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protocols::flexpack::interaction_graph::OTFFlexbbNode Class Reference

#include <OTFFlexbbInteractionGraph.hh>

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

Public Types

typedef FlexbbNode parent
typedef core::conformation::Residue Residue
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::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...
EdgeBasefind_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 * >
edge_list_begin ()
std::list< EdgeBase * >
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...
EdgeBaseget_incident_edge (int index)
int get_index_of_adjacent_node (int index) const
NodeBase const * get_adjacent_node (int index) const
NodeBaseget_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...
OTFFlexbbEdgeget_incident_otfflexbb_edge (int index)
OTFFlexbbNode const * get_adjacent_otfflexbb_node (int index) const
OTFFlexbbNodeget_adjacent_otfflexbb_node (int index)
OTFFlexbbInteractionGraph const * get_otfflexbbig_owner () const
OTFFlexbbInteractionGraphget_otfflexbbig_owner ()
- Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbNode
FlexbbEdge const * get_incident_flexbb_edge (int index) const
FlexbbEdgeget_incident_flexbb_edge (int index)
FlexbbNode const * get_adjacent_flexbb_node (int index) const
FlexbbNodeget_adjacent_flexbb_node (int index)
FlexbbInteractionGraph const * get_flexbbig_owner () const
FlexbbInteractionGraphget_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
InteractionGraphBaseget_owner ()

Private Attributes

utility::vector1< ResidueCOProtamers_
< utility::vector1< Real > > 
utility::vector1< unsigned char > rotamer_is_proline_
utility::vector1< unsigned char > rotamer_is_glycine_

Member Typedef Documentation

Constructor & Destructor Documentation

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

Member Function Documentation

OTFFlexbbNode::Real protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers ( int  aatype,
int  bb 
) const
unsigned int protocols::flexpack::interaction_graph::OTFFlexbbNode::count_dynamic_memory ( ) const
void protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized ( )
OTFFlexbbNode const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int  index) const
OTFFlexbbNode * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int  index)
OTFFlexbbEdge const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_incident_otfflexbb_edge ( int  index) const

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)
OTFFlexbbInteractionGraph const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner ( ) const
OTFFlexbbInteractionGraph * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner ( )
void protocols::flexpack::interaction_graph::OTFFlexbbNode::print ( ) const
Residue const& protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer ( int  index) const
bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine ( int  state) const
bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline ( int  state) const
void protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer ( int  state,
ResidueCOP  rotamer 

Member Data Documentation

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

Referenced by rotamer_is_glycine(), and set_rotamer().

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

Referenced by rotamer_is_proline(), and set_rotamer().

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

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