#include <MinimalistFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::MinimalistFlexbbNode:

Collaboration diagram for protocols::flexpack::interaction_graph::MinimalistFlexbbNode:

Public Types
typedef OTFFlexbbNode	parent

typedef FlexbbNode	grandparent

Public Types inherited from protocols::flexpack::interaction_graph::OTFFlexbbNode
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
	MinimalistFlexbbNode (MinimalistFlexbbInteractionGraph *owner, int node_id, int num_states)

	~MinimalistFlexbbNode ()

virtual void	assign_zero_state ()
	Virtual functions from NodeBase not covered by FlexbbNode. More...

virtual void	prepare_for_simulated_annealing ()

virtual void	print () const

PackerEnergy	project_deltaE_for_substitution (int alternate_state, PackerEnergy &prev_energy_for_node)
	Virtual functions from OTFFlexbbNode. More...

bool	prepare_for_altbb_move_to_state (int alt_state)
	Traverse incident edges and inform them of the alternate state being considered at this node. Return true if the alternate state is valid. More...

bool	prepare_for_altbb_move_to_closest_state (int alt_bb)
	Set the alternate state to be the one on the alternate backbone most similar to the currently assigned state. Traverse incident edges and inform them of the alternate state being considered at this node. Return true if the alternate state is valid. More...

PackerEnergy	get_frag_energy_for_alt_bb_state ()

PackerEnergy	get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total ()

void	commit_considered_substitution ()

void	commit_considered_substitution (ObjexxFCL::FArray1_int &state_on_node)

void	commit_alt_bb_substitution (ObjexxFCL::FArray1_int &state_on_node)

void	acknowledge_neighbors_substitution (int which_edge, PackerEnergy alternate_energy)

void	resolve_uncommitted_substitution ()

PackerEnergy	assign_state (int new_state)
	assign a new state to this node and return the change in energy induced More...

void	partially_assign_state (int new_state)
	For assinging network states to the interaction graph: when substituting two adjacent nodes i and j from states r and s to states r' and s', this function, along with its partner function, complete_partial_state_assignment, guarantees that neither the energies r' with s nor s' with r are computed which would be wasteful. This function is meant to be called by the owning interaction graph and not meant to be called by the outside world. More...

void	complete_partial_state_assignment ()
	See description of partially_assign_state. More...

virtual unsigned int	count_static_memory () const

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

Public Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbNode
	OTFFlexbbNode (OTFFlexbbInteractionGraph *, int node_id, int num_states)

virtual	~OTFFlexbbNode ()

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

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	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...

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
MinimalistFlexbbEdge const *	get_incident_minimalistflexbb_edge (int index) const
	Downcast pointers to incident edges, adjacent nodes, and the owning graph. More...

MinimalistFlexbbEdge *	get_incident_minimalistflexbb_edge (int index)

MinimalistFlexbbNode const *	get_adjacent_minimalistflexbb_node (int index) const

MinimalistFlexbbNode *	get_adjacent_minimalistflexbb_node (int index)

MinimalistFlexbbInteractionGraph const *	get_minimalistflexbbig_owner () const

MinimalistFlexbbInteractionGraph *	get_minimalistflexbbig_owner ()

PackerEnergy	get_altE_for_bb_move (PackerEnergy &curr_frag_etotal)

Protected Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbNode
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 ()

Member Typedef Documentation

typedef FlexbbNode protocols::flexpack::interaction_graph::MinimalistFlexbbNode::grandparent

typedef OTFFlexbbNode protocols::flexpack::interaction_graph::MinimalistFlexbbNode::parent

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::MinimalistFlexbbNode::MinimalistFlexbbNode	(	MinimalistFlexbbInteractionGraph *	owner,
		int	node_id,
		int	num_states
	)

Referenced by count_static_memory().

protocols::flexpack::interaction_graph::MinimalistFlexbbNode::~MinimalistFlexbbNode ( )

Member Function Documentation

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::acknowledge_neighbors_substitution	(	int	which_edge,
		PackerEnergy	alternate_energy
	)

References protocols::flexpack::interaction_graph::FlexbbNode::curr_state_two_body_energies(), protocols::flexpack::interaction_graph::FlexbbNode::inc_curr_state_total_energy(), and protocols::flexpack::interaction_graph::FlexbbNode::set_curr_state_two_body_energies().

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

MinimalistFlexbbNode::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_state ( int new_state)

assign a new state to this node and return the change in energy induced

References complete_partial_state_assignment(), protocols::flexpack::interaction_graph::FlexbbNode::curr_state_total_energy(), and partially_assign_state().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node().

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::assign_zero_state ( )

virtual

Virtual functions from NodeBase not covered by FlexbbNode.

Virtual functions from NodeBase.

Implements core::pack::interaction_graph::NodeBase.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0().

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_alt_bb_substitution ( ObjexxFCL::FArray1_int & state_on_node)

References protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(), protocols::flexpack::interaction_graph::FlexbbNode::alternate_state(), protocols::flexpack::interaction_graph::FlexbbNode::copy_alternate_to_current(), get_incident_minimalistflexbb_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current_following_flexbb_accept().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move().

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution ( )

References protocols::flexpack::interaction_graph::MinimalistFlexbbEdge::acknowledge_substitution(), protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_is_being_considered(), protocols::flexpack::interaction_graph::FlexbbNode::copy_alternate_to_current(), get_incident_minimalistflexbb_edge(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and protocols::flexpack::interaction_graph::FlexbbNode::have_edges_copy_alternate_to_current().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move(), commit_considered_substitution(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution().

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::commit_considered_substitution ( ObjexxFCL::FArray1_int & state_on_node)

References commit_considered_substitution(), protocols::flexpack::interaction_graph::FlexbbNode::current_state(), and core::pack::interaction_graph::NodeBase::get_node_index().

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::complete_partial_state_assignment ( )

See description of partially_assign_state.

Referenced by assign_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state().

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

virtual

memory accounting scheme

Reimplemented from protocols::flexpack::interaction_graph::OTFFlexbbNode.

References protocols::flexpack::interaction_graph::OTFFlexbbNode::count_dynamic_memory().

unsigned int protocols::flexpack::interaction_graph::MinimalistFlexbbNode::count_static_memory ( ) const

virtual

Implements core::pack::interaction_graph::NodeBase.

References MinimalistFlexbbNode().

MinimalistFlexbbNode const * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_adjacent_minimalistflexbb_node ( int index) const

inlineprotected

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

MinimalistFlexbbNode * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_adjacent_minimalistflexbb_node ( int index)

inlineprotected

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

PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_altE_for_bb_move ( PackerEnergy & curr_frag_etotal)

protected

MinimalistFlexbbNode::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_alt_bb_state ( )

This function call will be parallelized with openMP. The calculations performed by different nodes may be performed in any order and in parallel without any data collision. After this function completes, a second pass across the nodes in the graph must be performed to compute the node alternate_state_total_energy – but this second traversal is fast.

References protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_one_body_energy(), protocols::flexpack::interaction_graph::FlexbbNode::alternate_state_two_body_energies(), protocols::flexpack::interaction_graph::FlexbbNode::edge_connects_flexsegmate(), get_incident_minimalistflexbb_edge(), core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_node_index(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), and protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state_two_body_energies().

MinimalistFlexbbNode::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total ( )

This method could be parallelized with openMP, but probably would not be worth parallelizing. It is the second step of computing the deltaE for a backbone move. The alternate_state_total_energy is computed here, as well as the curr_frag_total_energy which is returned.

MinimalistFlexbbEdge const * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_incident_minimalistflexbb_edge ( int index) const

inlineprotected

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

Node Downcast.

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

Referenced by assign_zero_state(), commit_alt_bb_substitution(), commit_considered_substitution(), complete_partial_state_assignment(), get_frag_energy_for_alt_bb_state(), get_frag_energy_for_curr_bb_state_and_finalize_alt_energy_total(), and resolve_uncommitted_substitution().

MinimalistFlexbbEdge * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_incident_minimalistflexbb_edge ( int index)

inlineprotected

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

MinimalistFlexbbInteractionGraph const * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_minimalistflexbbig_owner ( ) const

inlineprotected

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

MinimalistFlexbbInteractionGraph * protocols::flexpack::interaction_graph::MinimalistFlexbbNode::get_minimalistflexbbig_owner ( )

inlineprotected

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

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::partially_assign_state ( int new_state)

For assinging network states to the interaction graph: when substituting two adjacent nodes i and j from states r and s to states r' and s', this function, along with its partner function, complete_partial_state_assignment, guarantees that neither the energies r' with s nor s' with r are computed which would be wasteful. This function is meant to be called by the owning interaction graph and not meant to be called by the outside world.

Referenced by assign_state(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state().

bool protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_closest_state ( int alt_bb)

Set the alternate state to be the one on the alternate backbone most similar to the currently assigned state. Traverse incident edges and inform them of the alternate state being considered at this node. Return true if the alternate state is valid.

References protocols::flexpack::interaction_graph::FlexbbNode::alt_bb(), protocols::flexpack::interaction_graph::FlexbbNode::closest_state_on_alt_bb(), protocols::flexpack::interaction_graph::FlexbbNode::curr_bb(), protocols::flexpack::interaction_graph::FlexbbNode::current_state(), protocols::flexpack::interaction_graph::FlexbbNode::get_num_distinct_backbones(), core::pack::interaction_graph::NodeBase::get_num_states(), and prepare_for_altbb_move_to_state().

bool protocols::flexpack::interaction_graph::MinimalistFlexbbNode::prepare_for_altbb_move_to_state ( int alt_state)

Traverse incident edges and inform them of the alternate state being considered at this node. Return true if the alternate state is valid.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution(), and prepare_for_altbb_move_to_closest_state().

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

virtual

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

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

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

virtual

Reimplemented from protocols::flexpack::interaction_graph::OTFFlexbbNode.

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

MinimalistFlexbbNode::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution	(	int	alternate_state,
		PackerEnergy &	prev_energy_for_node
	)

Virtual functions from OTFFlexbbNode.

Other functions

void protocols::flexpack::interaction_graph::MinimalistFlexbbNode::resolve_uncommitted_substitution ( )

References protocols::flexpack::interaction_graph::FlexbbNode::current_state(), get_incident_minimalistflexbb_edge(), core::pack::interaction_graph::NodeBase::get_num_incident_edges(), protocols::flexpack::interaction_graph::FlexbbEdge::reset_alternate_states_for_uncommited_substitution(), and protocols::flexpack::interaction_graph::FlexbbNode::set_alternate_state().

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution().

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

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

Public Types

Public Member Functions

Protected Member Functions

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation