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

#include <HPatchInteractionGraph.hh>

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

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

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

typedef V	grandparent

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
	HPatchNode (G *owner, int node_index, int num_states)
	HPatchNode constructor. More...

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

void	set_rotamers (rotamer_set::RotamerSetCOP rotamers)

conformation::ResidueCOP	get_rotamer (int state) const
	Returns a constant OP to the rotamer/residue object for the given state. More...

conformation::ResidueCOP	curr_state_rotamer () const

conformation::ResidueCOP	alt_state_rotamer () const

virtual void	set_rotamer_dots_for_state (Size state, RotamerDots const &rd)
	stores the coordinates for a state. More...

bool	overlaps (HPatchNode< V, E, G > *neighbor)
	returns true if any sphere for any atom of any state on this vertex overlaps with any atom on any sphere on a neighboring vertex. More...

bool	detect_any_overlap_with_rotamer (RotamerDots const &rotamer) const
	determines if any atom for any rotamer of this vertex overlaps with any atom from some background residue. called by BGNodes for the detect_background_residue_and_first_class_residue_overlap phase of the prep for simA call in the HPatchIG. More...

virtual void	prepare_for_simulated_annealing ()
	invokes V's prep_for_simA method. Also computes the "self-overlap" that each of its rotamers has. More...

void	initialize_overlap_with_background (RotamerDots const &bg_rotamer, std::vector< RotamerDotsCache > &overlap, std::vector< utility::vector1< utility::vector1< bool > > > &states_atom_atom_overlap_on_bg_res)
	This method computes and caches each set of overlaps this node's states have with a background residue. More...

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

void	acknowledge_neighbors_substitution ()
	bookkeeping to follow a neighbors state substitution. this method gets called when a HPatchNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident HPatchEdges. 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 HPatchNode to know what other HPatchNodes are connected to it except via HPatchEdges, the calls seem a bit complicated. A HPatchNode 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 HPatchNode. The inform_non_changing method can not be removed, because it's used during the substitution evaluations as well. More...

core::PackerEnergy	calculate_PD_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_PDenergies_for_node)
	Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only. More...

core::PackerEnergy	get_pd_energy_delta ()
	Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub(). More...

Real	consider_alternate_state ()
	Instructs the Node to update the alt state information held by it and its neighbors in response to switching from the current state to an alternate state. More...

Real	get_current_state_sasa () const
	returns the amount of sasa this node has in its current state assignment More...

Real	get_current_state_sasa (Size atom_index) const
	Returns the current state SASA for the passed in atom index. More...

Real	get_alternate_state_sasa (Size atom_index) const
	Returns the alternate state SASA for the passed in atom index. More...

utility::vector1 < utility::vector1< bool > > const &	get_atom_atom_self_overlaps_for_state (Size state) const
	Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, in the given state. More...

Size	get_current_state_num_atoms () const

Size	get_alt_state_num_atoms () const

int	wt_seqpos_for_node () const

conformation::Residue const &	wt_residue_for_node () const

Real	update_state_for_neighbors_substitution (HPatchNode< V, E, G > *node_considering_substitution, RotamerDots &neighbors_alternate_state, RotamerDotsCache const &neighbors_curr_state_overlap_with_this, RotamerDotsCache &this_overlap_with_neighbors_alternate, RotamerDotsCache &neighbors_alternate_overlap_with_this, utility::vector1< utility::vector1< bool > > &alt_state_atom_atom_overlaps_cache)
	returns the change in sasa for this node induced by a state substitution at a neighboring node. The node increments the dot coverage count for the RotamerDots object representing the alternate state dots for that neighbor. More...

void	reset_alt_state_dots ()
	Sets the alt state rotamer dots to the current state rotamer dots. See comments in SIG and commit_considered_substitution for more information about why this method exists. More...

void	commit_considered_substitution ()
	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...

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...

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

RotamerDots const &	get_current_state_rotamer_dots ()
	Returns current state. Only used by the unit tests. More...

RotamerDots const &	get_alt_state_rotamer_dots ()
	Returns current state. Only used by the unit tests. More...

