Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...

#include <HPatchInteractionGraph.hh>

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

Public Member Functions
	HPatchEdge (G *owner, int node1, int node2)
	main constructor. No default, or copy constructors, no assignment operator More...

virtual	~HPatchEdge ()

virtual void	prepare_for_simulated_annealing ()
	drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself. More...

void	acknowledge_state_zeroed (int node_index)
	respond to when one of its vertices enters the "unassigned" state. More...

Real	update_state_at_neighbor (int node_considering_substitution, int alt_state, RotamerDots &alt_state_dots)
	returns the change in sasa for the neighbor of a node that is produced by the state substitution it is considering. More...

void	acknowledge_substitution ()
	bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider. More...

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

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

virtual void	declare_energies_final ()
	Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter. More...

virtual unsigned int	getMemoryUsageInBytes () const

virtual unsigned int	count_static_memory () const

virtual unsigned int	count_dynamic_memory () const

Real	get_current_two_body_energy () const

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

	FirstClassEdge (G *owner, int first_node_ind, int second_node_ind)
	FirstClassEdge constructor. More...

Protected Member Functions
HPatchNode< V, E, G > *	get_hpatch_node (int index)

Private Member Functions
void	inform_non_changing_node_of_neighbors_change ()
	tells the node that isn't considering a substitution or changing state that its neighbor who is has changed. More...

	HPatchEdge ()

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

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

Private Attributes
int	node_changing_

int	node_not_changing_

int	nodes_curr_states_ [2]

int	nodes_alt_states_ [2]

RotamerDotsCache	nodes_curr_pair_dot_counts_ [2]

RotamerDotsCache	nodes_alt_pair_dot_counts_ [2]

utility::vector1 < utility::vector1< bool > >	current_state_atom_atom_overlaps_

utility::vector1 < utility::vector1< bool > >	alt_state_atom_atom_overlaps_

utility::vector1< std::pair < Size, Size > >	curr_state_exolap_hphobes_
	pairs of hphobes that have exposed overlap More...

utility::vector1< std::pair < Size, Size > >	alt_state_exolap_hphobes_

Detailed Description

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

Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast.

HPatchEdge

Member Typedef Documentation

template<typename V, typename E, typename G>

typedef FirstClassEdge< V, E, G > core::pack::interaction_graph::HPatchEdge< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >

core::pack::interaction_graph::HPatchEdge< V, E, G >::HPatchEdge	(	G *	owner,
		int	node1,
		int	node2
	)

main constructor. No default, or copy constructors, no assignment operator

HPatchEdge::HPatchEdge

Parameters

owner - [in] - the owning interaction graph object node1 - [in] - the index of the lower-indexed HPatchNode node2 - [in] - the index of the higher-indexed HPatchNode

References core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_alt_states_, and core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_curr_states_.

template<typename V , typename E , typename G >

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

virtual

HPatchEdge::~HPatchEdge

template<typename V, typename E, typename G>

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

private

template<typename V, typename E, typename G>

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

private

Member Function Documentation

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_state_zeroed ( int node_that_changed )

respond to when one of its vertices enters the "unassigned" state.

HPatchEdge::acknowledge_state_zeroed

Detailed:: called during the HIG::blanket_assign_state_0 -> HPatchNode::assign_zero_state() cascade of calls.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_substitution ( )

bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider.

HPatchEdge::acknowledge_substitution

References core::io::serialization::size().

template<typename V , typename E , typename G >

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

virtual

HPatchEdge::count_dynamic_memory

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

References core::io::serialization::size().

template<typename V , typename E , typename G >

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

virtual

HPatchEdge::count_static_memory

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchEdge< V, E, G >::declare_energies_final ( )

virtual

Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter.

HPatchEdge::declare_energies_final

Remarks: (all by apl) In the PDEdge's version of this method, after invoking two_body_energies_.drop_zero_submatrices_where_possible(); the PDEdge checks if the two body energy table it now holds is empty. If the table is empty, the edge deletes itself.

