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Rosetta 3.5
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Rosetta 3.5
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#include <SimpleInteractionGraph.hh>
Public Member Functions | |
| SimpleNode (graph::Graph *owner, Size resnum) | |
| virtual | ~SimpleNode () |
| virtual void | copy_from (graph::Node const *) |
| invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node. More... | |
| virtual void | print () const |
| send summaray data about this node to the screen More... | |
| virtual platform::Size | count_static_memory () const |
| memory accounting scheme More... | |
| virtual platform::Size | count_dynamic_memory () const |
| memory accounting scheme More... | |
| Real | one_body_energy () const |
| Real | proposed_one_body_energy () const |
| Real | current_one_body_energy () const |
| bool | moved () const |
| Is this node considering a state substitution? More... | |
| void | commit_change () |
| Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges. More... | |
| void | commit_change_no_res_pointer_update () |
| Copy the alternate energies to the current energies for this node and its incident edges. More... | |
| void | reject_change () |
| Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation. More... | |
| void | set_current (conformation::ResidueCOP res) |
| Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies. More... | |
| void | set_alternate (conformation::ResidueCOP res) |
| Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies. More... | |
| void | set_current_no_E_update (conformation::ResidueCOP res) |
| Passive mode behavior: set the current residue pointer without updating the current one body or two body energies. More... | |
| void | set_alternate_no_E_update (conformation::ResidueCOP res) |
| Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies. More... | |
| void | update_energies_after_passive_change () |
| conformation::ResidueCOP | get_current () const |
| return the pointer to the current state (might be 0) More... | |
| conformation::ResidueCOP | get_alternate () const |
| return the pointer to the alternate state (might be 0) More... | |
| Vector const & | bb_centroid () const |
| Real | bb_radius () const |
| Vector const & | curr_sc_centroid () const |
| Real | curr_sc_radius () const |
| Vector const & | alt_sc_centroid () const |
| Real | alt_sc_radius () const |
 Public Member Functions inherited from core::graph::Node | |
| virtual | ~Node () |
| virtual destructor More... | |
| Node (Graph *, platform::Size node_id) | |
| Main constructor, no default constructor nor copy constructor. More... | |
| void | add_edge (Edge *edge_ptr, EdgeListIter &) |
| adds edge pointer to edge list; returns an iterator to the new list element More... | |
| void | drop_edge (EdgeListIter edge_iterator) |
| removes an edge iterator from the node's edge list. Only called by Edge class. More... | |
| void | drop_all_edges () |
| deletes all edges incident upon this node More... | |
| void | set_num_neighbors_counting_self_static (platform::Size neighbor) |
| Edge const * | find_edge (platform::Size other_node_index) const |
| a "slow" (linear) search for an edge. More... | |
| Edge * | find_edge (platform::Size other_node_index) |
| non-const edge finding method; changes no data, but returns a non-const pointer More... | |
| EdgeListIter | edge_list_begin () |
| returns a non-const iterator to the beginning of its edge list More... | |
| EdgeListConstIter | const_edge_list_begin () const |
| returns a const iterator to the beginning of its edge list More... | |
| EdgeListIter | edge_list_end () |
| returns a non-const iterator to the end of its edge list More... | |
| EdgeListConstIter | const_edge_list_end () const |
| returns a const iterator to the end of its edge list More... | |
| EdgeListIter | lower_edge_list_begin () |
| returns a non-const iterator to the beginning of its lower-edge list More... | |
| EdgeListConstIter | const_lower_edge_list_begin () const |
| returns a const iterator to the beginning of its lower-edge list More... | |
| EdgeListIter | lower_edge_list_end () |
| returns a non-const iterator to the end of its lower-edge list More... | |
| EdgeListConstIter | const_lower_edge_list_end () const |
| returns a const iterator to the end of its lower-edge list More... | |
| EdgeListIter | upper_edge_list_begin () |
| returns a non-const iterator to the beginning of its upper-edge list More... | |
| EdgeListConstIter | const_upper_edge_list_begin () const |
| returns a const iterator to the beginning of its upper-edge list More... | |
| EdgeListIter | upper_edge_list_end () |
| returns a non-const iterator to the end of its upper-edge list More... | |
| EdgeListConstIter | const_upper_edge_list_end () const |
| returns a const iterator to the end of its upper-edge list More... | |
| platform::Size | get_node_index () const |
| the index for this node More... | |
| platform::Size | num_edges () const |
| the number of edges incident on this node, which may include a loop edge More... | |
| platform::Size | num_neighbors_counting_self () const |
| the number of neighbors counting "self" as a neighbor. More... | |
| platform::Size | num_neighbors_counting_self_static () const |
| the number of neighbors counting "self" as neighbor. Defaults to num_neighbors_counting_self() but can be set to other values as well. Useful in calculation of symmetrical structures. More... | |
| platform::Size | get_num_edges_to_smaller_indexed_nodes () const |
| the number of lower neighbors More... | |
| platform::Size | get_num_edges_to_larger_indexed_nodes () const |
| the number of upper neighbors – which "self" neighborness is counted if a loop edge is present More... | |
| bool | loop_incident () const |
| NOTE TO SELF: remove loop support. More... | |
Private Member Functions | |
| void | update_current_one_body_energy () |
| void | update_alternate_one_body_energy () |
| void | initialize () |
Additional Inherited Members | |
| Public Types inherited from core::graph::Node | |
| typedef EdgeListIterator | EdgeListIter |
| typedef EdgeListConstIterator | EdgeListConstIter |
| Protected Member Functions inherited from core::graph::Node | |
| Graph * | get_owner () const |
| derived class access to the owner More... | |
Definition at line 38 of file SimpleInteractionGraph.hh.
| core::pack::interaction_graph::SimpleNode::SimpleNode | ( | graph::Graph * | owner, |
| Size | resnum | ||
| ) |
Definition at line 49 of file SimpleInteractionGraph.cc.
References initialize().
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virtual |
Definition at line 59 of file SimpleInteractionGraph.cc.
| Vector const & core::pack::interaction_graph::SimpleNode::alt_sc_centroid | ( | ) | const |
Definition at line 246 of file SimpleInteractionGraph.cc.
References alt_sc_centroid_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Real core::pack::interaction_graph::SimpleNode::alt_sc_radius | ( | ) | const |
Definition at line 252 of file SimpleInteractionGraph.cc.
References alt_sc_radius_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Vector const & core::pack::interaction_graph::SimpleNode::bb_centroid | ( | ) | const |
Definition at line 222 of file SimpleInteractionGraph.cc.
References bb_centroid_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Real core::pack::interaction_graph::SimpleNode::bb_radius | ( | ) | const |
Definition at line 228 of file SimpleInteractionGraph.cc.
References bb_radius_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| void core::pack::interaction_graph::SimpleNode::commit_change | ( | ) |
Copy the alternate_residue_ pointer to the current_residue_ pointer; copy the alternate energies to the current energies for this node and its incident edges.
Definition at line 94 of file SimpleInteractionGraph.cc.
References alternate_residue_, commit_change_no_res_pointer_update(), and current_residue_.
| void core::pack::interaction_graph::SimpleNode::commit_change_no_res_pointer_update | ( | ) |
Copy the alternate energies to the current energies for this node and its incident edges.
Definition at line 101 of file SimpleInteractionGraph.cc.
References alternate_one_body_energy_, core::pack::interaction_graph::SimpleEdge::commit_change(), current_one_body_energy_, core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), and moved_.
Referenced by commit_change().
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inlinevirtual |
invoked during graph assignment operators to copy any node data from one graph to another graph. The source node must be the same type as this node.
copy-from for use in Graph::operator= and copy ctors; derived classes must define their own version of this function
Reimplemented from core::graph::Node.
Definition at line 46 of file SimpleInteractionGraph.hh.
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inlinevirtual |
memory accounting scheme
recursively descend through heirarchy accounting for heap memory usage. Each derived class in the heirarchy should recursively add the amount of dynamic memory its parent allocates by calling parent::count_dynamic_memory
Reimplemented from core::graph::Node.
Definition at line 51 of file SimpleInteractionGraph.hh.
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inlinevirtual |
memory accounting scheme
called on most-derived class. The most-derived class should NOT recursively call this method on its parent class. The sizeof function will handle the whole Node (or DerivedNode).
Reimplemented from core::graph::Node.
Definition at line 50 of file SimpleInteractionGraph.hh.
| Vector const & core::pack::interaction_graph::SimpleNode::curr_sc_centroid | ( | ) | const |
Definition at line 234 of file SimpleInteractionGraph.cc.
References curr_sc_centroid_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Real core::pack::interaction_graph::SimpleNode::curr_sc_radius | ( | ) | const |
Definition at line 240 of file SimpleInteractionGraph.cc.
References curr_sc_radius_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| Real core::pack::interaction_graph::SimpleNode::current_one_body_energy | ( | ) | const |
Definition at line 88 of file SimpleInteractionGraph.cc.
References current_one_body_energy_.
Referenced by core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().
| conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_alternate | ( | ) | const |
return the pointer to the alternate state (might be 0)
Definition at line 216 of file SimpleInteractionGraph.cc.
References alternate_residue_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
| conformation::ResidueCOP core::pack::interaction_graph::SimpleNode::get_current | ( | ) | const |
return the pointer to the current state (might be 0)
Definition at line 210 of file SimpleInteractionGraph.cc.
References current_residue_.
Referenced by core::pack::interaction_graph::SimpleEdge::compute_energy().
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private |
Definition at line 62 of file SimpleInteractionGraph.cc.
Referenced by SimpleNode().
| bool core::pack::interaction_graph::SimpleNode::moved | ( | ) | const |
Is this node considering a state substitution?
Definition at line 119 of file SimpleInteractionGraph.cc.
References moved_.
Referenced by core::pack::interaction_graph::SimpleEdge::update_proposed_energy().
| Real core::pack::interaction_graph::SimpleNode::one_body_energy | ( | ) | const |
Definition at line 72 of file SimpleInteractionGraph.cc.
References alternate_one_body_energy_, current_one_body_energy_, and moved_.
Referenced by core::pack::interaction_graph::SimpleInteractionGraph::total_energy().
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inlinevirtual |
send summaray data about this node to the screen
virtual function to print node to standard out
Reimplemented from core::graph::Node.
Definition at line 48 of file SimpleInteractionGraph.hh.
| Real core::pack::interaction_graph::SimpleNode::proposed_one_body_energy | ( | ) | const |
Definition at line 82 of file SimpleInteractionGraph.cc.
References alternate_one_body_energy_.
Referenced by core::pack::compare_simple_inteaction_graph_alt_state_and_energy_graph(), and core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().
| void core::pack::interaction_graph::SimpleNode::reject_change | ( | ) |
Reset state on this node so that its incident edges will no longer think it is considering an alternate conformation.
Definition at line 113 of file SimpleInteractionGraph.cc.
References moved_.
| void core::pack::interaction_graph::SimpleNode::set_alternate | ( | conformation::ResidueCOP | res) |
Set the alternate residue COP and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "proposed" energies.
Definition at line 162 of file SimpleInteractionGraph.cc.
References alt_sc_centroid_, alt_sc_radius_, alternate_residue_, core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), moved_, core::pack::interaction_graph::TR(), update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleEdge::update_proposed_energy().
Referenced by core::pack::interaction_graph::SimpleInteractionGraph::consider_substitution().
| void core::pack::interaction_graph::SimpleNode::set_alternate_no_E_update | ( | conformation::ResidueCOP | res) |
Passive mode behavior: set the current residue pointer without updating the alternate one body or proposed two body energies.
Definition at line 191 of file SimpleInteractionGraph.cc.
References alternate_residue_, and moved_.
| void core::pack::interaction_graph::SimpleNode::set_current | ( | conformation::ResidueCOP | res) |
Set the current residue COP, and follow by computing the energy for this residue with its neighbors and storing those computed energies on this node's edges as their "current" energies.
Definition at line 124 of file SimpleInteractionGraph.cc.
