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Rosetta 3.5
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Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it. More...
#include <SurfaceInteractionGraph.hh>


Public Types | |
| typedef BackgroundNode< V, E, G > | parent |
Public Types inherited from core::pack::interaction_graph::BackgroundNode< V, E, G > | |
| typedef std::list < BackgroundToFirstClassEdge < V, E, G > * >::iterator | BackgroundEdgeListIter |
| typedef std::list < BackgroundToFirstClassEdge < V, E, G > * > | BackgroundEdgeList |
| typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * > | BackgroundEdgeVector |
| typedef std::vector < BackgroundToFirstClassEdge < V, E, G > * >::iterator | BackgroundEdgeVectorIter |
| typedef std::vector < FirstClassNode< V, E, G > * > | FirstClassNodeVector |
Public Member Functions | |
| SurfaceBackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index) | |
| main constructor. No default constructor, copy constructor or assignment operator More... | |
| virtual | ~SurfaceBackgroundNode () |
| destructor - no dynamicly allocated memory to manage -> empty More... | |
| bool | detect_neighborship (SurfaceNode< V, E, G > *node) const |
| returns true if this background residue neighbors with any rotamer of a SurfaceNode More... | |
| Real | project_surface_deltaE_for_substitution (SurfaceNode< V, E, G > *fc_node_changing, int changing_nodes_curr_state, int changing_nodes_alt_state) |
| returns the change in surface induced by a SurfaceNode undergoing a state substitution. More... | |
| void | acknowledge_substitution_surface () |
| bookkeeping to reflect a SurfaceNode's state substitution. More... | |
| Real | get_surface_score () const |
| returns the surface score under the current state assignment More... | |
| virtual void | prepare_for_simulated_annealing () |
| Sets the hASA of surface exposed hydrophobic neighbors using the pose's neighbor graph. There's no need for BGNodes to keep track of which Nodes are really neighbors (energy graph vs neighbor graph) because they never broadcast changes to their neighboring Nodes. More... | |
| void | print () const |
| used only for debugging More... | |
| virtual unsigned int | count_static_memory () const |
| virtual unsigned int | count_dynamic_memory () const |
| conformation::Residue const & | wt_residue_for_node () const |
| bool | is_surface_exposed () const |
| Returns the value of surface_exposed_ which gets set during the SIG initialize() method. More... | |
| void | surface_exposed (bool value) |
| using this for debugging More... | |
| bool | is_below_buried_residue_no_hsasa_cutoff () const |
| Returns the value of is_below_buried_residue_no_hsasa_cutoff_ which gets set during the SIG initialize() method. More... | |
| void | is_below_buried_residue_no_hsasa_cutoff (bool value) |
| setter for the is_below_buried_residue_no_hsasa_cutoff_ bool More... | |
| void | reset_alt_state_total_hASA () |
| Sets the alt state total hASA to the current state total hASA. See comments in SIG and commit_considered_substitution_surface for more information about why this method exists. More... | |
| void | initialize_num_neighbors_counting_self () const |
| Returns the number of neighbors within the interaction threshold, counting self. A member variable stores the value so that this method only has to run once and lookups can be performed thereafter. More... | |
| int | num_neighbors_counting_self () const |
| Returns the value stored in the member variable. More... | |
| void | init_hASA_variables () |
| Real | calculate_amount_total_hydrophobic_ASA () |
| Real | average_residue_hASA () const |
| Returns the amount of hydrophobic ASA this residue adds to a patch. More... | |
| Real | average_residue_hASA (chemical::AA residue_type, Size num_nbs) const |
| Same function as above, but this one allows you to specify what type and num_nbs. This function is meant to be used only when initializing all of the Nodes/BGNodes because at that point we have to use the wild-type residue type, not the new rotamers residue type (which is what the above function will do). More... | |
| Real | hASA_energy (Real patch_area) const |
| Calls a SurfacePotential class method to get the energy for a given patch area. Not sure if I should take num neighbors as a parameter to the function, or just use the class method num_neighbors_counting_self(). More... | |
