#include <SymmOnTheFlyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::SymmOnTheFlyEdge:

Public Member Functions
	~SymmOnTheFlyEdge () override

	SymmOnTheFlyEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

void	add_ProCorrection_values (int node_not_necessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E)

void	add_GlyCorrection_values (int node_not_necessarily_glycine, int state, core::PackerEnergy bb_nonglybb_E, core::PackerEnergy bb_glybb_E, core::PackerEnergy sc_nonglybb_E, core::PackerEnergy sc_glybb_E)

core::PackerEnergy	get_proline_correction_for_node (int node_ind, int state) const

core::PackerEnergy	get_glycine_correction_for_node (int node_ind, int state) const

unsigned int	count_static_memory () const override=0

unsigned int	count_dynamic_memory () const override

bool	long_range_interactions_exist () const

bool	short_range_interactions_exist () const

void	note_long_range_interactions_exist ()

void	note_short_range_interactions_exist ()

ResiduePairEvalType	eval_type (int node_index) const

void	set_residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit)

unsigned char	residues_adjacent_for_subunit_pair (int which_node, int other_node_subunit, int whichnode_restypegroup, int othernode_restypegroup) const

void	set_sparse_aa_info (ObjexxFCL::FArray2_bool const &) override
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

bool	get_sparse_aa_info (int, int) const override
	fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true. More...

void	force_aa_neighbors (int, int) override
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

void	force_all_aa_neighbors () override
	fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop. More...

core::PackerEnergy	get_two_body_energy (int const, int const ) const override=0

Public Member Functions inherited from core::pack::interaction_graph::FixedBBEdge
	~FixedBBEdge () override

	FixedBBEdge (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)

Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual	~EdgeBase ()
	copy constructor, do not use More...

	EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
	main constructor for edge, no default nor copy constructors More...

int	get_other_ind (int callers_index) const
	returns the index of the other node that the edge is incident upon More...

NodeBase *	get_other_node (int callers_index) const
	returns a pointer to the other node that the edge is incident upon More...

int	get_first_node_ind () const
	returns the index of the smaller-indexed node More...

int	get_second_node_ind () const
	returns the index of the larger-indexed node More...

void	set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
	edge keeps iterator to its position in it's owner's edge list More...

void	set_pos_in_node_edgevector (int callers_index, int position)
	edge keeps index it has in node_ind's edge vector More...

bool	same_edge (int node1, int node2) const
	returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...

virtual void	declare_energies_final ()=0

virtual void	prepare_for_simulated_annealing ()=0

Real	edge_weight () const

virtual void	set_edge_weight (Real weight)=0

bool	marked_for_deletion () const
	Has this edge indicated that it can be deleted? More...

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

Protected Member Functions
core::PackerEnergy	get_proline_correction (int which_node, int state) const

core::PackerEnergy	get_glycine_correction (int which_node, int state) const

SymmOnTheFlyNode const *	get_otf_node (int which_node) const

SymmOnTheFlyNode *	get_otf_node (int which_node)

SymmOnTheFlyInteractionGraph const *	get_otf_owner () const

SymmOnTheFlyInteractionGraph *	get_otf_owner ()

Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
void	mark_edge_for_deletion ()
	Mark this edge so that it can be deleted. More...

int	get_node_index (int index) const

int	get_num_states_for_node (int index) const

NodeBase const *	get_node (int index) const

NodeBase *	get_node (int index)

int	get_edges_position_in_nodes_edge_vector (int index) const

int	which_node (int node_index) const
	is a node the first or second node this edge is incident upon? More...

void	edge_weight (Real)
	protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting. More...

Private Attributes
ObjexxFCL::FArray4D< unsigned char >	restypegroup_adjacency_

utility::vector1 < core::PackerEnergy >	proline_corrections_ [2]

utility::vector1 < core::PackerEnergy >	glycine_corrections_ [2]

ResiduePairEvalType	eval_types_ [2]

bool	long_range_interactions_exist_

bool	short_range_interactions_exist_

Constructor & Destructor Documentation

core::pack::interaction_graph::SymmOnTheFlyEdge::~SymmOnTheFlyEdge ( )

overridedefault

core::pack::interaction_graph::SymmOnTheFlyEdge::SymmOnTheFlyEdge	(	InteractionGraphBase *	owner,
		int	first_node_ind,
		int	second_node_ind
	)

References core::pack::interaction_graph::SymmOnTheFlyNode::distinguish_backbone_and_sidechain(), core::sequence::end, eval_types_, core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), get_otf_node(), glycine_corrections_, proline_corrections_, core::pack::interaction_graph::sc_sc, core::pack::interaction_graph::sc_whole, core::pack::interaction_graph::whole_sc, and core::pack::interaction_graph::whole_whole.