References bb_centroid_, bb_radius_, core::scoring::compute_bb_centroid(), core::scoring::compute_bb_radius(), core::scoring::compute_sc_centroid(), core::scoring::compute_sc_radius(), curr_sc_centroid_, curr_sc_radius_, current_residue_, core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), moved_, core::pack::interaction_graph::SimpleEdge::update_current_energy(), and update_current_one_body_energy().
Referenced by core::pack::interaction_graph::SimpleInteractionGraph::initialize(), and core::pack::interaction_graph::SimpleInteractionGraph::set_pose_no_initialize().
| void core::pack::interaction_graph::SimpleNode::set_current_no_E_update | ( | conformation::ResidueCOP | res) |
Passive mode behavior: set the current residue pointer without updating the current one body or two body energies.
Definition at line 186 of file SimpleInteractionGraph.cc.
References current_residue_.
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private |
Definition at line 271 of file SimpleInteractionGraph.cc.
References alternate_one_body_energy_, alternate_residue_, core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_cd_intrares_energy(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::eval_ci_intrares_energy(), core::graph::Node::get_owner(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), core::pack::interaction_graph::SimpleInteractionGraph::scorefunction(), and core::scoring::ScoreFunction::weights().
Referenced by set_alternate(), and update_energies_after_passive_change().
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private |
Definition at line 258 of file SimpleInteractionGraph.cc.
References current_one_body_energy_, current_residue_, core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_1b(), core::scoring::ScoreFunction::eval_cd_intrares_energy(), core::scoring::ScoreFunction::eval_ci_1b(), core::scoring::ScoreFunction::eval_ci_intrares_energy(), core::graph::Node::get_owner(), core::pack::interaction_graph::SimpleInteractionGraph::pose(), core::pack::interaction_graph::SimpleInteractionGraph::scorefunction(), and core::scoring::ScoreFunction::weights().
Referenced by set_current().
| void core::pack::interaction_graph::SimpleNode::update_energies_after_passive_change | ( | ) |
Definition at line 197 of file SimpleInteractionGraph.cc.
References core::graph::Node::edge_list_begin(), core::graph::Node::edge_list_end(), update_alternate_one_body_energy(), and core::pack::interaction_graph::SimpleEdge::update_proposed_energy().
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Definition at line 159 of file SimpleInteractionGraph.hh.
Referenced by alt_sc_centroid(), and set_alternate().
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Definition at line 160 of file SimpleInteractionGraph.hh.
Referenced by alt_sc_radius(), and set_alternate().
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Definition at line 148 of file SimpleInteractionGraph.hh.
Referenced by commit_change_no_res_pointer_update(), one_body_energy(), proposed_one_body_energy(), and update_alternate_one_body_energy().
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Definition at line 151 of file SimpleInteractionGraph.hh.
Referenced by commit_change(), get_alternate(), set_alternate(), set_alternate_no_E_update(), and update_alternate_one_body_energy().
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Definition at line 153 of file SimpleInteractionGraph.hh.
Referenced by bb_centroid(), and set_current().
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Definition at line 154 of file SimpleInteractionGraph.hh.
Referenced by bb_radius(), and set_current().
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Definition at line 156 of file SimpleInteractionGraph.hh.
Referenced by curr_sc_centroid(), and set_current().
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Definition at line 157 of file SimpleInteractionGraph.hh.
Referenced by curr_sc_radius(), and set_current().
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Definition at line 147 of file SimpleInteractionGraph.hh.
Referenced by commit_change_no_res_pointer_update(), current_one_body_energy(), one_body_energy(), and update_current_one_body_energy().
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Definition at line 150 of file SimpleInteractionGraph.hh.
Referenced by commit_change(), get_current(), set_current(), set_current_no_E_update(), and update_current_one_body_energy().
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Definition at line 145 of file SimpleInteractionGraph.hh.
Referenced by commit_change_no_res_pointer_update(), moved(), one_body_energy(), reject_change(), set_alternate(), set_alternate_no_E_update(), and set_current().
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Definition at line 146 of file SimpleInteractionGraph.hh.
1.8.4