| Real | get_current_hASA () |
| Returns current hASA. Only used by the unit tests. Should not exist in release mode. More... | |
| Real | get_alt_hASA () |
| Returns current hASA. Only used by the unit tests. Should not exist in release mode. More... | |
Public Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G > | |
| virtual | ~BackgroundNode () |
| BackgroundNode destructor. More... | |
| BackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index) | |
| BackgroundNode constructor - no default or copy constructors; no operator =. More... | |
| BackgroundEdgeListIter | add_edge (BackgroundToFirstClassEdge< V, E, G > *edge_ptr) |
| Adds a BackgroundToFirstClassEdge to the edge list for this node. Returns an iterator to the new list element. More... | |
| void | drop_edge (BackgroundEdgeListIter edge) |
| removes an edge from the nodes edge list in constant time More... | |
| BackgroundToFirstClassEdge< V, E, G > * | find_edge (int fc_node_index) |
| Linear time edge lookup function. More... | |
Protected Member Functions | |
| SurfaceInteractionGraph< V, E, G > * | get_surface_owner () const |
| SurfaceBackgroundEdge< V, E, G > * | get_surface_bg_edge (int index) |
Protected Member Functions inherited from core::pack::interaction_graph::BackgroundNode< V, E, G > | |
| void | update_edge_vector () |
| Syncs the edge vector with the edge list. More... | |
| int | get_node_index () const |
| int | get_num_incident_edges () const |
| BackgroundToFirstClassEdge< V, E, G > * | get_incident_edge (int index) const |
| int | get_index_of_adjacent_first_class_node (int index) const |
| FirstClassNode< V, E, G > * | get_adjacent_first_class_node (int index) const |
| bool | get_edge_vector_up_to_date () const |
| AdditionalBackgroundNodesInteractionGraph < V, E, G > * | get_owner () const |
Private Member Functions | |
| SurfaceBackgroundNode () | |
| SurfaceBackgroundNode (SurfaceBackgroundNode< V, E, G > const &) | |
| SurfaceBackgroundNode< V, E, G > & | operator= (SurfaceBackgroundNode< V, E, G > const &) |
Static Private Attributes | |
| static Real | surface_energy_weight_ = 1.0 |
| static const int | MAX_SURFACE_ENERGY = 100 |
| static const int | INTERACTION_RADIUS = 10 |
| static const int | SURFACE_EXPOSED_CUTOFF = 20 |
| static const int | BURIED_RESIDUE_NO_HSASA_CUTOFF = 24 |
| static const int | MAX_PATCH_SURFACE_AREA = 1100 |
Defines a BackgroundResidue node which will contribute to changes in surface energy due to state changes on neighboring nodes, and not because of state changes to it.
Definition at line 62 of file SurfaceInteractionGraph.hh.
| typedef BackgroundNode< V, E, G > core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::parent |
Definition at line 239 of file SurfaceInteractionGraph.hh.
| core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::SurfaceBackgroundNode | ( | AdditionalBackgroundNodesInteractionGraph< V, E, G > * | owner, |
| int | node_index | ||
| ) |
main constructor. No default constructor, copy constructor or assignment operator
SurfaceBackgroundNode::SurfaceBackgroundNode
| owner | - [in] - the owning interaction graph node_id - [in] - the index for this node amongst its owners set |
Definition at line 2171 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_owner(), core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::surface_energy_weight_, and core::pack::interaction_graph::TR_BGNODE().
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destructor - no dynamicly allocated memory to manage -> empty
SurfaceBackgroundNode::~SurfaceBackgroundNode
Definition at line 2194 of file SurfaceInteractionGraph.hh.
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| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::acknowledge_substitution_surface | ( | ) |
bookkeeping to reflect a SurfaceNode's state substitution.
SurfaceBackgroundNode::acknowledge_substitution
Definition at line 2393 of file SurfaceInteractionGraph.hh.
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::average_residue_hASA | ( | ) | const |
Returns the amount of hydrophobic ASA this residue adds to a patch.
SurfaceBackgroundNode::average_residue_hASA
Definition at line 2670 of file SurfaceInteractionGraph.hh.
