core::pack::interaction_graph::HPatchNode< V, E, G > Class Template Reference

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 >:

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

List of all members.

Public Types
typedef FirstClassNode< V, E, G >	parent
typedef V	grandparent
Public Member Functions
	HPatchNode (G *owner, int node_index, int num_states)
	HPatchNode constructor.
virtual	~HPatchNode ()
	destructor -- no dynamically allocated data, does nothing
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.
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.
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.
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.
virtual void	prepare_for_simulated_annealing ()
	invokes V's prep_for_simA method. Also computes the "self-overlap" that each of its rotamers has.
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.
virtual void	assign_zero_state ()
	Assign the node to state 0 -- the "unassigned" state.
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.
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.
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().
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.
Real	get_current_state_sasa () const
	returns the amount of sasa this node has in its current state assignment
Real	get_current_state_sasa (Size atom_index) const
	Returns the current state SASA for the passed in atom index.
Real	get_alternate_state_sasa (Size atom_index) const
	Returns the alternate state SASA for the passed in atom index.
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.
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.
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.
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.
virtual unsigned int	getMemoryUsageInBytes () const
	Not implemented, but needs to be!
virtual unsigned int	count_static_memory () const
	Returns the amount of static memory used by this Node object.
virtual unsigned int	count_dynamic_memory () const
	Returns the amount of dynamic memory used by this Node object.
virtual void	print () const
	useful for debugging
RotamerDots const &	get_current_state_rotamer_dots ()
	Returns current state. Only used by the unit tests.
RotamerDots const &	get_alt_state_rotamer_dots ()
	Returns current state. Only used by the unit tests.
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
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.

---

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.

---

Member Typedef Documentation

template<typename V, typename E, typename G>

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

template<typename V, typename E, typename G>

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

---

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

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

---

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

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]

template<typename V, typename E, typename G>

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

(

)

const [inline]

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]

References 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]

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.

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.

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.

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()

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 >.

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

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]

template<typename V, typename E, typename G>

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

(

)

const [inline]

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]

References 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]

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

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]

References 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

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()

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

template<typename V, typename E, typename G>

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

(

)

const [inline]

References 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

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()

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.

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 [inline, protected]

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 [inline, protected]

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 [inline, protected]

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()

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

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().

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

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

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

template<typename V, typename E, typename G>

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

(

)

const [inline]

template<typename V, typename E, typename G>

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

(

)

const [inline]

template<typename V, typename E, typename G>

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

(

)

const [inline]

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]

template<typename V, typename E, typename G>

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

(

)

const [inline]

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

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)

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

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

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

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().

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

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 >

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_;

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]

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]

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().

---

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

• src/core/pack/interaction_graph/HPatchInteractionGraph.hh