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Rosetta
2021.07
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#include <OnTheFlyInteractionGraph.hh>
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 |
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~FixedBBNode () override | |
FixedBBNode (InteractionGraphBase *owner, int node_id, int num_states) | |
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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 |
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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_ |
typedef std::pair< Vector, Real > core::pack::interaction_graph::OnTheFlyNode::BoundingSphere |
core::pack::interaction_graph::OnTheFlyNode::OnTheFlyNode | ( | InteractionGraphBase * | owner, |
int | node_id, | ||
int | num_states | ||
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main constructor, no default or copy constructors
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overridedefault |
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overridevirtual |
Implements core::pack::interaction_graph::NodeBase.
References one_body_energies_.
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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().
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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().
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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().
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overridepure virtual |
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inline |
void core::pack::interaction_graph::OnTheFlyNode::distinguish_backbone_and_sidechain | ( | bool | setting | ) |
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inlineprotected |
References core::pack::interaction_graph::NodeBase::get_adjacent_node().
Referenced by compute_rotamer_pair_energy().
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inlineprotected |
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inlineprotected |
References core::pack::interaction_graph::NodeBase::get_incident_edge().
Referenced by compute_rotamer_pair_energy().
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inlineprotected |
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inline |
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inline |
References num_states_for_aatype_.
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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().
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inline |
References num_states_for_aatype_.
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inlineprotected |
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inlineprotected |
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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().
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inlineprotected |
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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().
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inline |
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inlineprotected |
References sc_bounding_spheres_.
Referenced by compute_rotamer_pair_energy().
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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().
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overridevirtual |
Implements core::pack::interaction_graph::NodeBase.
References protocols::buns::energy, and one_body_energies_.
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overridevirtual |
Implements core::pack::interaction_graph::NodeBase.
References one_body_energies_.
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References one_body_energies_.
Referenced by core::pack::interaction_graph::OnTheFlyInteractionGraph::zero_one_body_energy_for_node_state().
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Referenced by bb_bounding_sphere(), and set_rotamers().
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Referenced by distinguish_backbone_and_sidechain().
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Referenced by get_num_aa_types().
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Referenced by count_dynamic_memory(), get_num_states_for_aa_type(), get_num_states_for_aa_types(), and set_rotamers().
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Referenced by set_rotamers().
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Referenced by count_dynamic_memory(), get_rotamer(), and set_rotamers().
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Referenced by count_dynamic_memory(), sc_bounding_sphere(), and set_rotamers().
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Referenced by count_dynamic_memory(), get_sparse_mat_info_for_state(), and set_rotamers().
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Referenced by count_dynamic_memory(), get_state_offset_for_aatype(), and set_rotamers().