Member Function Documentation

void core::pack::interaction_graph::SymmOnTheFlyEdge::add_GlyCorrection_values	(	int	node_not_necessarily_glycine,
		int	state,
		core::PackerEnergy	bb_nonglybb_E,
		core::PackerEnergy	bb_glybb_E,
		core::PackerEnergy	sc_nonglybb_E,
		core::PackerEnergy	sc_glybb_E
	)

References core::pack::interaction_graph::EdgeBase::get_node_index(), glycine_corrections_, and core::pack::interaction_graph::EdgeBase::which_node().

void core::pack::interaction_graph::SymmOnTheFlyEdge::add_ProCorrection_values	(	int	node_not_necessarily_proline,
		int	state,
		core::PackerEnergy	bb_nonprobb_E,
		core::PackerEnergy	bb_probb_E,
		core::PackerEnergy	sc_nonprobb_E,
		core::PackerEnergy	sc_probb_E
	)

References core::pack::interaction_graph::EdgeBase::get_node_index(), proline_corrections_, and core::pack::interaction_graph::EdgeBase::which_node().

unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_dynamic_memory ( ) const

overridevirtual

Reimplemented from core::pack::interaction_graph::EdgeBase.

References core::pack::interaction_graph::EdgeBase::count_dynamic_memory(), glycine_corrections_, and proline_corrections_.

Referenced by core::pack::interaction_graph::SymmMinimalistEdge::count_dynamic_memory(), and core::pack::interaction_graph::SymmLinearMemEdge::count_dynamic_memory().

unsigned int core::pack::interaction_graph::SymmOnTheFlyEdge::count_static_memory ( ) const

overridepure virtual

Implements core::pack::interaction_graph::EdgeBase.

Implemented in core::pack::interaction_graph::SymmLinearMemEdge, and core::pack::interaction_graph::SymmMinimalistEdge.

ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_type ( int node_index ) const

inline

References eval_types_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().

void core::pack::interaction_graph::SymmOnTheFlyEdge::force_aa_neighbors	(	int	,
		int
	)

inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

void core::pack::interaction_graph::SymmOnTheFlyEdge::force_all_aa_neighbors ( )

inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_glycine_correction	(	int	which_node,
		int	state
	)		const

inlineprotected

References glycine_corrections_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by get_glycine_correction_for_node().

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_glycine_correction_for_node	(	int	node_ind,
		int	state
	)		const

inline

References get_glycine_correction(), core::pack::interaction_graph::EdgeBase::get_node_index(), and core::pack::interaction_graph::EdgeBase::which_node().

SymmOnTheFlyNode const* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int which_node ) const

inlineprotected

References core::pack::interaction_graph::EdgeBase::get_node().

Referenced by set_residues_adjacent_for_subunit_pair(), and SymmOnTheFlyEdge().

SymmOnTheFlyNode* core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_node ( int which_node )

inlineprotected

References core::pack::interaction_graph::EdgeBase::get_node().

SymmOnTheFlyInteractionGraph const * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( ) const

inlineprotected

References core::pack::interaction_graph::EdgeBase::get_owner().

Referenced by set_residues_adjacent_for_subunit_pair().

SymmOnTheFlyInteractionGraph * core::pack::interaction_graph::SymmOnTheFlyEdge::get_otf_owner ( )

inlineprotected

References core::pack::interaction_graph::EdgeBase::get_owner().

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction	(	int	which_node,
		int	state
	)		const

inlineprotected

References proline_corrections_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by get_proline_correction_for_node().

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_proline_correction_for_node	(	int	node_ind,
		int	state
	)		const

inline

References core::pack::interaction_graph::EdgeBase::get_node_index(), get_proline_correction(), and core::pack::interaction_graph::EdgeBase::which_node().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::get_sparse_aa_info	(	int	,
		int
	)		const

inlineoverridevirtual

fullfilling base class virtual member request – however, this function does not quite make sense for a symmetric otf ig, so this is just stubbed out to return true.

