#include <OTFFlexbbInteractionGraph.hh>

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...

virtual	~OTFFlexbbEdge ()

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 ()

virtual unsigned int	count_dynamic_memory () const

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)

virtual void	prepare_for_simulated_annealing ()

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)

virtual	~FlexbbEdge ()

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 void	declare_energies_final ()=0

virtual unsigned int	count_static_memory () const =0

virtual void	set_edge_weight (Real weight)=0

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)

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
bool	compute_bbbb_and_scbb_otf_

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_, 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 ( )

virtual

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.

References core::conformation::Residue::aa(), all_vs_bb_energies_, all_vs_bb_energy_alt_conf_, all_vs_bb_energy_curr_conf_, protocols::flexpack::interaction_graph::FlexbbEdge::alt_energy(), alt_rot(), compact_bbindex(), core::pack::interaction_graph::SparseMatrixIndex::get_aa_type(), protocols::flexpack::interaction_graph::FlexbbSparseMatrixIndex::get_bb(), protocols::flexpack::interaction_graph::FlexbbEdge::get_flexbb_node(), glycorr_alt_conf_, glycorr_curr_conf_, glycorr_energies_, lr_energies_exist_, protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_info(), protocols::flexpack::interaction_graph::FlexbbEdge::nodes_alt_state(), pose_, procorr_alt_conf_, procorr_curr_conf_, procorr_energies_, scsc_energy_alt_conf_, scsc_energy_curr_conf_, protocols::flexpack::interaction_graph::FlexbbEdge::set_alt_energy(), sfxn_, sr_aa_neighbors_, state_is_glycine(), and state_is_proline().

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

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbEdge.

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.

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

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

inlineprotected

Referenced by OTFFlexbbEdge().

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

inlineprotected

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 ( )

virtual

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

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbEdge.

References protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers(), compact_bbindex(), numeric::xyzVector< class >::distance_squared(), 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_, 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(), and glycorr_energies_.

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(), and procorr_energies_.

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

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().

bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_bbbb_and_scbb_otf_

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.

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:

symlinks/rosetta/src/protocols/flexpack/interaction_graph/OTFFlexbbInteractionGraph.hh
symlinks/rosetta/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