|
| | OTFFlexbbInteractionGraph (int num_nodes) |
| | GRAPH. More...
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| |
| | ~OTFFlexbbInteractionGraph () override |
| |
| void | initialize (core::pack_basic::RotamerSetsBase const &) override |
| |
| void | set_ProCorrection_values_for_edge (int node1, int node2, int node_not_necessarily_proline, int state, int other_bb, PackerEnergy bb_nonprobb_E, PackerEnergy bb_probb_E, PackerEnergy sc_nonprobb_E, PackerEnergy sc_probb_E) |
| |
| void | set_GlyCorrection_values_for_edge (int node1, int node2, int node_not_necessarily_glycine, int state, int other_bb, PackerEnergy bb_nonglybb_E, PackerEnergy bb_glybb_E, PackerEnergy sc_nonglybb_E, PackerEnergy sc_glybb_E) |
| |
| unsigned int | count_dynamic_memory () const override |
| |
| virtual void | set_pose (Pose const &pose) |
| | Pose must be set before any edges are added to the graph. More...
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| |
| virtual void | set_scorefxn (ScoreFunction const &sfxn) |
| | Score function must be set before any edges are added to the graph. More...
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| PoseCOP | get_pose () const |
| | Edges request the pose and the score function at the time of their creation. More...
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| ScoreFunctionCOP | get_scorefxn () const |
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| void | note_long_range_interactions_exist_for_edge (int node1, int node2) |
| | Informs the edge connecting nodes 1 and 2 that they require long range interactions. Note – the edge must already exist. More...
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| void | debug_note_considered_substitution (core::conformation::Residue const &alt_rotamer, int index) |
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| void | debug_note_projected_deltaE_of_considered_substitution (PackerEnergy deltaE, PackerEnergy node_alt_total, bool require_match=true) |
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| void | debug_note_accepted_substitution () |
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| void | debug_note_rejected_substitution () |
| |
| | ~FlexbbInteractionGraph () override |
| | GRAPH. More...
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| |
| | FlexbbInteractionGraph (int num_nodes) |
| |
| int | get_num_aa_types () const |
| |
utility::vector1< core::Size >
const & | flexseg_members (int flexseg) const |
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| int | get_flexseg_for_bb (int bb) const |
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| int | get_flexseg_bb_offset (int flexseg_id) const |
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| bool | nodes_from_same_flexseg (int node1, int node2) const |
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| int | get_num_states_per_backbone_for_node (int node, int bb) const |
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| int | get_bb_for_state (int node, int state) const |
| |
| virtual void | consider_backbone_move (int bb_id, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_flexseg_energy, bool &valid_motion, int &num_nodes_changing_state)=0 |
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| virtual void | consider_bbmove_w_state_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state)=0 |
| |
| virtual PackerEnergy | commit_considered_backbone_move (ObjexxFCL::FArray1_int &rotamer_on_node)=0 |
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| void | get_accessible_states (Subsitution move_mode, utility::vector1< core::Size > &rotlist) const |
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| void | get_backbone_list (utility::vector1< core::Size > &bblist) const |
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| bool | get_backbone_currently_assigned (int bbid) const |
| | Is the backbone conformation (in the global enumertion of backbone conformations) already assigned to the network? False if any residue on the flexible segment that this bbid corresponds to is assigned state 0. More...
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| |
| bool | get_enforce_bb_contiguity () const |
| | FlexbbNodes will ask: am I allowed to have a state that breaks the backbone? There are brief periods when the backbone is "broken" as the graph assigns new states to nodes on the same flexible segment. More...
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| |
| void | increment_count_nodes_in_flexseg () |
| | Owner keeps a count of the number of nodes undergoing a simultaneous rotamer substitution as the backbone moves. More...
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| |
| | ~InteractionGraphBase () override |
| | destructor More...
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| |
| | InteractionGraphBase (int num_nodes) |
| | main constructor More...
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| |
| int | get_num_nodes () const override |
| | Get the number of nodes in the graph. More...
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| |
| 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...
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| |
| int | get_num_states_for_node (int node) const override |
| | returns the number of states for a particular node More...