InvRotamerDots const &	curr_state_inv_dots () const

InvRotamerDots const &	alt_state_inv_dots () const

Size	max_hphobe_atoms_any_restype () const

utility::vector1< Size > const &	curr_state_hphobes () const

utility::vector1< Size > const &	alt_state_hphobes () const

Size	n_curr_state_hphobes () const

Size	n_alt_state_hphobes () const

utility::vector1< Size > const &	curr_state_exp_hphobes () const

utility::vector1< Size > const &	alt_state_exp_hphobes () const

Size	n_curr_state_exp_hphobes () const

Size	n_alt_state_exp_hphobes () const

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...

Protected Member Functions
HPatchEdge< V, E, G > *	get_incident_hpatch_edge (int index) const

HPatchBackgroundEdge< V, E, G > *	get_edge_to_hpatch_bg_node (int index) const

HPatchInteractionGraph< V, E, G > *	get_hpatch_owner () const

Real	get_sasa_difference () const
	Returns alt_state_rotamer_dots_.get_sasa() - curr_state_dots.get_sasa() except when either the current state or the alternate state is the unassigned state; state 0. More...

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
void	update_alt_state_exphphobes ()
	Updates the vector alt_state_exp_hphobes_ by checking the sasa of every atom in the residue currently on this Node. More...

void	initialize_self_overlap ()
	Initializes rotamer self overlap; called by HPatchInteractionGraph;:prepare_for_sim_annealing right before simulated annealing begins. More...

void	initialize_atom_atom_overlap_cache ()
	Initializes the atom_atom_overlaps vector. More...

	HPatchNode ()

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

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

Detailed Description

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

Defines a FirstClass node which will keep track of changes in the SASA and hpatch score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph.

HPatchNode

Remarks: No public default constructor makes this class uncopyable.

Definition at line 93 of file HPatchInteractionGraph.hh.

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef V core::pack::interaction_graph::HPatchNode< V, E, G >::grandparent

Definition at line 119 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

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

Definition at line 118 of file HPatchInteractionGraph.hh.

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

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

HPatchNode constructor.

HPatchNode< V, E, G >::HPatchNode

Definition at line 806 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::restype_group_for_rotamers_, core::pack::interaction_graph::HPatchNode< V, E, G >::rotamers_vector_, and core::pack::interaction_graph::HPatchNode< V, E, G >::self_and_bg_dots_for_states_.

template<typename V , typename E , typename G >

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

virtual

destructor – no dynamically allocated data, does nothing

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

Definition at line 825 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::acknowledge_neighbors_substitution ( )

bookkeeping to follow a neighbors state substitution. this method gets called when a HPatchNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident HPatchEdges. 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 HPatchNode to know what other HPatchNodes are connected to it except via HPatchEdges, the calls seem a bit complicated. A HPatchNode 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 HPatchNode. The inform_non_changing method can not be removed, because it's used during the substitution evaluations as well.

HPatchNode::acknowledge_neighbors_substitution

Definition at line 1279 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_exp_hphobes ( ) const

inline

Definition at line 225 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_exp_hphobes_.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_hphobes ( ) const

inline

Definition at line 217 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::hphobe_ats_for_restype_group_, and core::pack::interaction_graph::HPatchNode< V, E, G >::restype_group_for_rotamers_.

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

template<typename V, typename E, typename G>

InvRotamerDots const& core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_inv_dots ( ) const

inline

Definition at line 201 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_inv_dots_, core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_rotamer_dots_, core::pack::interaction_graph::RotamerDots::rotamer(), and core::pack::interaction_graph::InvRotamerDots::rotamer().

template<typename V, typename E, typename G>

conformation::ResidueCOP core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_rotamer ( ) const

inline

Definition at line 132 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::rotamers_vector_.

template<typename V , typename E , typename G >

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

virtual

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

HPatchNode::assign_zero_state

Detailed:: A node in state 0 produces no hpatch 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 1227 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::HPatchNode< V, E, G >::calculate_PD_deltaE_for_substitution	(	int	alternate_state,
		core::PackerEnergy &	prev_PDenergies_for_node
	)

Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only.

HPatchNode::calculate_PD_deltaE_for_substitution

Detailed:: This function always gets called for every substitution. Only the consider_alt_state() call can get procrastinated.

Definition at line 1359 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::commit_considered_substitution ( )

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.

HPatchNode::commit_considered_substitution

Detailed:: 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 states 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!

