#include <OTFFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::OTFFlexbbNode:

Collaboration diagram for protocols::flexpack::interaction_graph::OTFFlexbbNode:

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

virtual	~OTFFlexbbNode ()

virtual void	print () const

virtual unsigned int	count_dynamic_memory () const
	memory accounting scheme More...

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

Public Member Functions inherited from core::pack::interaction_graph::NodeBase
virtual	~NodeBase ()
	virtual destructor More...

	NodeBase (InteractionGraphBase *, int node_id, int num_states)
	Main constructor, no default constructor nor copy constructor. More...

int	get_num_states () const
	returns the number of states for this node More...

std::list< EdgeBase * >::iterator	add_edge (EdgeBase *edge_ptr)
	adds edge pointer to edge list; returns an iterator to the new list element More...

void	drop_edge (std::list< EdgeBase * >::iterator edge_iterator)
	removes an edge iterator from the node's edge list More...

void	drop_all_edges ()
	deletes all edges incident upon this node More...

EdgeBase *	find_edge (int other_node_index) const
	a slow (linear) search for an edge. The edge is identified by the index of the node to which the edge connects this node. Returns NULL when there is no such connecting edge. More...

virtual void	assign_zero_state ()=0

virtual void	add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)=0

void	depth_first_connected_component_counting ()
	performs a depth first traversal of the graph. Each node informs the graph that the traversal resulted in arriving at the node. More...

virtual unsigned int	count_static_memory () const =0

std::list< EdgeBase * > ::const_iterator	edge_list_begin ()

std::list< EdgeBase * > ::const_iterator	edge_list_end ()

int	get_node_index () const

int	get_num_incident_edges () const

int	get_num_edges_to_smaller_indexed_nodes () const

int	get_num_edges_to_larger_indexed_nodes () const

EdgeBase const *	get_incident_edge (int index) const
	These functions are public for the sake of writing good unit tests. More...

EdgeBase *	get_incident_edge (int index)

int	get_index_of_adjacent_node (int index) const

NodeBase const *	get_adjacent_node (int index) const

NodeBase *	get_adjacent_node (int index)

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...

Protected Member Functions inherited from core::pack::interaction_graph::NodeBase
void	update_edge_vector ()
	converts edge-list to edge-vector representation More...

bool	get_edge_vector_up_to_date () const

InteractionGraphBase const *	get_owner () const

InteractionGraphBase *	get_owner ()

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

memory accounting scheme

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

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

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

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 bounding_volumes_for_bb_for_aa_, core::sequence::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

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

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

inlineprotected

References core::pack::interaction_graph::NodeBase::get_adjacent_node().

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.

References core::pack::interaction_graph::NodeBase::get_incident_edge().

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

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

inlineprotected

References core::pack::interaction_graph::NodeBase::get_incident_edge().

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

inlineprotected

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

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

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

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

Public Member Functions

Protected Member Functions

Private Attributes

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation