SurfaceInteractionGraph.hh.

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

src/core/pack/interaction_graph/SurfaceInteractionGraph.fwd.hh
src/core/pack/interaction_graph/SurfaceInteractionGraph.hh

Private Attributes
int	num_total_residues_

int	num_residues_assigned_as_background_

utility::vector1< int >	resid_2_bgenumeration_

utility::vector1< int >	bgenumeration_2_resid_

int	num_commits_since_last_update_

core::PackerEnergy	total_energy_current_state_assignment_

core::PackerEnergy	total_energy_alternate_state_assignment_

int	node_considering_alt_state_

Real	deltaE_threshold_for_avoiding_surface_calcs_

bool	prepared_for_simulated_annealing_

pose::PoseOP	pose_

task::PackerTaskOP	packer_task_

rotamer_set::RotamerSetsOP	rotamer_sets_

core::Real	surface_score_weight_

Public Types

Public Member Functions

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::SurfaceInteractionGraph< 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::SurfaceInteractionGraph< V, E, G >