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::average_residue_hASA | ( | chemical::AA | residue_type, |
| Size | num_nbs | ||
| ) | const |
Same function as above, but this one allows you to specify what type and num_nbs. This function is meant to be used only when initializing all of the Nodes/BGNodes because at that point we have to use the wild-type residue type, not the new rotamers residue type (which is what the above function will do).
SurfaceBackgroundNode::average_residue_hASA
Definition at line 2683 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::SurfacePotential::average_residue_hASA(), and core::pack::interaction_graph::SurfacePotential::get_instance().
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::calculate_amount_total_hydrophobic_ASA | ( | ) |
SurfaceBackgroundNode::calculate_amount_total_hydrophobic_ASA
Definition at line 2604 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::TR_BGNODE().
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SurfaceBackgroundNode::count_dynamic_memory
Reimplemented from core::pack::interaction_graph::BackgroundNode< V, E, G >.
Definition at line 2446 of file SurfaceInteractionGraph.hh.
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SurfaceBackgroundNode::count_static_memory
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
Definition at line 2437 of file SurfaceInteractionGraph.hh.
| bool core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::detect_neighborship | ( | SurfaceNode< V, E, G > * | node) | const |
returns true if this background residue neighbors with any rotamer of a SurfaceNode
SurfaceBackgroundNode::detect_neighborship
Definition at line 2231 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::SurfaceNode< V, E, G >::detect_neighborship_with_node().
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_alt_hASA | ( | ) |
Returns current hASA. Only used by the unit tests. Should not exist in release mode.
SurfaceBackgroundNode::get_alt_hASA
Definition at line 4203 of file SurfaceInteractionGraph.hh.
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_current_hASA | ( | ) |
Returns current hASA. Only used by the unit tests. Should not exist in release mode.
SurfaceBackgroundNode::get_current_count
Definition at line 4148 of file SurfaceInteractionGraph.hh.
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Definition at line 292 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_incident_edge().
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Definition at line 287 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_owner().
Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::SurfaceBackgroundNode(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::wt_residue_for_node().
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_score | ( | ) | const |
returns the surface score under the current state assignment
SurfaceBackgroundNode< V, E, G >::get_surface_score
Definition at line 2405 of file SurfaceInteractionGraph.hh.
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::hASA_energy | ( | Real | patch_area) | const |
Calls a SurfacePotential class method to get the energy for a given patch area. Not sure if I should take num neighbors as a parameter to the function, or just use the class method num_neighbors_counting_self().
SurfaceBackgroundNode::hASA_energy()
Definition at line 2698 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::SurfacePotential::get_instance(), and core::pack::interaction_graph::SurfacePotential::hASA_patch_energy().
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::init_hASA_variables | ( | ) |
SurfaceBackgroundNode::init_hASA_variables
Definition at line 2590 of file SurfaceInteractionGraph.hh.
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::initialize_num_neighbors_counting_self | ( | ) | const |
Returns the number of neighbors within the interaction threshold, counting self. A member variable stores the value so that this method only has to run once and lookups can be performed thereafter.
SurfaceBackgroundNode::initialize_num_neighbors_counting_self
Definition at line 2532 of file SurfaceInteractionGraph.hh.
References core::graph::Graph::get_node(), core::graph::Node::num_neighbors_counting_self(), and core::pack::interaction_graph::TR_BGNODE().
| bool core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff | ( | ) | const |
Returns the value of is_below_buried_residue_no_hsasa_cutoff_ which gets set during the SIG initialize() method.
SurfaceBackgroundNode::is_below_buried_residue_no_hsasa_cutoff
Definition at line 2485 of file SurfaceInteractionGraph.hh.
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff | ( | bool | value) |
setter for the is_below_buried_residue_no_hsasa_cutoff_ bool
SurfaceBackgroundNode::is_below_buried_residue_no_hsasa_cutoff
Definition at line 2496 of file SurfaceInteractionGraph.hh.
| bool core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::is_surface_exposed | ( | ) | const |
Returns the value of surface_exposed_ which gets set during the SIG initialize() method.
