#include <OTFFlexbbInteractionGraph.hh>

Public Member Functions
	OTFFlexbbNode (OTFFlexbbInteractionGraph *, int node_id, int num_states)

virtual	~OTFFlexbbNode ()

virtual void	print () const

virtual unsigned int	count_dynamic_memory () const

Residue const &	rotamer (int index) const

void	set_rotamer (int state, ResidueCOP rotamer)

void	declare_all_rotamers_initialized ()

Real	bounding_radius_for_rotamers (int aatype, int bb) const

bool	rotamer_is_proline (int state) const

bool	rotamer_is_glycine (int state) const

Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbNode
	FlexbbNode (FlexbbInteractionGraph *owner, int node_id, int num_states)

virtual	~FlexbbNode ()

void	set_num_distinct_backbones (int nbbconfs)

int	get_num_distinct_backbones () const

void	set_num_states_per_backbone (utility::vector1< int > const &)

int	get_bb_for_state (int state) const

int	get_num_states_for_bb (int bbconf) const

int	get_state_offset_for_bb (int bbconf) const

void	get_states_on_curr_bb (utility::vector1< Size > &state_list, int offset) const

void	get_all_states (utility::vector1< Size > &rotlist, int offset) const

void	set_closest_states_on_other_bbs (ObjexxFCL::FArray2D_int const &)

void	set_amino_acid_types (utility::vector1< int > const &)

ObjexxFCL::FArray1A_int	getNumStatesPerAAPerBB (int aa)

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< PackerEnergy > &energies)

virtual void	add_to_one_body_energy (int state, PackerEnergy energy)

virtual void	update_one_body_energy (int state, PackerEnergy energy)

virtual void	zero_one_body_energies ()

virtual bool	state_unassigned () const

PackerEnergy	get_one_body_energy (int state) const

virtual void	prepare_for_simulated_annealing ()

int	get_current_state () const

int	get_backbone_for_current_state () const

void	write_current_state_to_state_array (ObjexxFCL::FArray1_int &nodes_states)

bool	inform_edges_of_alt_state_before_bbjump ()
	Preliminatry bookkeeping for the node the Graph contacted about a backbone move. This node is the "root" of the DFS traversal. More...

bool	state_has_same_backbone_as_current (int state) const
	Did the alterenate state assigned during a flexbb move actually preserve the currently assigned bb? More...

int	get_num_states_for_aa_type_for_bb (int aa_type, int bb) const

void	print_internal_energies ()

void	update_internal_energy_sums ()

int	num_aa_types () const
	Read access to private data to both derived classes and the world. More...

int	num_bbconfs () const

utility::vector1< int > const &	num_states_for_bb ()

utility::vector1< int > const &	state_offsets_for_bb ()

ObjexxFCL::FArray2D_int const &	num_states_for_aa_for_bb ()

ObjexxFCL::FArray2D_int const &	state_offsets_for_aa_for_bb ()

ObjexxFCL::FArray2D_int const &	closest_state_on_alt_bb () const

FlexbbSparseMatrixIndex const &	state_info (int state) const

utility::vector1< PackerEnergy > const &	one_body_energies () const

int	current_state () const

FlexbbSparseMatrixIndex const &	current_state_info () const

int	curr_bb () const

PackerEnergy	curr_state_one_body_energy () const

PackerEnergy	curr_state_total_energy () const

utility::vector1< PackerEnergy > const &	curr_state_two_body_energies ()

int	alternate_state () const

FlexbbSparseMatrixIndex const &	alternate_state_info () const

int	alt_bb () const

PackerEnergy	alternate_state_one_body_energy () const

PackerEnergy	alternate_state_total_energy () const

utility::vector1< PackerEnergy > const &	alternate_state_two_body_energies () const

PackerEnergy	alternate_state_two_body_energies (int ind) const

utility::vector1< bool > const &	edge_connects_flexsegmate () const

bool	count_energy_to_node_in_my_fragtotalE (int edge_index) const
	Convention for acumulating energies between flexsegmates during a backbone move: The smaller-indexed node counts the interaction, the larger-indexed node does not. More...

bool	alternate_state_is_being_considered () const

Protected Member Functions
OTFFlexbbEdge const *	get_incident_otfflexbb_edge (int index) const
	Downcast pointers to incident edges, adjacent nodes, and the owning graph. More...

OTFFlexbbEdge *	get_incident_otfflexbb_edge (int index)

OTFFlexbbNode const *	get_adjacent_otfflexbb_node (int index) const

OTFFlexbbNode *	get_adjacent_otfflexbb_node (int index)

OTFFlexbbInteractionGraph const *	get_otfflexbbig_owner () const

OTFFlexbbInteractionGraph *	get_otfflexbbig_owner ()

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

FlexbbEdge *	get_incident_flexbb_edge (int index)

FlexbbNode const *	get_adjacent_flexbb_node (int index) const

FlexbbNode *	get_adjacent_flexbb_node (int index)

FlexbbInteractionGraph const *	get_flexbbig_owner () const

FlexbbInteractionGraph *	get_flexbbig_owner ()

void	update_internal_vectors ()

void	inform_edges_considered_fixedbb_substition_uncommitted ()

void	set_considering_alternate_state ()
	Limited write acces to private data. More...

void	set_current_state (int setting)

void	set_curr_state_one_body_energy (PackerEnergy setting)

void	set_curr_state_total_energy (PackerEnergy setting)

void	inc_curr_state_total_energy (PackerEnergy setting)

void	set_curr_state_two_body_energies (Size index, PackerEnergy setting)

void	set_alternate_state (int setting)

void	set_alternate_state_one_body_energy (PackerEnergy setting)

void	set_alternate_state_total_energy (PackerEnergy setting)

void	inc_alternate_state_total_energy (PackerEnergy setting)

void	set_alternate_state_two_body_energies (Size index, PackerEnergy setting)

void	reset_all_rotamer_substitution_bookkeeping_data ()

void	partial_state_assignment (int new_state)

void	inform_incident_edges_about_partial_state_assignment ()

void	copy_alternate_to_current ()
	bookkeeping for DFS traversal. Derived classes should consult this at the beginning of node "get_energies" traversals. Calling this function for a node effectively declares that the code which follows will project the delta energy: after the first time this functio is called, it will return true. Must be proceeded by a call to prepare_for_bb_jump(). Depricated. bool energies_already_projected() const; More...

void	have_edges_copy_alternate_to_current ()
	Have all incident edges copy their data from "alternate_" to "current_". More...

void	have_edges_copy_alternate_to_current_following_flexbb_accept ()
	Have a subset of the incident edges copy their data from "alternate_" to "current_" where this subset includes all edges to non-flexsegmates as well as all all upper edges to flexsegmates. Threadsafe if it can be fruitfully parallelized. More...

Private Attributes
utility::vector1< ResidueCOP >	rotamers_

utility::vector1 < utility::vector1< Real > >	bounding_volumes_for_bb_for_aa_

utility::vector1< unsigned char >	rotamer_is_proline_

utility::vector1< unsigned char >	rotamer_is_glycine_

Member Typedef Documentation

typedef core::DistanceSquared protocols::flexpack::interaction_graph::OTFFlexbbNode::DistanceSquared

typedef core::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbNode::PackerEnergy

typedef FlexbbNode protocols::flexpack::interaction_graph::OTFFlexbbNode::parent

typedef core::Real protocols::flexpack::interaction_graph::OTFFlexbbNode::Real

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

typedef core::conformation::ResidueCOP protocols::flexpack::interaction_graph::OTFFlexbbNode::ResidueCOP

typedef core::Size protocols::flexpack::interaction_graph::OTFFlexbbNode::Size

typedef core::Vector protocols::flexpack::interaction_graph::OTFFlexbbNode::Vector

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::OTFFlexbbNode::OTFFlexbbNode	(	OTFFlexbbInteractionGraph *	owner,
		int	node_id,
		int	num_states
	)

protocols::flexpack::interaction_graph::OTFFlexbbNode::~OTFFlexbbNode ( )

virtual

Member Function Documentation

OTFFlexbbNode::Real protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers	(	int	aatype,
		int	bb
	)		const

References bounding_volumes_for_bb_for_aa_.

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

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

virtual

Reimplemented from protocols::flexpack::interaction_graph::FlexbbNode.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

References protocols::flexpack::interaction_graph::FlexbbNode::count_dynamic_memory(), rotamers_, and protocols::analysis::total.

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

void protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized ( )

compute bounding radii for the rotamers that actually exist – maybe they're tighter than the nbr_radius for the residue type... maybe I could find the minimal bounding sphere for each. maybe I could keep two nbr_radii, one for all atoms and one for just the sidechain atoms?

References begin, bounding_volumes_for_bb_for_aa_, numeric::xyzVector< class >::distance_squared(), end, protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones(), core::conformation::Residue::nbr_atom(), core::conformation::Residue::nheavyatoms(), protocols::flexpack::interaction_graph::FlexbbNode::num_aa_types(), protocols::flexpack::interaction_graph::FlexbbNode::num_states_for_aa_for_bb(), rotamers_, protocols::flexpack::interaction_graph::FlexbbNode::state_offsets_for_aa_for_bb(), and core::conformation::Residue::xyz().

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

OTFFlexbbNode const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int index ) const

inlineprotected

OTFFlexbbNode * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int index )

inlineprotected

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

inlineprotected

Downcast pointers to incident edges, adjacent nodes, and the owning graph.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

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

inlineprotected

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

inlineprotected

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

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

inlineprotected

void protocols::flexpack::interaction_graph::OTFFlexbbNode::print ( ) const

virtual

Reimplemented from protocols::flexpack::interaction_graph::FlexbbNode.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbNode.

References protocols::flexpack::interaction_graph::FlexbbNode::print().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::print().

Residue const& protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer ( int index ) const

inline

References rotamers_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::alt_rot(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state(), protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing(), protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution(), and set_rotamer().

bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine ( int state ) const

inline

References rotamer_is_glycine_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_glycine().

bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline ( int state ) const

inline

References rotamer_is_proline_.

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_proline().

void protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer	(	int	state,
		ResidueCOP	rotamer
	)

References core::chemical::aa_gly, core::chemical::aa_pro, rotamer(), rotamer_is_glycine_, rotamer_is_proline_, and rotamers_.

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

Member Data Documentation

utility::vector1< utility::vector1< Real > > protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_volumes_for_bb_for_aa_

private

Referenced by bounding_radius_for_rotamers(), and declare_all_rotamers_initialized().

utility::vector1< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine_

private

Referenced by rotamer_is_glycine(), and set_rotamer().

utility::vector1< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline_

private

Referenced by rotamer_is_proline(), and set_rotamer().

utility::vector1< ResidueCOP > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamers_

private

Referenced by count_dynamic_memory(), declare_all_rotamers_initialized(), rotamer(), and set_rotamer().

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
typedef FlexbbNode	parent

typedef core::conformation::Residue	Residue

typedef core::conformation::ResidueCOP	ResidueCOP

typedef core::Size	Size

typedef core::PackerEnergy	PackerEnergy

typedef core::Real	Real

typedef core::Vector	Vector

typedef core::DistanceSquared	DistanceSquared

Public Types inherited from protocols::flexpack::interaction_graph::FlexbbNode
typedef core::pack::interaction_graph::NodeBase	parent

typedef core::PackerEnergy	PackerEnergy

typedef core::Size	Size

Public Types

Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation