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

#include <OnTheFlyInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::OnTheFlyNode:
Inheritance graph
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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...
 
 ~OnTheFlyNode () override
 
void set_rotamers (rotamer_set::RotamerSetCOP rotamers)
 
void zero_one_body_energies () override
 
void add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &energy1b) override
 
void update_one_body_energy (int state, core::PackerEnergy energy) override
 
virtual void set_one_body_energy (int state, core::PackerEnergy energy)
 
void add_to_one_body_energy (int state, core::PackerEnergy energy) override
 
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)
 
unsigned int count_static_memory () const override=0
 
unsigned int count_dynamic_memory () const override
 
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
 ~FixedBBNode () override
 
 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
 
- 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

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_
 

Member Typedef Documentation

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

Constructor & Destructor Documentation

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

main constructor, no default or copy constructors

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

Member Function Documentation

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

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

References one_body_energies_.

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

increments one body energies for a given state

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

References protocols::buns::energy, and 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

References bb_bounding_sphere_.

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

References protocols::cluster::calibur::aa, core::conformation::Residue::aa(), core::chemical::aa_gly, core::chemical::aa_pro, 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::weighted_sum(), 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
overridevirtual

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

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

References core::pack::interaction_graph::NodeBase::count_dynamic_memory(), num_states_for_aatype_, one_body_energies_, rotamers_, sc_bounding_spheres_, 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().

unsigned int core::pack::interaction_graph::OnTheFlyNode::count_static_memory ( ) const
overridepure 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

References distinguish_backbone_and_sidechain_.

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)

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

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

Referenced by compute_rotamer_pair_energy().

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

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

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

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

Referenced by compute_rotamer_pair_energy().

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

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

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

References num_aa_types_.

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

References num_states_for_aatype_.

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

References num_states_for_aatype_.

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

References num_states_for_aatype_.

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

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

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

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

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

References one_body_energies_.

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

References rotamers_.

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

References core::pack::interaction_graph::NodeBase::get_num_states(), and sparse_mat_info_for_state_.

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

References state_offset_for_aatype_.

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

References sc_bounding_spheres_.

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

References protocols::buns::energy, and 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.

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(), core::chemical::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 
)
overridevirtual

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

References protocols::buns::energy, and one_body_energies_.

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

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

References one_body_energies_.

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

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

Referenced by bb_bounding_sphere(), and set_rotamers().

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

Referenced by distinguish_backbone_and_sidechain().

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

Referenced by get_num_aa_types().

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

Referenced by count_dynamic_memory(), get_num_states_for_aa_type(), get_num_states_for_aa_types(), and set_rotamers().

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

Referenced by add_to_one_body_energies(), add_to_one_body_energy(), count_dynamic_memory(), get_one_body_energy(), 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

Referenced by set_rotamers().

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

Referenced by count_dynamic_memory(), get_rotamer(), and set_rotamers().

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

Referenced by count_dynamic_memory(), sc_bounding_sphere(), and set_rotamers().

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

Referenced by count_dynamic_memory(), get_sparse_mat_info_for_state(), and set_rotamers().

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

Referenced by count_dynamic_memory(), get_state_offset_for_aatype(), and set_rotamers().

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