#include <OTFFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::OTFFlexbbEdge:

Public Types
typedef FlexbbEdge	parent

typedef core::conformation::Residue	Residue

typedef ObjexxFCL::FArray2D < PackerEnergy >	FArray2D_PackerEnergy

Public Types inherited from protocols::flexpack::interaction_graph::FlexbbEdge
typedef core::pack::interaction_graph::EdgeBase	parent

typedef core::PackerEnergy	PackerEnergy

typedef core::Real	Real

typedef core::Size	Size

Public Member Functions
	OTFFlexbbEdge (OTFFlexbbInteractionGraph *owner, int node1, int node2)
	EDGE. More...

	~OTFFlexbbEdge () override

PackerEnergy	compute_samebbconf_alternate_state_energy_first_node ()

PackerEnergy	compute_samebbconf_alternate_state_energy_second_node ()

PackerEnergy	compute_altbbconf_alternate_state_energy ()

void	otfedge_note_substitution_accepted ()

unsigned int	count_dynamic_memory () const override

void	set_ProCorrection_values (int node_not_necessarily_proline, int state, int other_bb, PackerEnergy bb_nonprobb_E, PackerEnergy bb_probb_E, PackerEnergy sc_nonprobb_E, PackerEnergy sc_probb_E)

void	set_GlyCorrection_values (int node_not_necessarily_glycine, int state, int other_bb, PackerEnergy bb_nonglybb_E, PackerEnergy bb_glybb_E, PackerEnergy sc_nonglybb_E, PackerEnergy sc_glybb_E)

void	prepare_for_simulated_annealing () override

void	note_long_range_interactions_exist ()

void	print_alt_energies () const

Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbEdge
	FlexbbEdge (FlexbbInteractionGraph *owner, int first_node_ind, int second_node_ind)

	~FlexbbEdge () override

bool	get_nodes_from_same_flexseg () const

void	set_alt_state (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)
	Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_. More...

void	acknowledge_partial_state_assignment (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)

void	note_state_substitution_accepted ()
	Copy alt data to current data after a state substitution. More...

void	reset_alternate_states_for_uncommited_substitution ()
	After a rejected state substitution, the FlexbbNode will call this function to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution. More...

PackerEnergy	cur_energy () const

PackerEnergy	alt_energy () const

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 unsigned int	count_static_memory () const =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
OTFFlexbbNode const *	get_otfflexbb_node (int index) const
	Downcasts. More...

OTFFlexbbNode *	get_otfflexbb_node (int index)

OTFFlexbbInteractionGraph const *	get_otfflexbbig_owner () const

OTFFlexbbInteractionGraph *	get_otfflexbbig_owner ()

Residue const &	alt_rot (int which_node) const

void	zero_state_on_node (int which_node)

Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbEdge
FlexbbNode const *	get_flexbb_node (int index) const

FlexbbNode *	get_flexbb_node (int index)

FlexbbInteractionGraph const *	get_flexbbig_owner () const

FlexbbInteractionGraph *	get_flexbbig_owner ()

int	num_bb (int node)

bool	nodes_part_of_same_flexseg () const

bool	nodes_considering_bb_move () const

void	set_nodes_considering_bb_move (bool status)

int	nodes_cur_state (int node) const

FlexbbSparseMatrixIndex const &	nodes_cur_info (int node) const

int	nodes_alt_state (int node) const

FlexbbSparseMatrixIndex const &	nodes_alt_info (int node) const

bool	alt_e_up_to_date () const

void	set_nodes_cur_state (int node, int setting)
	Set the currently assigned state for a node; node == 0 \|\| 1. More...

void	set_nodes_cur_info (int node, FlexbbSparseMatrixIndex const &setting)

void	set_nodes_alt_state (int node, int setting)
	Set the altnernate state being considered for a node; node == 0 \|\| 1. More...

void	set_nodes_alt_info (int node, FlexbbSparseMatrixIndex const &setting)

void	set_cur_energy (PackerEnergy setting)

void	set_alt_energy (PackerEnergy setting)

void	copy_alternate_to_current ()

void	set_node_state_to_zero (int which_node)

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 Member Functions
bool	state_is_proline (int which_node, int state) const

bool	state_is_glycine (int which_node, int state) const

int	compact_bbindex (int index) const

Private Attributes
PackerEnergy	all_vs_bb_energy_curr_conf_ [2]

PackerEnergy	procorr_curr_conf_ [2]

PackerEnergy	glycorr_curr_conf_ [2]

PackerEnergy	scsc_energy_curr_conf_

PackerEnergy	all_vs_bb_energy_alt_conf_ [2]

PackerEnergy	procorr_alt_conf_ [2]

PackerEnergy	glycorr_alt_conf_ [2]

PackerEnergy	scsc_energy_alt_conf_

FArray2D_PackerEnergy	all_vs_bb_energies_ [2]

FArray2D_PackerEnergy	procorr_energies_ [2]
	Farray indexed ( state_this, compact bb_other ) More...