I'm not sure the above is really a problem in the case of this IG. It seems like even if a non-committed consider() call occurs that alters the alt state counts/dots at some set of nodes, when a following sub does get commit'd(), then the nodes that will get the commit message should have all been updated. Some nodes will still have alt_state counts that are weird, but when a consider() call comes back around to them, it should reset the alt_state before doing anything.

Definition at line 1677 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::consider_alternate_state ( )

Instructs the Node to update the alt state information held by it and its neighbors in response to switching from the current state to an alternate state.

HPatchNode< V, E, G >::consider_alternate_state()

Definition at line 1397 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

virtual

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

HPatchNode::count_dynamic_memory

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

Definition at line 1737 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

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

HPatchNode::count_static_memory

Definition at line 1726 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_exp_hphobes ( ) const

inline

Definition at line 224 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_exp_hphobes_.

template<typename V, typename E, typename G>

utility::vector1< Size > const& core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_hphobes ( ) const

inline

Definition at line 212 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::hphobe_ats_for_restype_group_, and core::pack::interaction_graph::HPatchNode< V, E, G >::restype_group_for_rotamers_.

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

template<typename V, typename E, typename G>

InvRotamerDots const& core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_inv_dots ( ) const

inline

Definition at line 197 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_inv_dots_, core::pack::interaction_graph::HPatchNode< V, E, G >::current_state_rotamer_dots_, core::pack::interaction_graph::RotamerDots::rotamer(), and core::pack::interaction_graph::InvRotamerDots::rotamer().

template<typename V, typename E, typename G>

conformation::ResidueCOP core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_rotamer ( ) const

inline

Definition at line 128 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::rotamers_vector_.

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::HPatchNode< V, E, G >::detect_any_overlap_with_rotamer ( RotamerDots const & bg_dots) const

determines if any atom for any rotamer of this vertex overlaps with any atom from some background residue. called by BGNodes for the detect_background_residue_and_first_class_residue_overlap phase of the prep for simA call in the HPatchIG.

HPatchNode::detect_any_overlap_with_rotamer

Definition at line 985 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::get_alt_state_num_atoms ( ) const

inline

Definition at line 162 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_rotamer_dots_, and core::pack::interaction_graph::RotamerDots::get_num_atoms().

template<typename V , typename E , typename G >

RotamerDots const & core::pack::interaction_graph::HPatchNode< V, E, G >::get_alt_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

HPatchNode::get_alt_state_rotamer_dots

Definition at line 4967 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::get_alternate_state_sasa ( Size atom_index) const

Returns the alternate state SASA for the passed in atom index.

HPatchNode::get_alternate_state_sasa()

Definition at line 1331 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchNode< V, E, G >::get_atom_atom_self_overlaps_for_state ( Size state) const

Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, in the given state.

HPatchNode< V, E, G >::get_atom_atom_self_overlaps_for_state

Definition at line 1344 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_num_atoms ( ) const

inline

Definition at line 161 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::current_state_rotamer_dots_, and core::pack::interaction_graph::RotamerDots::get_num_atoms().

template<typename V , typename E , typename G >

RotamerDots const & core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

HPatchNode::get_current_state_rotamer_dots

Definition at line 4959 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_sasa ( ) const

returns the amount of sasa this node has in its current state assignment

HPatchNode::get_current_state_sasa()

Detailed:: RotamerDots objects know when they are in the unassigned state, so nothing special needs to be done to handle the 0 state. But, we could also query parent using get_current_state() to check if it's nonzero as an alternative.

Definition at line 1307 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_sasa ( Size atom_index) const

Returns the current state SASA for the passed in atom index.

HPatchNode::get_current_state_sasa()

Definition at line 1319 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

HPatchBackgroundEdge< V, E, G >* core::pack::interaction_graph::HPatchNode< V, E, G >::get_edge_to_hpatch_bg_node ( int index) const

inlineprotected

Definition at line 236 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

HPatchInteractionGraph< V, E, G >* core::pack::interaction_graph::HPatchNode< V, E, G >::get_hpatch_owner ( ) const

inlineprotected

Definition at line 241 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

HPatchEdge< V, E, G >* core::pack::interaction_graph::HPatchNode< V, E, G >::get_incident_hpatch_edge ( int index) const

inlineprotected

Definition at line 231 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

core::PackerEnergy core::pack::interaction_graph::HPatchNode< V, E, G >::get_pd_energy_delta ( )

Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub().

HPatchNode< V, E, G >::get_pd_energy_delta()

Definition at line 1384 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

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

Returns a constant OP to the rotamer/residue object for the given state.

HPatchNode::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 908 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::get_sasa_difference ( ) const

protected

Returns alt_state_rotamer_dots_.get_sasa() - curr_state_dots.get_sasa() except when either the current state or the alternate state is the unassigned state; state 0.

HPatchNode::get_sasa_difference

Detailed:: This method requires that the variables current_state_ and alternate_state_ correspond to the rotamers held in current_state_rotamer_dots_ and alt_state_rotamer_dots_. Usually, alternate_state_ holds meaningful data only if a vertex is considering a state substitution. This method will be invoked by a vertex as it considers a state substitition; it will also be invoked by each of its neighbors. That means the statement alternate_state_ = current_state_; must be present in HPatchNode::update_state_for_neighbors_substitution().

Definition at line 1604 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

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

virtual

Not implemented, but needs to be!

HPatchNode::getMemoryUsageInBytes

Definition at line 1715 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_atom_atom_overlap_cache ( )

private

Initializes the atom_atom_overlaps vector.

HPatchNode::initialize_atom_atom_overlap_cache

Detailed:: The atom_atom_overlaps vector stores a boolean for the intra-residue atom-atom overlap for every state possible at this Node. During simulated annealing, the IG has to determine the connected components after every sub. To do this, it has to know which atoms are exposed as well as overlapping. Instead of recomputing atom-atom overlaps after every sub, do it once and cache the values on the Node.

Definition at line 1069 of file HPatchInteractionGraph.hh.

References core::kinematics::tree::distance_squared(), core::pack::interaction_graph::RotamerDots::get_atom_radius(), and core::scoring::get_overlap().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_overlap_with_background	(	RotamerDots const &	bg_rotamer_dots,
		std::vector< RotamerDotsCache > &	node_states_coverage_of_bg_res_,
		std::vector< utility::vector1< utility::vector1< bool > > > &	states_atom_atom_overlap_on_bg_res
	)

This method computes and caches each set of overlaps this node's states have with a background residue.

HPatchNode< V, E, G >::initialize_overlap_with_background

Detailed:: The node stores these overlaps in two places: 1) in the input vector from the HPatchBackgroundEdge object, and 2) in its own array of dot coverage counts for the self-and-background sphere overlaps.

Parameters

bg_rotamer - [in] - the RotamerDots object for the background residue node_states_coverage_of_bg_res_ -[out] - the array of RotamerDotsCache objects that the HPatchBackgroundEdge stores for the overlap of each state in this residue on the background residue. states_atom_atom_overlap_on_bg_res -[out] - an array that holds the atom-atom overlap each state on this Node has on the background residue

Definition at line 1166 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::RotamerDots::get_num_atoms().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::initialize_self_overlap ( )

private

Initializes rotamer self overlap; called by HPatchInteractionGraph;:prepare_for_sim_annealing right before simulated annealing begins.

HPatchNode::initialize_self_overlap

Definition at line 1046 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::max_hphobe_atoms_any_restype ( ) const

inline

Definition at line 207 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::max_hphobes_.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::n_alt_state_exp_hphobes ( ) const

inline

Definition at line 227 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_exp_hphobes_.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::n_alt_state_hphobes ( ) const

inline

Definition at line 222 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_hphobes().

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::n_curr_state_exp_hphobes ( ) const

inline

Definition at line 226 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_exp_hphobes_.

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::n_curr_state_hphobes ( ) const

inline

Definition at line 221 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_hphobes().

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

bool core::pack::interaction_graph::HPatchNode< V, E, G >::overlaps ( HPatchNode< V, E, G > * neighbor)

returns true if any sphere for any atom of any state on this vertex overlaps with any atom on any sphere on a neighboring vertex.

HPatchNode::overlaps

Detailed:: neighbor - [in] - the vertex that neighbors this vertex

Remarks: This method could be faster if I built a rotamer trie for each vertex, so I've got code in here to measure just how much time I spend on this task. In a complete redesign of UBQ, I spend 8 to 10 seconds in this method. In comparison, I spend 15 minutes in simulated annealing. (apl)

Definition at line 949 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::self_and_bg_dots_for_states_.

template<typename V , typename E , typename G >

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

virtual

invokes V's prep_for_simA method. Also computes the "self-overlap" that each of its rotamers has.