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| |
| int | get_num_total_states () const override |
| | Get the total number of states. More...
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| |
| 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...
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| bool | get_edge_exists (int node1, int node2) const |
| | returns true if an edge between node1 and node2 exists More...
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| |
| void | drop_all_edges_for_node (int node) |
| | deletes all edges adjacent to the node specified More...
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| |
| void | print_vertices () const |
| | calls print() on each of the nodes in the graph More...
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| |
| virtual void | print () const |
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| void | output_connectivity (std::ostream &os) const |
| | writes out a list of all the edges in the graph More...
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| |
| 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...
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| |
| void | set_onebody_energies_multithreaded (core::Size const node_index, core::pack::rotamer_set::RotamerSetCOP rotset, core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, basic::thread_manager::RosettaThreadAssignmentInfo const &thread_assignments) |
| | Compute and store the onebody energy for all rotamers at a position. Safe for a multithreaded context. More...
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| |
| void | prepare_graph_for_simulated_annealing () override |
| | iterate across edges and nodes and allow them to prepare for simulated annealing More...
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| |
| void | blanket_assign_state_0 () override=0 |
| | State initialization. More...
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| |
| core::PackerEnergy | set_state_for_node (int node_ind, int new_state) override=0 |
| | Explicit state modification for a node. More...
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| |
| core::PackerEnergy | set_network_state (ObjexxFCL::FArray1_int &node_states) override=0 |
| | Explicit state modification for the network. More...
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| |
| void | consider_substitution (int node_ind, int new_state, core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_node) override=0 |
| | Consider switching node "node_ind" to state "new_state". More...
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| core::PackerEnergy | commit_considered_substitution () override=0 |
| | Accept a considered substitution (i.e. make the substitution permanent; commit it). More...
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| |
| core::PackerEnergy | get_energy_current_state_assignment () override=0 |
| | Get the energy resulting from the current set of state assignments. More...
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| |
| 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 |
| |
| void | set_errorfull_deltaE_threshold (core::PackerEnergy deltaE) override=0 |
| | Set an error threshold. More...
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| |
| bool | any_vertex_state_unassigned () const override |
| | Returns true if any node in the graph is in state 0, the unassigned state. More...
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| |
| 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...
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| |
| 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...
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| void | zero_one_body_energies_for_node (int node) |
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| void | add_to_nodes_one_body_energy (int node_ind, utility::vector1< core::PackerEnergy > const &one_body_energies) |
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| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| |
| 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...
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| |
| void | increment_edge_list_iterator () const |
| | increment the (single) edge list iterator to the next element More...
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| |
| bool | edge_list_iterator_at_end () const |
| | test: have we arrived at the edge list end? More...
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| |
| EdgeBase const & | get_edge () const |
| | return a const reference to an edge pointed at by the list iterator More...
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| |
| virtual void | declare_all_edge_energies_final () |
| | Iterates over all edges and calls declare_energies_final() on all of them. Takes O(N) time, where N is the number of edges. More...
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| |
| EdgeBase const * | find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) const |
| | Find an edge and return a const pointer to it. More...
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| |
| EdgeBase * | find_edge (int node1, int node2, bool const use_threadsafe_lookup=false) |
| | Find an edge and return a nonconst pointer to it. More...
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| |
| 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 () |
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| std::list< EdgeBase * >::iterator | get_edge_list_end () |
| |
std::list< EdgeBase * >
::const_iterator | get_edge_list_begin () const |
| |
std::list< EdgeBase * >
::const_iterator | get_edge_list_end () const |
| |
| | AnnealableGraphBase () |
| | Constructor. More...
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| |
| | AnnealableGraphBase (AnnealableGraphBase const &src) |
| | Copy constructor. More...
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| |
| | ~AnnealableGraphBase () override |
| | Destructor. More...
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| |
| virtual void | clean_up_after_packing (core::pose::Pose &pose) |
| | Provide the opportunity for an AnnealableGraph to clean up cached data in the pose or inside itself after packing. More...
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| |
Public Types inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
1.8.7