Implements core::pack::interaction_graph::FixedBBEdge.

core::PackerEnergy core::pack::interaction_graph::SymmOnTheFlyEdge::get_two_body_energy	(	int	const,
		int	const
	)		const

overridepure virtual

Implements core::pack::interaction_graph::FixedBBEdge.

Implemented in core::pack::interaction_graph::SymmLinearMemEdge, and core::pack::interaction_graph::SymmMinimalistEdge.

bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist ( ) const

inline

References long_range_interactions_exist_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().

void core::pack::interaction_graph::SymmOnTheFlyEdge::note_long_range_interactions_exist ( )

inline

References long_range_interactions_exist_.

void core::pack::interaction_graph::SymmOnTheFlyEdge::note_short_range_interactions_exist ( )

inline

References short_range_interactions_exist_.

unsigned char core::pack::interaction_graph::SymmOnTheFlyEdge::residues_adjacent_for_subunit_pair	(	int	which_node,
		int	other_node_subunit,
		int	whichnode_restypegroup,
		int	othernode_restypegroup
	)		const

References restypegroup_adjacency_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().

void core::pack::interaction_graph::SymmOnTheFlyEdge::set_residues_adjacent_for_subunit_pair	(	int	which_node,
		int	other_node_subunit
	)

References core::kinematics::tree::distance_squared(), core::pack::interaction_graph::SymmOnTheFlyNode::get_asu_rotamer(), core::pack::interaction_graph::SymmOnTheFlyNode::get_num_restype_groups(), get_otf_node(), get_otf_owner(), core::pack::interaction_graph::SymmOnTheFlyNode::get_rotamer(), core::pack::interaction_graph::SymmOnTheFlyNode::get_state_offset_for_restype_group(), core::scoring::ScoreFunction::max_atomic_interaction_cutoff(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nbr_radius(), restypegroup_adjacency_, core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::score_function(), and core::conformation::Residue::xyz().

Referenced by core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::set_residues_adjacent_for_subunit_pair_for_edge().

void core::pack::interaction_graph::SymmOnTheFlyEdge::set_sparse_aa_info ( ObjexxFCL::FArray2_bool const & )

inlineoverridevirtual

fullfilling base class virtual member request – however, this funciton does not quite make sense for a symmetric oft ig so this is just stubbed out as a noop.

Implements core::pack::interaction_graph::FixedBBEdge.

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist ( ) const

inline

References short_range_interactions_exist_.

Referenced by core::pack::interaction_graph::SymmOnTheFlyNode::compute_rotamer_pair_energy().

Member Data Documentation

ResiduePairEvalType core::pack::interaction_graph::SymmOnTheFlyEdge::eval_types_[2]

private

Referenced by eval_type(), and SymmOnTheFlyEdge().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyEdge::glycine_corrections_[2]

private

Referenced by add_GlyCorrection_values(), count_dynamic_memory(), get_glycine_correction(), and SymmOnTheFlyEdge().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::long_range_interactions_exist_

private

Referenced by long_range_interactions_exist(), and note_long_range_interactions_exist().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::SymmOnTheFlyEdge::proline_corrections_[2]

private

Referenced by add_ProCorrection_values(), count_dynamic_memory(), get_proline_correction(), and SymmOnTheFlyEdge().

ObjexxFCL::FArray4D< unsigned char > core::pack::interaction_graph::SymmOnTheFlyEdge::restypegroup_adjacency_

private

Dimensions: naatypes x naatypes x n_subunits x 2 aa_adjacency( l, k, j, i ); i = 1 or 2, repesnting either the lower or upper node respectively, the residue of which lives in the asymmetric unit j = 1..n_subunits, representing the subunit of origin for the other node's residue k = amino acid type for node i l = amino acid type for the other node

Referenced by residues_adjacent_for_subunit_pair(), and set_residues_adjacent_for_subunit_pair().

bool core::pack::interaction_graph::SymmOnTheFlyEdge::short_range_interactions_exist_

private

Referenced by note_short_range_interactions_exist(), and short_range_interactions_exist().

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

src/core/pack/interaction_graph/SymmOnTheFlyInteractionGraph.hh
src/core/pack/interaction_graph/SymmOnTheFlyInteractionGraph.cc

Public Member Functions

Protected Member Functions

Private Attributes

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation