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core::pack::interaction_graph::OnTheFlyNode Class Referenceabstract

#include <OnTheFlyInteractionGraph.hh>

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Public Types

typedef std::pair< Vector, Real > BoundingSphere
 

Public Member Functions

 OnTheFlyNode (InteractionGraphBase *owner, int node_id, int num_states)
 main constructor, no default or copy constructors More...
 
virtual ~OnTheFlyNode ()
 
void set_rotamers (rotamer_set::RotamerSetCOP rotamers)
 
virtual void zero_one_body_energies ()
 
virtual void add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b)
 
virtual void update_one_body_energy (int state, core::PackerEnergy energy)
 
virtual void set_one_body_energy (int state, core::PackerEnergy energy)
 
virtual void add_to_one_body_energy (int state, core::PackerEnergy energy)
 
virtual void zero_one_body_energy (int state)
 
int get_num_aa_types () const
 
utility::vector1< int > & get_num_states_for_aa_types ()
 
utility::vector1< int > const & get_num_states_for_aa_types () const
 
int get_num_states_for_aa_type (int aa_type)
 
SparseMatrixIndex const & get_sparse_mat_info_for_state (int state) const
 
int get_state_offset_for_aatype (int aatype) const
 
core::PackerEnergy get_one_body_energy (int state) const
 
bool distinguish_backbone_and_sidechain () const
 
void distinguish_backbone_and_sidechain (bool setting)
 
virtual unsigned int count_static_memory () const =0
 
virtual unsigned int count_dynamic_memory () const
 
core::PackerEnergy compute_rotamer_pair_energy (int edge_making_energy_request, int state_this, int state_other) const
 
- Public Member Functions inherited from core::pack::interaction_graph::FixedBBNode
virtual ~FixedBBNode ()
 
 FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states)
 
- 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 prepare_for_simulated_annealing ()=0
 
virtual void print () const =0
 
virtual bool state_unassigned () const =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

OnTheFlyEdge * get_incident_otf_edge (int edge)
 
OnTheFlyEdge const * get_incident_otf_edge (int edge) const
 
OnTheFlyNode * get_adjacent_otf_node (int index)
 
OnTheFlyNode const * get_adjacent_otf_node (int index) const
 
OnTheFlyInteractionGraph * get_on_the_fly_owner ()
 
OnTheFlyInteractionGraph const * get_on_the_fly_owner () const
 
conformation::Residue const & get_rotamer (int state) const
 
BoundingSphere const & sc_bounding_sphere (int state) const
 
BoundingSphere const & bb_bounding_sphere () const
 

Private Attributes

rotamer_set::RotamerSetCOP rotamer_set_
 
utility::vector1
< conformation::ResidueCOP > 		rotamers_
 
utility::vector1< BoundingSphere > sc_bounding_spheres_
 
BoundingSphere bb_bounding_sphere_
 
int num_aa_types_
 
utility::vector1< int > num_states_for_aatype_
 
utility::vector1< int > state_offset_for_aatype_
 
utility::vector1
< SparseMatrixIndex > 		sparse_mat_info_for_state_
 
utility::vector1
< core::PackerEnergy > 		one_body_energies_
 
bool distinguish_backbone_and_sidechain_
 

Detailed Description

Definition at line 67 of file OnTheFlyInteractionGraph.hh.

Member Typedef Documentation

typedef std::pair< Vector, Real > core::pack::interaction_graph::OnTheFlyNode::BoundingSphere

Definition at line 70 of file OnTheFlyInteractionGraph.hh.

Constructor & Destructor Documentation

core::pack::interaction_graph::OnTheFlyNode::OnTheFlyNode ( InteractionGraphBase *  owner,
int  node_id,
int  num_states 
)

main constructor, no default or copy constructors

Detailed:

Definition at line 46 of file OnTheFlyInteractionGraph.cc.

core::pack::interaction_graph::OnTheFlyNode::~OnTheFlyNode ( )
virtual

Definition at line 67 of file OnTheFlyInteractionGraph.cc.

Member Function Documentation

void core::pack::interaction_graph::OnTheFlyNode::add_to_one_body_energies ( ObjexxFCL::FArray1< core::PackerEnergy > &  energy1b)
virtual

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

Definition at line 126 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::OnTheFlyNode::add_to_one_body_energy ( int  state,
core::PackerEnergy  energy 
)
virtual

increments one body energies for a given state

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

Definition at line 149 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::add_to_one_body_energy_for_node_state().

BoundingSphere const& core::pack::interaction_graph::OnTheFlyNode::bb_bounding_sphere ( ) const
inlineprotected

Definition at line 199 of file OnTheFlyInteractionGraph.hh.

core::PackerEnergy core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy ( int  edge_making_energy_request,
int  state_this,
int  state_other 
) const

Definition at line 180 of file OnTheFlyInteractionGraph.cc.

References core::conformation::Residue::aa(), core::chemical::aa_pro, core::scoring::EMapVector::dot(), core::pack::interaction_graph::EdgeBase::edge_weight(), core::scoring::ScoreFunction::eval_cd_2b(), core::scoring::ScoreFunction::eval_cd_2b_bb_sc(), core::scoring::ScoreFunction::eval_cd_2b_sc_sc(), core::scoring::ScoreFunction::eval_ci_2b(), core::scoring::ScoreFunction::eval_ci_2b_bb_sc(), core::scoring::ScoreFunction::eval_ci_2b_sc_sc(), core::scoring::eval_scsc_sr2b_energies(), core::pack::interaction_graph::OnTheFlyEdge::eval_type(), get_adjacent_otf_node(), core::pack::interaction_graph::NodeBase::get_incident_edge(), get_incident_otf_edge(), core::pack::interaction_graph::NodeBase::get_index_of_adjacent_node(), core::pack::interaction_graph::NodeBase::get_node_index(), get_on_the_fly_owner(), get_rotamer(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::pack::interaction_graph::OnTheFlyEdge::long_range_interactions_exist(), core::pack::interaction_graph::OnTheFlyInteractionGraph::note_rpe_calculated(), core::pack::interaction_graph::OnTheFlyInteractionGraph::pose(), sc_bounding_sphere(), core::pack::interaction_graph::sc_sc, core::pack::interaction_graph::sc_whole, core::pack::interaction_graph::OnTheFlyInteractionGraph::score_function(), core::pack::interaction_graph::OnTheFlyEdge::short_range_interactions_exist(), core::scoring::ScoreFunction::weights(), core::pack::interaction_graph::whole_sc, and core::pack::interaction_graph::whole_whole.

Referenced by core::pack::interaction_graph::LinearMemNode::compute_pair_energy_for_alternate_state(), core::pack::interaction_graph::LazyNode::compute_pair_energy_for_current_state(), core::pack::interaction_graph::DoubleLazyNode::compute_pair_energy_for_current_state(), core::pack::interaction_graph::LinearMemNode::compute_pair_energy_for_current_state(), core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(), core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies(), core::pack::interaction_graph::LazyEdge::get_two_body_energy(), and core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy_smi().

unsigned int core::pack::interaction_graph::OnTheFlyNode::count_dynamic_memory ( ) const
virtual

reports the amount of dynamic memory this node allocates recursing to its base class

Reimplemented from core::pack::interaction_graph::NodeBase.

Reimplemented in core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::DoubleLazyNode, and core::pack::interaction_graph::LazyNode.

Definition at line 165 of file OnTheFlyInteractionGraph.cc.

References core::pack::interaction_graph::NodeBase::count_dynamic_memory(), num_states_for_aatype_, one_body_energies_, rotamers_, sparse_mat_info_for_state_, and state_offset_for_aatype_.

Referenced by core::pack::interaction_graph::LazyNode::count_dynamic_memory(), core::pack::interaction_graph::DoubleLazyNode::count_dynamic_memory(), and core::pack::interaction_graph::LinearMemNode::count_dynamic_memory().

virtual unsigned int core::pack::interaction_graph::OnTheFlyNode::count_static_memory ( ) const
pure virtual

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

Implemented in core::pack::interaction_graph::LinearMemNode, core::pack::interaction_graph::DoubleLazyNode, and core::pack::interaction_graph::LazyNode.

bool core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain ( ) const
inline

Definition at line 141 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::distinguish_backbone_and_sidechain_for_node(), and core::pack::interaction_graph::OnTheFlyEdge::OnTheFlyEdge().

void core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain ( bool  setting)

Definition at line 110 of file OnTheFlyInteractionGraph.cc.

References distinguish_backbone_and_sidechain_, and core::pack::interaction_graph::NodeBase::get_num_incident_edges().

OnTheFlyNode * core::pack::interaction_graph::OnTheFlyNode::get_adjacent_otf_node ( int  index)
inlineprotected

Definition at line 487 of file OnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy().

OnTheFlyNode const * core::pack::interaction_graph::OnTheFlyNode::get_adjacent_otf_node ( int  index) const
inlineprotected

Definition at line 495 of file OnTheFlyInteractionGraph.hh.

OnTheFlyEdge * core::pack::interaction_graph::OnTheFlyNode::get_incident_otf_edge ( int  edge)
inlineprotected

Definition at line 471 of file OnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy().

OnTheFlyEdge const * core::pack::interaction_graph::OnTheFlyNode::get_incident_otf_edge ( int  edge) const
inlineprotected

Definition at line 479 of file OnTheFlyInteractionGraph.hh.

int core::pack::interaction_graph::OnTheFlyNode::get_num_aa_types ( ) const
inline

Definition at line 93 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LazyNode::update_internal_vectors(), and core::pack::interaction_graph::LinearMemNode::update_internal_vectors().

int core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_type ( int  aa_type)
inline

Definition at line 114 of file OnTheFlyInteractionGraph.hh.

utility::vector1< int >& core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types ( )
inline

Definition at line 100 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LazyEdge::get_second_node_num_states_per_aa(), core::pack::interaction_graph::DoubleLazyEdge::potential_twobody_memory_use(), core::pack::interaction_graph::DoubleLazyEdge::prep_aa_submatrix(), and core::pack::interaction_graph::DoubleLazyEdge::submatrix_size().

utility::vector1< int > const& core::pack::interaction_graph::OnTheFlyNode::get_num_states_for_aa_types ( ) const
inline

Definition at line 107 of file OnTheFlyInteractionGraph.hh.

OnTheFlyInteractionGraph * core::pack::interaction_graph::OnTheFlyNode::get_on_the_fly_owner ( )
inlineprotected

Definition at line 504 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), and compute_rotamer_pair_energy().

OnTheFlyInteractionGraph const * core::pack::interaction_graph::OnTheFlyNode::get_on_the_fly_owner ( ) const
inlineprotected

Definition at line 512 of file OnTheFlyInteractionGraph.hh.

core::PackerEnergy core::pack::interaction_graph::OnTheFlyNode::get_one_body_energy ( int  state) const
inline

Definition at line 135 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LazyNode::complete_state_assignment(), core::pack::interaction_graph::DoubleLazyNode::complete_state_assignment(), core::pack::interaction_graph::LinearMemNode::complete_state_assignment(), and core::pack::interaction_graph::OnTheFlyInteractionGraph::get_one_body_energy_for_node_state().

conformation::Residue const& core::pack::interaction_graph::OnTheFlyNode::get_rotamer ( int  state) const
inlineprotected

Definition at line 186 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LinearMemNode::commit_considered_substitution(), compute_rotamer_pair_energy(), and core::pack::interaction_graph::LinearMemNode::get_current_rotamer().

SparseMatrixIndex const& core::pack::interaction_graph::OnTheFlyNode::get_sparse_mat_info_for_state ( int  state) const
inline

Definition at line 121 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::LazyNode::aatype_for_state(), core::pack::interaction_graph::DoubleLazyNode::aatype_for_state(), core::pack::interaction_graph::LazyNode::assign_state(), core::pack::interaction_graph::DoubleLazyNode::assign_state(), core::pack::interaction_graph::LinearMemNode::assign_state(), core::pack::interaction_graph::LazyNode::get_sparse_mat_info_for_curr_state(), core::pack::interaction_graph::DoubleLazyNode::get_sparse_mat_info_for_curr_state(), core::pack::interaction_graph::LinearMemNode::get_sparse_mat_info_for_curr_state(), core::pack::interaction_graph::LazyEdge::get_two_body_energy(), core::pack::interaction_graph::DoubleLazyEdge::get_two_body_energy(), core::pack::interaction_graph::LazyNode::partial_assign_state(), core::pack::interaction_graph::DoubleLazyNode::partial_assign_state(), core::pack::interaction_graph::LinearMemNode::partial_assign_state(), and core::pack::interaction_graph::LazyEdge::wipe_two_body_energies_for_node_state().

int core::pack::interaction_graph::OnTheFlyNode::get_state_offset_for_aatype ( int  aatype) const
inline

Definition at line 129 of file OnTheFlyInteractionGraph.hh.

Referenced by core::pack::interaction_graph::DoubleLazyEdge::get_aa_submatrix_energies(), and core::pack::interaction_graph::LazyEdge::get_aa_submatrix_energies().

BoundingSphere const& core::pack::interaction_graph::OnTheFlyNode::sc_bounding_sphere ( int  state) const
inlineprotected

Definition at line 193 of file OnTheFlyInteractionGraph.hh.

Referenced by compute_rotamer_pair_energy().

void core::pack::interaction_graph::OnTheFlyNode::set_one_body_energy ( int  state,
core::PackerEnergy  energy 
)
virtual

sets one body energies for a given state

Definition at line 142 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::set_one_body_energy_for_node_state().

void core::pack::interaction_graph::OnTheFlyNode::set_rotamers ( rotamer_set::RotamerSetCOP  rotamers)

avoid polymorphic lookup later by nabbing rotamers now.

Definition at line 72 of file OnTheFlyInteractionGraph.cc.

References bb_bounding_sphere_, core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::pack::interaction_graph::NodeBase::get_num_states(), num_aa_types_, num_states_for_aatype_, rotamer_set_, rotamers_, sc_bounding_spheres_, sparse_mat_info_for_state_, and state_offset_for_aatype_.

Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::initialize().

void core::pack::interaction_graph::OnTheFlyNode::update_one_body_energy ( int  state,
core::PackerEnergy  energy 
)
virtual

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

Definition at line 134 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::OnTheFlyNode::zero_one_body_energies ( )
virtual

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

Definition at line 120 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

void core::pack::interaction_graph::OnTheFlyNode::zero_one_body_energy ( int  state)
virtual

Definition at line 157 of file OnTheFlyInteractionGraph.cc.

References one_body_energies_.

Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::zero_one_body_energy_for_node_state().

Member Data Documentation

BoundingSphere core::pack::interaction_graph::OnTheFlyNode::bb_bounding_sphere_
private

Definition at line 205 of file OnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

bool core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain_
private

Definition at line 212 of file OnTheFlyInteractionGraph.hh.

Referenced by distinguish_backbone_and_sidechain().

int core::pack::interaction_graph::OnTheFlyNode::num_aa_types_
private

Definition at line 207 of file OnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

utility::vector1< int > core::pack::interaction_graph::OnTheFlyNode::num_states_for_aatype_
private

Definition at line 208 of file OnTheFlyInteractionGraph.hh.

Referenced by count_dynamic_memory(), and set_rotamers().

utility::vector1< core::PackerEnergy > core::pack::interaction_graph::OnTheFlyNode::one_body_energies_
private

Definition at line 211 of file OnTheFlyInteractionGraph.hh.

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), count_dynamic_memory(), set_one_body_energy(), update_one_body_energy(), zero_one_body_energies(), and zero_one_body_energy().

rotamer_set::RotamerSetCOP core::pack::interaction_graph::OnTheFlyNode::rotamer_set_
private

Definition at line 202 of file OnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

utility::vector1< conformation::ResidueCOP > core::pack::interaction_graph::OnTheFlyNode::rotamers_
private

Definition at line 203 of file OnTheFlyInteractionGraph.hh.

Referenced by count_dynamic_memory(), and set_rotamers().

utility::vector1< BoundingSphere > core::pack::interaction_graph::OnTheFlyNode::sc_bounding_spheres_
private

Definition at line 204 of file OnTheFlyInteractionGraph.hh.

Referenced by set_rotamers().

utility::vector1< SparseMatrixIndex > core::pack::interaction_graph::OnTheFlyNode::sparse_mat_info_for_state_
private

Definition at line 210 of file OnTheFlyInteractionGraph.hh.

Referenced by count_dynamic_memory(), and set_rotamers().

utility::vector1< int > core::pack::interaction_graph::OnTheFlyNode::state_offset_for_aatype_
private

Definition at line 209 of file OnTheFlyInteractionGraph.hh.

Referenced by count_dynamic_memory(), and set_rotamers().

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