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Rosetta
2021.16
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Rosetta
2021.16
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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... | |
| ~SurfaceBackgroundNode () override | |
| 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... | |
| void | prepare_for_simulated_annealing () override |
| 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 override |
| used only for debugging More... | |
| unsigned int | count_static_memory () const override |
| unsigned int | count_dynamic_memory () const override |
| Returns an int representing the amount of memory in bytes used by this node. More... | |
| 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.
| typedef BackgroundNode< V, E, G > core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::parent |
| 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
| owner | - [in] - the owning interaction graph node_id - [in] - the index for this node amongst its owners set |
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
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| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::acknowledge_substitution_surface | ( | ) |
bookkeeping to reflect a SurfaceNode's state substitution.
| 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.
This method is oblivious to whether a given residue should contribute to the patch area. This function just does the lookup for the hASA (using the SurfacePotential class). Calls to this function should be surrounded by is-this- a-surface-exposed-hydrophobic checks. Since background nodes don't actually change type, whatever the wild type residue's aa type is what we use for the score.
References protocols::cluster::calibur::aa.
| 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).
| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::calculate_amount_total_hydrophobic_ASA | ( | ) |
See comments in SurfaceNode for more info.
References protocols::cluster::calibur::aa, and core::pack::interaction_graph::TR_BGNODE().
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Returns an int representing the amount of memory in bytes used by this node.
| total_memory | - [out] - the amount of memory used by this node |
Reimplemented from core::pack::interaction_graph::BackgroundNode< V, E, G >.
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overridevirtual |
| 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
If this node is in the list of neighbors for the passed in SurfaceNode, return true. Leave the responsibility of figuring out neighborship to the first class node.
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.
| 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.
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| Real core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::get_surface_score | ( | ) | const |
returns the surface score under the current state assignment
| 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().
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::init_hASA_variables | ( | ) |
| 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.
See comments in SurfaceNode::initialize_num_neighbors_counting_self for details.
References 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.
| 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
| 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.
| int core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::num_neighbors_counting_self | ( | ) | const |
Returns the value stored in the member variable.
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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.
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
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used only for debugging
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
| 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.
Is it possible for a background node to have a state of zero (or unassigned state). Not really - there's no state for background nodes since they're not changing. What happens if the first class node undergoing sub is in the unassigned state? We have to figure out what the wild-type residue at the changing position is. Should I pass in the node index to this method? I have to pass in a pointer to the node because that's how to get the rotamer information stored there. But get_node_index() is a protected method so I can't call that using the pointer.
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.
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.
References core::pack::interaction_graph::TR_BGNODE().
| void core::pack::interaction_graph::SurfaceBackgroundNode< V, E, G >::surface_exposed | ( | bool | value | ) |
using this for debugging
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1.8.7