A HPatchEdge should not delete itself if the pair energies are all zero since the Minkowski sum of a water and a van der Waal's sphere extends further out from an atoms center than its (lj_atr, lj_rep, lksolv) interaction sphere. However, if a HPatchEdge holds no pair energies, it's a very good candidate for removal – it just first needs to check that no (vdw + 1.4 A) spheres overlap between any pair of rotamers on the edges it connects.

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchEdge< V, E, G >::get_alt_state_atom_atom_overlaps ( ) const

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

HPatchEdge< V, E, G >::get_alt_state_atom_atom_overlaps

template<typename V , typename E , typename G >

utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchEdge< V, E, G >::get_current_state_atom_atom_overlaps ( ) const

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

HPatchEdge< V, E, G >::get_current_state_atom_atom_overlaps

template<typename V, typename E, typename G>

Real core::pack::interaction_graph::HPatchEdge< V, E, G >::get_current_two_body_energy ( ) const

template<typename V, typename E, typename G>

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

inlineprotected

template<typename V , typename E , typename G >

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

virtual

HPatchEdge::getMemoryUsageInBytes

Remarks: Not implemented.

template<typename V , typename E , typename G >

void core::pack::interaction_graph::HPatchEdge< V, E, G >::inform_non_changing_node_of_neighbors_change ( )

inlineprivate

tells the node that isn't considering a substitution or changing state that its neighbor who is has changed.

HPatchEdge::inform_non_changing_node_of_neighbors_change

template<typename V, typename E, typename G>

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

private

template<typename V , typename E , typename G >

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

virtual

drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself.

HPatchEdge::prepare_for_simulated_annealing

References core::pack::interaction_graph::TR_EDGE.

template<typename V , typename E , typename G >

Real core::pack::interaction_graph::HPatchEdge< V, E, G >::update_state_at_neighbor	(	int	node_considering_substitution,
		int	alt_state,
		RotamerDots &	changing_node_alt_state_dots
	)

returns the change in sasa for the neighbor of a node that is produced by the state substitution it is considering.

HPatchEdge::update_state_at_neighbor

Detailed:: Very complicated. See HPatchNode::project_deltaE_for_neighbors_state_sub This edge collects cached sphere overlaps and hands this cached data to the node that is not considering the state substitution. That node computes more sphere overlaps and returns a delta sasa; this method then passes that delta sasa along.

See more comments inline.

Parameters

changing_node_alt_state_dots - [in] - the RotamerDots object for the alternate state at the changing Node

References core::pack::interaction_graph::RotamerDots::get_num_atoms(), and core::io::serialization::size().

Member Data Documentation

template<typename V, typename E, typename G>

utility::vector1< utility::vector1< bool > > core::pack::interaction_graph::HPatchEdge< V, E, G >::alt_state_atom_atom_overlaps_

private

template<typename V, typename E, typename G>

utility::vector1< std::pair< Size, Size > > core::pack::interaction_graph::HPatchEdge< V, E, G >::alt_state_exolap_hphobes_

private

template<typename V, typename E, typename G>

utility::vector1< std::pair< Size, Size > > core::pack::interaction_graph::HPatchEdge< V, E, G >::curr_state_exolap_hphobes_

private

pairs of hphobes that have exposed overlap

template<typename V, typename E, typename G>

utility::vector1< utility::vector1< bool > > core::pack::interaction_graph::HPatchEdge< V, E, G >::current_state_atom_atom_overlaps_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchEdge< V, E, G >::node_changing_

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchEdge< V, E, G >::node_not_changing_

private

template<typename V, typename E, typename G>

RotamerDotsCache core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_alt_pair_dot_counts_[2]

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_alt_states_[2]

private

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

template<typename V, typename E, typename G>

RotamerDotsCache core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_curr_pair_dot_counts_[2]

private

template<typename V, typename E, typename G>

int core::pack::interaction_graph::HPatchEdge< V, E, G >::nodes_curr_states_[2]

private

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

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

src/core/pack/interaction_graph/HPatchInteractionGraph.hh

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::HPatchEdge< 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::HPatchEdge< V, E, G >