FArray2D_PackerEnergy	glycorr_energies_ [2]
	Farray indexed ( state_this, compact bb_other ) More...

ObjexxFCL::FArray4D< unsigned char >	sr_aa_neighbors_

bool	lr_energies_exist_

core::pose::PoseCOP	pose_

core::scoring::ScoreFunctionCOP	sfxn_

Member Typedef Documentation

typedef ObjexxFCL::FArray2D< PackerEnergy > protocols::flexpack::interaction_graph::OTFFlexbbEdge::FArray2D_PackerEnergy

typedef FlexbbEdge protocols::flexpack::interaction_graph::OTFFlexbbEdge::parent

typedef core::conformation::Residue protocols::flexpack::interaction_graph::OTFFlexbbEdge::Residue

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::OTFFlexbbEdge::OTFFlexbbEdge	(	OTFFlexbbInteractionGraph *	owner,
		int	node1,
		int	node2
	)

EDGE.

References all_vs_bb_energies_, all_vs_bb_energy_alt_conf_, all_vs_bb_energy_curr_conf_, core::pack::interaction_graph::EdgeBase::get_num_states_for_node(), get_otfflexbbig_owner(), glycorr_alt_conf_, glycorr_curr_conf_, glycorr_energies_, protocols::flexpack::interaction_graph::FlexbbEdge::nodes_part_of_same_flexseg(), protocols::flexpack::interaction_graph::FlexbbEdge::num_bb(), procorr_alt_conf_, procorr_curr_conf_, procorr_energies_, scsc_energy_alt_conf_, scsc_energy_curr_conf_, and sr_aa_neighbors_.

protocols::flexpack::interaction_graph::OTFFlexbbEdge::~OTFFlexbbEdge ( )

overridedefault

Member Function Documentation

Residue const& protocols::flexpack::interaction_graph::OTFFlexbbEdge::alt_rot ( int which_node ) const

inlineprotected

References get_otfflexbb_node(), protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_state(), and protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer().

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), and compute_samebbconf_alternate_state_energy_second_node().

int protocols::flexpack::interaction_graph::OTFFlexbbEdge::compact_bbindex ( int index ) const

inlineprivate

References protocols::flexpack::interaction_graph::FlexbbEdge::nodes_part_of_same_flexseg().

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), prepare_for_simulated_annealing(), set_GlyCorrection_values(), and set_ProCorrection_values().

OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy ( )

Prerequisit: alternate state(s) must have already been set.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::get_alt_stateE().

OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node ( )

compute sc/sc energy while node 0 (first node) is considering a fixed-backbone state substitution. Prerequisit: alternate state must have already been set.

OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node ( )

Prerequisit: alternate state must have already been set.

unsigned int protocols::flexpack::interaction_graph::OTFFlexbbEdge::count_dynamic_memory ( ) const

overridevirtual

Reimplemented from protocols::flexpack::interaction_graph::FlexbbEdge.

References all_vs_bb_energies_, protocols::flexpack::interaction_graph::FlexbbEdge::count_dynamic_memory(), glycorr_energies_, procorr_energies_, sr_aa_neighbors_, and protocols::analysis::total.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::count_dynamic_memory().

OTFFlexbbNode const * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbb_node ( int index ) const

inlineprotected

Downcasts.

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

Referenced by alt_rot(), prepare_for_simulated_annealing(), state_is_glycine(), and state_is_proline().

OTFFlexbbNode * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbb_node ( int index )

inlineprotected

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

OTFFlexbbInteractionGraph const * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbbig_owner ( ) const

inlineprotected

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

Referenced by OTFFlexbbEdge().

