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Rosetta 3.5
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Rosetta 3.5
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#include <SymmLinMemInteractionGraph.hh>
Public Member Functions | |
| SymmLinearMemoryInteractionGraph (int numNodes) | |
| virtual | ~SymmLinearMemoryInteractionGraph () |
| virtual void | blanket_assign_state_0 () |
| virtual core::PackerEnergy | set_state_for_node (int node_ind, int new_state) |
| virtual core::PackerEnergy | set_network_state (ObjexxFCL::FArray1_int &node_states) |
| virtual void | consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) |
| virtual core::PackerEnergy | commit_considered_substitution () |
| virtual core::PackerEnergy | get_energy_current_state_assignment () |
| virtual int | get_edge_memory_usage () const |
| virtual void | print_current_state_assignment () const |
| virtual void | set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) |
| virtual core::PackerEnergy | get_energy_sum_for_vertex_group (int group_id) |
| virtual void | prepare_for_simulated_annealing () |
| iterate across edges and nodes and allow them to prepare for simulated annealing More... | |
| virtual unsigned int | count_static_memory () const |
| virtual unsigned int | count_dynamic_memory () const |
 Public Member Functions inherited from core::pack::interaction_graph::SymmOnTheFlyInteractionGraph | |
| SymmOnTheFlyInteractionGraph (int num_nodes) | |
| ~SymmOnTheFlyInteractionGraph () | |
| virtual void | initialize (rotamer_set::RotamerSetsBase const &rot_sets) |
| virtual int | get_num_aatypes () const |
| int | get_num_restype_groups () const |
| bool | distinguish_backbone_and_sidechain_for_node (int node) const |
| void | distinguish_backbone_and_sidechain_for_node (int node, bool setting) |
| void | set_score_function (ScoreFunction const &) |
| void | set_pose (Pose const &) |
| Pose const & | pose () const |
| conformation::symmetry::SymmetryInfoCOP | symm_info () const |
| Pose & | non_const_pose () |
| debugging only – modify the pose during simulated annealing, if you're so inclined More... | |
| ScoreFunction const & | score_function () const |
| void | zero_one_body_energy_for_node_state (int node_ind, int state) |
| void | add_to_one_body_energy_for_node_state (int node_ind, int state, core::PackerEnergy one_body_energy) |
| void | set_one_body_energy_for_node_state (int node_ind, int state, core::PackerEnergy one_body_energy) |
| virtual core::PackerEnergy | get_one_body_energy_for_node_state (int node, int state) |
| void | set_residues_adjacent_for_subunit_pair_for_edge (int node1, int node2, int asu_node_index, int other_node_subunit) |
| void | reset_rpe_calculations_count () |
| Size | get_num_rpe_calculations_count () const |
| void | note_rpe_calculated () const |
| to be called by owned OTF node only More... | |
| void | add_ProCorrection_values_for_edge (int node1, int node2, int node_not_neccessarily_proline, int state, core::PackerEnergy bb_nonprobb_E, core::PackerEnergy bb_probb_E, core::PackerEnergy sc_nonprobb_E, core::PackerEnergy sc_probb_E) |
| void | note_short_range_interactions_exist_for_edge (int node1, int node2) |
| void | note_long_range_interactions_exist_for_edge (int node1, int node2) |
| HTReal const & | symmetric_transform (Size dst_subunit) const |
| Return the homogeneous transform to translate and rotate coordinates originally in the asymmetric unit into a given destination subunit. More... | |
| SymmOnTheFlyNode * | get_on_the_fly_node (int node_index) |
| SymmOnTheFlyNode const * | get_on_the_fly_node (int node_index) const |
| Public Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph | |
| virtual | ~FixedBBInteractionGraph () |
| FixedBBInteractionGraph (int num_nodes) | |
| virtual bool | aa_submatrix_energies_retrievable () const |
| virtual int | aatype_for_node_state (int node_ind, int node_state) const |
| virtual ObjexxFCL::FArray2D < core::PackerEnergy > | get_aa_submatrix_energies_for_edge (int node1, int node2, int node1aa, int node2aa) const |
| void | set_sparse_aa_info_for_edge (int node1, int node2, ObjexxFCL::FArray2_bool const &sparse_conn_info) |
| interface to PDEdge::set_sparse_aa_info More... | |
| bool | get_sparse_aa_info_for_edge (int node1, int node2, int node1aa, int node2aa) |
| returns true if node1aa and node2aa are amino acid neighbors More... | |
| void | force_aa_neighbors_for_edge (int node1, int node2, int node1aa, int node2aa) |
| interface to FixedBBEdge::force_aa_neighbors More... | |
| void | force_all_aa_neighbors_for_edge (int node1, int node2) |
| interface to PDEdge::force_aa_neighbors More... | |
| virtual core::PackerEnergy | get_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) const |
| interface to FixedBBEdge::get_two_body_energy More... | |
| Public Member Functions inherited from core::pack::interaction_graph::InteractionGraphBase | |
| virtual | ~InteractionGraphBase () |
| destructor More... | |
| InteractionGraphBase (int num_nodes) | |
| main constructor More... | |
| virtual int | get_num_nodes_v () const |
| int | get_num_nodes () const |
| void | set_num_states_for_node (int node, int num_states) |
| sets the number of states for a node of a particular index NEW REQUIREMENT: Nodes must have their num-states set in ascending order by node index; that is, node 1 must go first, node 2 next, and so on. More... | |
| int | get_num_states_for_node (int node) const |
| returns the number of states for a particular node More... | |
| int | get_num_total_states () const |
| void | add_edge (int node1, int node2) |
| creates a new edge between nodes index1 and index2. Nodes do not have to be listed in order More... | |
| bool | get_edge_exists (int node1, int node2) |
| returns true if an edge between node1 and node2 exists More... | |
| void | drop_all_edges_for_node (int node) |
| deletes all edges adjacent to the node specified More... | |
| void | print_vertices () const |
| calls print() on each of the nodes in the graph More... | |
| virtual void | print () const |
| void | output_connectivity (std::ostream &os) const |
| writes out a list of all the edges in the graph More... | |
| void | output_dimacs (std::ostream &os) const |
| writes out a connectivity description of the graph in the famous dimacs format. (where the first column "DIMACS:" should be sed'ed out) More... | |
| void | set_edge_weight (int node1, int node2, Real edge_weight) |
| Real | get_edge_weight (int node1, int node2) const |
| bool | any_vertex_state_unassigned () const |
| Returns true if any node in the graph is in state 0, the unassigned state. More... | |
| void | add_to_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &one_body_energies) |
| takes one FArray of energies – one energy for each state for each node More... | |
| void | update_one_body_energies (ObjexxFCL::FArray1< core::PackerEnergy > &old_energy1b, ObjexxFCL::FArray1< core::PackerEnergy > &new_energy1b) |
| decrements the one body energies by the values held in old_energy1b, increments the one body energies by the values held in new_energy1b, and copies new_energy1b into old_energy1b. More... | |
| void | zero_one_body_energies_for_node (int node) |
| void | add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies) |
| void | add_to_nodes_one_body_energy (int node_ind, ObjexxFCL::FArray1< core::PackerEnergy > const &one_body_energies) |
| void | add_to_nodes_one_body_energy (int node_ind, int state_id, core::PackerEnergy const one_body_energy) |
| interface to PrecomputedPairEnergiesNode::add_to_nodes_one_body_energy More... | |
| void | set_number_of_energy_sum_vertex_groups (int num_groups) |
| a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More... | |
| void | set_vertex_member_of_group (int vertex, int group) |
| a user may define subsets of the vertex set for which they would like to know the internal energy sum. For instance in a graph with 6 vertices, {a,b,c,d,e,f} a user may be interested in the sum of the one- and two-body energies for vertices {a,b,c}. The graph will return sum of the one body energies for vertices a b and c and also any two-body energies for the edges in the subgraph induced by a,b, and c. (In this case, edges {a,b}, {a,c} and {b,c} if these edges are part of the graph. The edge {a,d} will not be counted if it is part of the graph.) More... | |
| void | print_vertex_groups () |
| int | count_connected_components_and_initialize_vertex_groups () |
| makes a depth first traversal of the graph, counting the number of connected components, and initializes the vertex group memberships to reflect the connected components. Returns the number of connected components in the graph. More... | |
| void | note_vertex_reached (int node_index) |
| marks a vertex as belonging to the connected component currently being traversed in the depth first traversal. More... | |
| bool | vertex_already_reached (int node_index) |
| used by class NodeBase during the depth-first traversal to determine the number of connected components in the graph. returns true if the dft has already reached the node. More... | |
| bool | get_vertex_member_of_energy_sum_group (int node_index, int group_id) |
| virtual unsigned int | getTotalMemoryUsage () const |
| void | reset_edge_list_iterator_for_node (int node_index) const |
| set the Graph's (single) edge list iterator to the beginning of the edge list for a particular node More... | |
| void | increment_edge_list_iterator () const |
| increment the (single) edge list iterator to the next element More... | |
| bool | edge_list_iterator_at_end () const |
| test: have we arrived at the edge list end? More... | |
| EdgeBase const & | get_edge () const |
| return a const reference to an edge pointed at by the list iterator More... | |
| EdgeBase const * | find_edge (int node1, int node2) const |
| returns the edge connecting node1 and node2 More... | |
| EdgeBase * | find_edge (int node1, int node2) |
| NodeBase * | get_node (int index) const |
| int | get_num_edges () const |
| std::list< EdgeBase * >::iterator | get_edge_list_begin () |
| std::list< EdgeBase * > ::const_iterator | get_edge_list_begin () const |
| std::list< EdgeBase * > ::const_iterator | get_edge_list_end () const |
Protected Member Functions | |
| virtual NodeBase * | create_new_node (int node_index, int num_states) |
| virtual EdgeBase * | create_new_edge (int index1, int index2) |
| core::PackerEnergy | get_energy_PD_current_state_assignment () |
| O(1) total energy report. Protected read access for derived classes. More... | |
| void | update_internal_energy_totals () |
| SymmLinearMemNode const * | get_symmlinmem_node (int index) const |
| SymmLinearMemNode * | get_symmlinmem_node (int index) |
Private Member Functions | |
| void | set_recent_history_sizes () |
| SymmLinearMemoryInteractionGraph () | |
| SymmLinearMemoryInteractionGraph (SymmLinearMemoryInteractionGraph const &) | |
| SymmLinearMemoryInteractionGraph & | operator= (SymmLinearMemoryInteractionGraph const &) |
Static Private Attributes | |
| static const int | COMMIT_LIMIT_BETWEEN_UPDATES = 1024 |
Additional Inherited Members | |
| Public Types inherited from core::pack::interaction_graph::SymmOnTheFlyInteractionGraph | |
| typedef pose::Pose | Pose |
| typedef pose::PoseOP | PoseOP |
| typedef scoring::ScoreFunction | ScoreFunction |
| typedef scoring::ScoreFunctionOP | ScoreFunctionOP |
| typedef numeric::HomogeneousTransform < Real > | HTReal |
Definition at line 302 of file SymmLinMemInteractionGraph.hh.
| core::pack::interaction_graph::SymmLinearMemoryInteractionGraph::SymmLinearMemoryInteractionGraph | ( | int | numNodes) |
Definition at line 1077 of file SymmLinMemInteractionGraph.cc.
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Definition at line 1090 of file SymmLinMemInteractionGraph.cc.
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Referenced by count_static_memory().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1094 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmLinearMemNode::assign_zero_state(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_symmlinmem_node(), have_not_committed_last_substitution_, and total_energy_current_state_assignment_.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1157 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmLinearMemNode::commit_considered_substitution(), COMMIT_LIMIT_BETWEEN_UPDATES, get_symmlinmem_node(), have_not_committed_last_substitution_, node_considering_alt_state_, num_commits_since_last_update_, total_energy_alternate_state_assignment_, total_energy_current_state_assignment_, and update_internal_energy_totals().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1134 of file SymmLinMemInteractionGraph.cc.
References get_symmlinmem_node(), have_not_committed_last_substitution_, node_considering_alt_state_, total_energy_alternate_state_assignment_, and total_energy_current_state_assignment_.
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Reimplemented from core::pack::interaction_graph::SymmOnTheFlyInteractionGraph.
Definition at line 1264 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::count_dynamic_memory().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1258 of file SymmLinMemInteractionGraph.cc.
References SymmLinearMemoryInteractionGraph().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1279 of file SymmLinMemInteractionGraph.cc.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1272 of file SymmLinMemInteractionGraph.cc.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1190 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), and core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1175 of file SymmLinMemInteractionGraph.cc.
References total_energy_current_state_assignment_, and update_internal_energy_totals().
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O(1) total energy report. Protected read access for derived classes.
Definition at line 1184 of file SymmLinMemInteractionGraph.cc.
References total_energy_current_state_assignment_.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1223 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), core::pack::interaction_graph::SymmLinearMemNode::get_one_body_energy_current_state(), get_symmlinmem_node(), and core::pack::interaction_graph::InteractionGraphBase::get_vertex_member_of_energy_sum_group().
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Definition at line 341 of file SymmLinMemInteractionGraph.hh.
References core::pack::interaction_graph::InteractionGraphBase::get_node().
Referenced by blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), get_energy_sum_for_vertex_group(), print_current_state_assignment(), set_network_state(), set_recent_history_sizes(), set_state_for_node(), and update_internal_energy_totals().
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Definition at line 347 of file SymmLinMemInteractionGraph.hh.
References core::pack::interaction_graph::InteractionGraphBase::get_node().
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iterate across edges and nodes and allow them to prepare for simulated annealing
Edges may decide to delete themselves during this subroutine; therefore edges are prepared first. Afterwards, the nodes must update their edge vector representation.
Reimplemented from core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1247 of file SymmLinMemInteractionGraph.cc.
References first_time_prepping_for_simA_, core::pack::interaction_graph::InteractionGraphBase::prepare_for_simulated_annealing(), and set_recent_history_sizes().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1202 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmLinearMemNode::get_current_state(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_symmlinmem_node(), core::pack::interaction_graph::SymmLinearMemNode::print(), core::pack::interaction_graph::T(), and total_energy_current_state_assignment_.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1219 of file SymmLinMemInteractionGraph.cc.
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1115 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmLinearMemNode::complete_state_assignment(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_symmlinmem_node(), have_not_committed_last_substitution_, core::pack::interaction_graph::SymmLinearMemNode::partial_assign_state(), total_energy_current_state_assignment_, and update_internal_energy_totals().
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Definition at line 1305 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_symmlinmem_node(), and core::pack::interaction_graph::SymmLinearMemNode::set_recent_history_size().
Referenced by prepare_for_simulated_annealing().
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Implements core::pack::interaction_graph::InteractionGraphBase.
Definition at line 1105 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::SymmLinearMemNode::assign_state(), get_symmlinmem_node(), have_not_committed_last_substitution_, total_energy_current_state_assignment_, and update_internal_energy_totals().
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Definition at line 1285 of file SymmLinMemInteractionGraph.cc.
References core::pack::interaction_graph::InteractionGraphBase::get_edge_list_begin(), core::pack::interaction_graph::InteractionGraphBase::get_edge_list_end(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), get_symmlinmem_node(), num_commits_since_last_update_, and total_energy_current_state_assignment_.
Referenced by commit_considered_substitution(), get_energy_current_state_assignment(), set_network_state(), and set_state_for_node().
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Definition at line 364 of file SymmLinMemInteractionGraph.hh.
Referenced by commit_considered_substitution().
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Definition at line 356 of file SymmLinMemInteractionGraph.hh.
Referenced by prepare_for_simulated_annealing().
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Definition at line 362 of file SymmLinMemInteractionGraph.hh.
Referenced by blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), set_network_state(), and set_state_for_node().
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Definition at line 360 of file SymmLinMemInteractionGraph.hh.
Referenced by commit_considered_substitution(), and consider_substitution().
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Definition at line 357 of file SymmLinMemInteractionGraph.hh.
Referenced by commit_considered_substitution(), and update_internal_energy_totals().
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Definition at line 359 of file SymmLinMemInteractionGraph.hh.
Referenced by commit_considered_substitution(), and consider_substitution().
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Definition at line 358 of file SymmLinMemInteractionGraph.hh.
Referenced by blanket_assign_state_0(), commit_considered_substitution(), consider_substitution(), get_energy_current_state_assignment(), get_energy_PD_current_state_assignment(), print_current_state_assignment(), set_network_state(), set_state_for_node(), and update_internal_energy_totals().
1.8.4