HPatchNode::prepare_for_simulated_annealing

Definition at line 1007 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

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

virtual

useful for debugging

HPatchNode::write_dot_kinemage HPatchNode::print

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

Definition at line 1766 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::reset_alt_state_dots ( )

Sets the alt state rotamer dots to the current state rotamer dots. See comments in SIG and commit_considered_substitution for more information about why this method exists.

HPatchNode::reset_alt_state_dots

Definition at line 1626 of file HPatchInteractionGraph.hh.

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

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::set_rotamer_dots_for_state	(	Size	state,
		RotamerDots const &	rd
	)

virtual

stores the coordinates for a state.

HPatchNode::set_rotamer_dots_for_state

Detailed:: Currently RotamerCoords stores the atoms in the order they are created for the pose. In the future, this might be changes to store the atoms in special trie order to reduce the number of sphere calculations necessary.

self_and_bg_dots_for_states_ is a vector1 of RotamerDots objects. the size of the vector is set during Node construction to parent::get_num_states().

Definition at line 928 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

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

HPatchNode::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 837 of file HPatchInteractionGraph.hh.

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::element(), core::chemical::ResidueType::nheavyatoms(), and core::pack::interaction_graph::TR_NODE().

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchNode< V, E, G >::update_alt_state_exphphobes ( )

private

Updates the vector alt_state_exp_hphobes_ by checking the sasa of every atom in the residue currently on this Node.

HPatchNode< V, E, G >::update_alt_state_exphphobes

Definition at line 1455 of file HPatchInteractionGraph.hh.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchNode< V, E, G >::update_state_for_neighbors_substitution	(	HPatchNode< V, E, G > *	node_considering_substitution,
		RotamerDots &	neighbors_alternate_state,
		RotamerDotsCache const &	neighbors_curr_state_overlap_with_this,
		RotamerDotsCache &	this_overlap_with_neighbors_alternate,
		RotamerDotsCache &	neighbors_alternate_overlap_with_this,
		utility::vector1< utility::vector1< bool > > &	atom_atom_overlaps_cache
	)

returns the change in sasa for this node induced by a state substitution at a neighboring node. The node increments the dot coverage count for the RotamerDots object representing the alternate state dots for that neighbor.

HPatchNode< V, E, G >::update_state_for_neighbors_substitution

Detailed:: The procedure is simple at heart – the caching makes it complex.

alt_state_rotamer_dots_ = current_state_rotamer_dots_; //copy dot coverage counts alt_state_rotamer_dots_.decrement( neighbors_curr_state_overlap_with_this ); alt_state_rotamer_dots_.increment_both( neighbors_alternate_state ); return ( alt_state_rotamer_dots_.get_score() - current_state_rotamer_dots_.get_score() );

Extensive caching techniques save time. Each HPatchEdge stores the dot coverage for each pair of HPatchNodes in their current state. These are stored in the RotamerDotsCache objects. Let's name the vertices: this vertex is vertex B. Vertex B is projecting its hpatch deltaE while vertex A is considering a substitution from one state to another. The edge connecting A and B provides node B with the set of masks for the overlap by the atoms of A's alternate state on all atoms of vertex B.

Parameters

neighbors_alternate_state - [in/out] - the RotamerDots object representing the alternate state vertex A (the neighbor) is considering. neighbors_curr_state_overlap_with_this - [in] - the RotamerDotsCache object held by the HPatchEdge connecting A and B that represents the coverage of A's current state of B's atoms. this_overlap_with_neighbors_alternate - [out] - the dot cache to store the results of computing the overlap of B's current state on A's alt state neighbors_alternate_overlap_with_this - [out] - the dot cache to store the results of computing the overlap of A's alt state on B's current state mask_this_covered_by_other - [in/out] - starting set of overlaps mask_other_covered_by_this - [in/out] - starting set of overlaps num_atoms_same - [in] - the number of atoms shared between A's current and alternate states.

What do we do when the current state is unassigned. Then that results in the alt_state starting from being unassigned and we get problems because the RotamerDots object doesn't have any memory assigned to it if it's in the unassigned state.

