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Rosetta 3.5
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Rosetta 3.5
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#include <PrecomputedPairEnergiesInteractionGraph.hh>
Public Member Functions | |
| virtual | ~PrecomputedPairEnergiesInteractionGraph () |
| PrecomputedPairEnergiesInteractionGraph (int num_nodes) | |
| void | add_to_two_body_energies_for_edge (int node1, int node2, ObjexxFCL::FArray2< core::PackerEnergy > const &res_res_energy_array) |
| interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies More... | |
| void | add_to_two_body_energies_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) |
| interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies More... | |
| void | set_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2, core::PackerEnergy const two_body_energy) |
| interface to PDEdge::set_two_body_energy More... | |
| void | clear_two_body_energy_for_edge (int node1, int node2, int state_node1, int state_node2) |
| interface to PDEdge::clear_two_body_energy More... | |
| virtual void | declare_edge_energies_final (int node1, int node2) |
| call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible More... | |
 Public Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph | |
| virtual | ~FixedBBInteractionGraph () |
| FixedBBInteractionGraph (int num_nodes) | |
| virtual int | get_num_aatypes () const =0 |
| 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 |
| virtual void | initialize (rotamer_set::RotamerSetsBase const &rot_sets)=0 |
| 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 |
| virtual core::PackerEnergy | get_one_body_energy_for_node_state (int node, int state)=0 |
| 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... | |
| virtual void | prepare_for_simulated_annealing () |
| iterate across edges and nodes and allow them to prepare for simulated annealing More... | |
| virtual void | blanket_assign_state_0 ()=0 |
| virtual core::PackerEnergy | set_state_for_node (int node_ind, int new_state)=0 |
| virtual core::PackerEnergy | set_network_state (ObjexxFCL::FArray1_int &node_states)=0 |
| virtual void | consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node)=0 |
| virtual core::PackerEnergy | commit_considered_substitution ()=0 |
| virtual core::PackerEnergy | get_energy_current_state_assignment ()=0 |
| void | set_edge_weight (int node1, int node2, Real edge_weight) |
| Real | get_edge_weight (int node1, int node2) const |
| virtual int | get_edge_memory_usage () const =0 |
| virtual void | print_current_state_assignment () const =0 |
| virtual void | set_errorfull_deltaE_threshold (core::PackerEnergy deltaE)=0 |
| 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 () |
| virtual core::PackerEnergy | get_energy_sum_for_vertex_group (int group_id)=0 |
| 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) |
| virtual NodeBase * | create_new_node (int node_index, int num_states)=0 |
| virtual EdgeBase * | create_new_edge (int index1, int index2)=0 |
| 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 |
Additional Inherited Members | |
| Protected Member Functions inherited from core::pack::interaction_graph::FixedBBInteractionGraph | |
| FixedBBNode const * | get_fixedbb_node (int node_index) const |
| Downcasts. More... | |
| FixedBBNode * | get_fixedbb_node (int node_index) |
| FixedBBEdge const * | get_fixedbb_edge (int node1, int node2) const |
| FixedBBEdge * | get_fixedbb_edge (int node1, int node2) |
Definition at line 74 of file PrecomputedPairEnergiesInteractionGraph.hh.
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inlinevirtual |
Definition at line 77 of file PrecomputedPairEnergiesInteractionGraph.hh.
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inline |
Definition at line 78 of file PrecomputedPairEnergiesInteractionGraph.hh.
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge | ( | int | node1, |
| int | node2, | ||
| ObjexxFCL::FArray2< core::PackerEnergy > const & | res_res_energy_array | ||
| ) |
interface for PrecomputedPairEnergiesEdge::add_to_two_body_energies
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::add_to_two_body_energies_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2, | ||
| core::PackerEnergy const | two_body_energy | ||
| ) |
interface to PrecomputedPairEnergiesEdge::add_to_two_body_energies
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
| two_body_energy | - [in] - the energy for this state pair |
Definition at line 60 of file PrecomputedPairEnergiesInteractionGraph.cc.
References core::pack::interaction_graph::PrecomputedPairEnergiesEdge::add_to_two_body_energy().
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::clear_two_body_energy_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2 | ||
| ) |
interface to PDEdge::clear_two_body_energy
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
Definition at line 107 of file PrecomputedPairEnergiesInteractionGraph.cc.
References core::pack::interaction_graph::PrecomputedPairEnergiesEdge::set_two_body_energy().
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virtual |
call this if you're done storing energies in an edge - it will reduce the memory usage for that edge if possible
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
Definition at line 127 of file PrecomputedPairEnergiesInteractionGraph.cc.
References core::pack::interaction_graph::EdgeBase::declare_energies_final().
| void core::pack::interaction_graph::PrecomputedPairEnergiesInteractionGraph::set_two_body_energy_for_edge | ( | int | node1, |
| int | node2, | ||
| int | state_node1, | ||
| int | state_node2, | ||
| core::PackerEnergy const | two_body_energy | ||
| ) |
interface to PDEdge::set_two_body_energy
| node1 | - [in] - the index of the smaller-indexed node |
| node2 | - [in] - the index of the larger-indexed node |
| state_node1 | - [in] - state on smaller-indexed node |
| state_node2 | - [in] - state on larger-indexed node |
| two_body_energy | - [in] - the energy for this state pair |
Definition at line 83 of file PrecomputedPairEnergiesInteractionGraph.cc.
References core::pack::interaction_graph::PrecomputedPairEnergiesEdge::set_two_body_energy().
1.8.4