SurfaceBackgroundNode::is_surface_exposed
Definition at line 2461 of file SurfaceInteractionGraph.hh.
| int core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::num_neighbors_counting_self | ( | ) | const |
Returns the value stored in the member variable.
SurfaceBackgroundNode::num_neighbors_counting_self
Definition at line 2576 of file SurfaceInteractionGraph.hh.
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Sets the hASA of surface exposed hydrophobic neighbors using the pose's neighbor graph. There's no need for BGNodes to keep track of which Nodes are really neighbors (energy graph vs neighbor graph) because they never broadcast changes to their neighboring Nodes.
SurfaceBackgroundNode::prepare_for_simulated_annealing
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
Definition at line 2206 of file SurfaceInteractionGraph.hh.
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used only for debugging
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
Definition at line 2426 of file SurfaceInteractionGraph.hh.
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::project_surface_deltaE_for_substitution | ( | SurfaceNode< V, E, G > * | fc_node_changing, |
| int | changing_nodes_curr_state, | ||
| int | changing_nodes_alt_state | ||
| ) |
returns the change in surface induced by a SurfaceNode undergoing a state substitution.
SurfaceBackgroundNode::project_surface_deltaE_for_substitution
Bug fix: Turns out that if you do multiple loops of pack_rotamers, then the method blanket assign state 0 gets called. Have to handle the case where the current state is some nonzero value and the alt_state is going to the zero state. If not, you get seg faults. But, if we're going into the unassigned state, does it make sense in actually calculating a "correct" surface deltaE. Doesn't seem like it. Going to just add a instant return of a bad value!
There's a potential problem with the setting of the alt state count that can creep up on multiple rounds of consider() without concomitant commit(). A separate method has been added to this class to handle these cases. It basically executes the following line each round of consider(). alt_state_num_se_hp_nbs_ = curr_state_num_se_hp_nbs_;
02/20/2009/ Updating the function to do everything with hASA rather than hp counts.
Definition at line 2263 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::SurfaceNode< V, E, G >::get_rotamer(), core::pack::interaction_graph::SurfaceNode< V, E, G >::is_below_buried_residue_no_hsasa_cutoff(), core::pack::interaction_graph::SurfaceNode< V, E, G >::num_neighbors_counting_self(), core::pack::interaction_graph::TR_BGNODE(), core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_residue_for_node(), and core::pack::interaction_graph::SurfaceNode< V, E, G >::wt_seqpos_for_node().
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::reset_alt_state_total_hASA | ( | ) |
Sets the alt state total hASA to the current state total hASA. See comments in SIG and commit_considered_substitution_surface for more information about why this method exists.
SurfaceBackgroundNode::reset_alt_state_total_hASA
Definition at line 2509 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::TR_BGNODE().
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::surface_exposed | ( | bool | value) |
using this for debugging
SurfaceBackgroundNode::surface_exposed
Definition at line 2473 of file SurfaceInteractionGraph.hh.
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Definition at line 261 of file SurfaceInteractionGraph.hh.
References core::pack::interaction_graph::BackgroundNode< V, E, G >::get_node_index(), and core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_owner().
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Definition at line 305 of file SurfaceInteractionGraph.hh.
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Definition at line 301 of file SurfaceInteractionGraph.hh.
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Definition at line 304 of file SurfaceInteractionGraph.hh.
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Definition at line 307 of file SurfaceInteractionGraph.hh.
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Definition at line 299 of file SurfaceInteractionGraph.hh.
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Definition at line 310 of file SurfaceInteractionGraph.hh.
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Definition at line 302 of file SurfaceInteractionGraph.hh.
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Definition at line 298 of file SurfaceInteractionGraph.hh.
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Definition at line 311 of file SurfaceInteractionGraph.hh.
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Definition at line 297 of file SurfaceInteractionGraph.hh.
Referenced by core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::SurfaceBackgroundNode().
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Definition at line 309 of file SurfaceInteractionGraph.hh.
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Definition at line 300 of file SurfaceInteractionGraph.hh.
1.8.4