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_;

Definition at line 1510 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

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

inline

Definition at line 170 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::get_hpatch_owner().

template<typename V, typename E, typename G>

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

inline

Definition at line 165 of file HPatchInteractionGraph.hh.

References core::pack::interaction_graph::HPatchNode< V, E, G >::get_hpatch_owner().

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

Member Data Documentation

template<typename V, typename E, typename G>

bool core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_dots_matches_current_state_dots_

private

Definition at line 278 of file HPatchInteractionGraph.hh.

template<typename V, typename E, typename G>

utility::vector1< Size > core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_exp_hphobes_

private

Definition at line 276 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_exp_hphobes(), and core::pack::interaction_graph::HPatchNode< V, E, G >::n_alt_state_exp_hphobes().

template<typename V, typename E, typename G>

InvRotamerDots core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_inv_dots_

private

Definition at line 273 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

RotamerDots core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_rotamer_dots_

private

Definition at line 270 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_inv_dots(), and core::pack::interaction_graph::HPatchNode< V, E, G >::get_alt_state_num_atoms().

template<typename V, typename E, typename G>

utility::vector1< Size > core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_exp_hphobes_

private

Definition at line 275 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_exp_hphobes(), and core::pack::interaction_graph::HPatchNode< V, E, G >::n_curr_state_exp_hphobes().

template<typename V, typename E, typename G>

InvRotamerDots core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_inv_dots_

private

Definition at line 272 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

RotamerDots core::pack::interaction_graph::HPatchNode< V, E, G >::current_state_rotamer_dots_

private

Definition at line 269 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_inv_dots(), and core::pack::interaction_graph::HPatchNode< V, E, G >::get_current_state_num_atoms().

template<typename V, typename E, typename G>

utility::vector1< utility::vector1< Size > > core::pack::interaction_graph::HPatchNode< V, E, G >::hphobe_ats_for_restype_group_

private

Definition at line 260 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_hphobes(), and core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_hphobes().

template<typename V, typename E, typename G>

Size core::pack::interaction_graph::HPatchNode< V, E, G >::max_hphobes_

private

Definition at line 261 of file HPatchInteractionGraph.hh.

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

template<typename V, typename E, typename G>

utility::vector1< Size > core::pack::interaction_graph::HPatchNode< V, E, G >::restype_group_for_rotamers_

private

Definition at line 259 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_hphobes(), core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_hphobes(), and core::pack::interaction_graph::HPatchNode< V, E, G >::HPatchNode().

template<typename V, typename E, typename G>

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

private

Definition at line 258 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::alt_state_rotamer(), core::pack::interaction_graph::HPatchNode< V, E, G >::curr_state_rotamer(), and core::pack::interaction_graph::HPatchNode< V, E, G >::HPatchNode().

template<typename V, typename E, typename G>

utility::vector1< RotamerDots > core::pack::interaction_graph::HPatchNode< V, E, G >::self_and_bg_dots_for_states_

private

Definition at line 267 of file HPatchInteractionGraph.hh.

Referenced by core::pack::interaction_graph::HPatchNode< V, E, G >::HPatchNode(), and core::pack::interaction_graph::HPatchNode< V, E, G >::overlaps().

template<typename V, typename E, typename G>

utility::vector1< utility::vector1< utility::vector1< bool > > > core::pack::interaction_graph::HPatchNode< V, E, G >::self_atom_atom_overlaps_

private

Definition at line 264 of file HPatchInteractionGraph.hh.

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

src/core/pack/interaction_graph/HPatchInteractionGraph.hh

Private Attributes
utility::vector1 < conformation::ResidueCOP >	rotamers_vector_

utility::vector1< Size >	restype_group_for_rotamers_

utility::vector1 < utility::vector1< Size > >	hphobe_ats_for_restype_group_

Size	max_hphobes_

utility::vector1 < utility::vector1 < utility::vector1< bool > > >	self_atom_atom_overlaps_

utility::vector1< RotamerDots >	self_and_bg_dots_for_states_

RotamerDots	current_state_rotamer_dots_

RotamerDots	alt_state_rotamer_dots_

InvRotamerDots	curr_state_inv_dots_

InvRotamerDots	alt_state_inv_dots_

utility::vector1< Size >	curr_state_exp_hphobes_

utility::vector1< Size >	alt_state_exp_hphobes_

bool	alt_state_dots_matches_current_state_dots_

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Detailed Description

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