OTFFlexbbInteractionGraph * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbbig_owner ( )

inlineprotected

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

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist ( )

References lr_energies_exist_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::note_long_range_interactions_exist_for_edge().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::otfedge_note_substitution_accepted ( )

References all_vs_bb_energy_alt_conf_, all_vs_bb_energy_curr_conf_, glycorr_alt_conf_, glycorr_curr_conf_, procorr_alt_conf_, procorr_curr_conf_, scsc_energy_alt_conf_, and scsc_energy_curr_conf_.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing ( )

overridevirtual

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

References protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers(), compact_bbindex(), protocols::flexpack::interaction_graph::FlexbbEdge::get_nodes_from_same_flexseg(), get_otfflexbb_node(), core::conformation::Residue::nbr_atom(), protocols::flexpack::interaction_graph::FlexbbEdge::num_bb(), protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer(), sfxn_, sr_aa_neighbors_, protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb(), and core::conformation::Residue::xyz().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::prepare_for_simulated_annealing().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies ( ) const

References all_vs_bb_energy_alt_conf_, all_vs_bb_energy_curr_conf_, core::pack::interaction_graph::EdgeBase::get_node_index(), glycorr_alt_conf_, glycorr_curr_conf_, procorr_alt_conf_, procorr_curr_conf_, scsc_energy_alt_conf_, and scsc_energy_curr_conf_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values	(	int	node_not_necessarily_glycine,
		int	state,
		int	other_bb,
		PackerEnergy	bb_nonglybb_E,
		PackerEnergy	bb_glybb_E,
		PackerEnergy	sc_nonglybb_E,
		PackerEnergy	sc_glybb_E
	)

References all_vs_bb_energies_, compact_bbindex(), glycorr_energies_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_GlyCorrection_values_for_edge().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_ProCorrection_values	(	int	node_not_necessarily_proline,
		int	state,
		int	other_bb,
		PackerEnergy	bb_nonprobb_E,
		PackerEnergy	bb_probb_E,
		PackerEnergy	sc_nonprobb_E,
		PackerEnergy	sc_probb_E
	)

References all_vs_bb_energies_, compact_bbindex(), procorr_energies_, and core::pack::interaction_graph::EdgeBase::which_node().

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_ProCorrection_values_for_edge().

bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_glycine	(	int	which_node,
		int	state
	)		const

inlineprivate

References get_otfflexbb_node(), and protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine().

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), and compute_samebbconf_alternate_state_energy_second_node().

bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_proline	(	int	which_node,
		int	state
	)		const

inlineprivate

References get_otfflexbb_node(), and protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline().

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), and compute_samebbconf_alternate_state_energy_second_node().

void protocols::flexpack::interaction_graph::OTFFlexbbEdge::zero_state_on_node ( int which_node )

protected

References all_vs_bb_energy_alt_conf_, all_vs_bb_energy_curr_conf_, procorr_alt_conf_, procorr_curr_conf_, scsc_energy_alt_conf_, scsc_energy_curr_conf_, and protocols::flexpack::interaction_graph::FlexbbEdge::set_node_state_to_zero().

Member Data Documentation

FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energies_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), count_dynamic_memory(), OTFFlexbbEdge(), set_GlyCorrection_values(), and set_ProCorrection_values().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energy_alt_conf_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energy_curr_conf_[2]

private

If this flag is "true" then the two tables below are not allocated, and instead sc/bb and bb/bb energies are calculated alongside sc/sc energies in the OTF calculations. Slower, but uses less memory.

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_alt_conf_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), and print_alt_energies().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_curr_conf_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), and print_alt_energies().

FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_energies_[2]

private

Farray indexed ( state_this, compact bb_other )

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), count_dynamic_memory(), OTFFlexbbEdge(), and set_GlyCorrection_values().

bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::lr_energies_exist_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), and note_long_range_interactions_exist().

core::pose::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbEdge::pose_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), and compute_samebbconf_alternate_state_energy_second_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_alt_conf_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_curr_conf_[2]

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_energies_[2]

private

Farray indexed ( state_this, compact bb_other )

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), count_dynamic_memory(), OTFFlexbbEdge(), and set_ProCorrection_values().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::scsc_energy_alt_conf_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::scsc_energy_curr_conf_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

core::scoring::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbEdge::sfxn_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), and prepare_for_simulated_annealing().

ObjexxFCL::FArray4D< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbEdge::sr_aa_neighbors_

private

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), count_dynamic_memory(), OTFFlexbbEdge(), and prepare_for_simulated_annealing().

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

src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.hh
src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.cc

Public Types

Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation