Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Member Functions | List of all members
protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph Class Reference

#include <MinimalistFlexbbInteractionGraph.hh>

Public Types

typedef OTFFlexbbInteractionGraph parent
 
- Public Types inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
typedef FlexbbInteractionGraph parent
 
typedef core::Real Real
 
typedef core::pose::PoseOP PoseOP
 
typedef core::pose::PoseCOP PoseCOP
 
typedef core::pose::Pose Pose
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::scoring::ScoreFunction 
ScoreFunction
 
- Public Types inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
enum  Subsitution { SC_ONLY, BOTH_SC_AND_BB }
 
typedef
core::pack::interaction_graph::InteractionGraphBase 
parent
 
typedef core::PackerEnergy PackerEnergy
 
typedef
core::pack::interaction_graph::EdgeBase 
EdgeBase
 

Public Member Functions

 MinimalistFlexbbInteractionGraph (int num_nodes)
 GRAPH. More...
 
virtual ~MinimalistFlexbbInteractionGraph ()
 
virtual void initialize (core::pack::rotamer_set::RotamerSetsBase const &rot_sets)
 Virtual functions from InteractionGraphBase. More...
 
virtual PackerEnergy get_one_body_energy_for_node_state (int node, int state)
 
virtual void blanket_assign_state_0 ()
 
virtual PackerEnergy set_state_for_node (int node_ind, int new_state)
 
virtual PackerEnergy set_network_state (ObjexxFCL::FArray1_int &node_states)
 
virtual void consider_substitution (int node_ind, int new_state, PackerEnergy &delta_energy, PackerEnergy &prev_energy_for_node)
 
virtual PackerEnergy commit_considered_substitution ()
 
virtual PackerEnergy get_energy_current_state_assignment ()
 
virtual int get_edge_memory_usage () const
 
virtual void print_current_state_assignment () const
 
virtual void set_errorfull_deltaE_threshold (PackerEnergy deltaE)
 
virtual PackerEnergy get_energy_sum_for_vertex_group (int group_id)
 
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)
 Virtual functions from FlexbbInteractionGraph. More...
 
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)
 
- Public Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
 OTFFlexbbInteractionGraph (int num_nodes)
 GRAPH. More...
 
virtual ~OTFFlexbbInteractionGraph ()
 
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)
 
virtual void set_pose (Pose const &pose)
 Pose must be set before any edges are added to the graph. More...
 
virtual void set_scorefxn (ScoreFunction const &sfxn)
 Score function must be set before any edges are added to the graph. More...
 
PoseCOP get_pose () const
 Edges request the pose and the score function at the time of their creation. More...
 
ScoreFunctionCOP get_scorefxn () const
 
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...
 
void debug_note_considered_substitution (core::conformation::Residue const &alt_rotamer, int index)
 
void debug_note_projected_deltaE_of_considered_substitution (PackerEnergy deltaE, PackerEnergy node_alt_total, bool require_match=true)
 
void debug_note_accepted_substitution ()
 
void debug_note_rejected_substitution ()
 
- Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
virtual ~FlexbbInteractionGraph ()
 GRAPH. More...
 
 FlexbbInteractionGraph (int num_nodes)
 
int get_num_aa_types () const
 
utility::vector1< Size > const & flexseg_members (int flexseg) const
 
int get_flexseg_for_bb (int bb) const
 
int get_flexseg_bb_offset (int flexseg_id) const
 
bool nodes_from_same_flexseg (int node1, int node2) const
 
int get_num_states_per_backbone_for_node (int node, int bb) const
 
int get_bb_for_state (int node, int state) const
 
void get_accessible_states (Subsitution move_mode, utility::vector1< Size > &rotlist) const
 
void get_backbone_list (utility::vector1< Size > &bblist) const
 
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...
 
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...
 
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...
 

Protected Member Functions

void complete_deltaE_prediction_for_bbmove (core::PackerEnergy &delta_energy, core::PackerEnergy &prev_energy_for_flexseg, bool &valid_motion, int &num_nodes_changing_state)
 
MinimalistFlexbbNode const * get_minimalistflexbb_node (int index) const
 Downcasts. More...
 
MinimalistFlexbbNodeget_minimalistflexbb_node (int index)
 
MinimalistFlexbbEdge const * find_minimalist_flexbb_edge (int node1, int node2) const
 
MinimalistFlexbbEdgefind_minimalist_flexbb_edge (int node1, int node2)
 
MinimalistFlexbbEdge const * cast_minimalist_flexbb_edge (EdgeBase const *edge) const
 
MinimalistFlexbbEdgecast_minimalist_flexbb_edge (EdgeBase *edge)
 
virtual unsigned int count_static_memory () const
 Virtual functions from InteractionGraphBase. More...
 
virtual unsigned int count_dynamic_memory () const
 
virtual
core::pack::interaction_graph::NodeBase
create_new_node (int node_index, int num_states)
 
virtual
core::pack::interaction_graph::EdgeBase
create_new_edge (int index1, int index2)
 
void resolve_uncommitted_substitution ()
 
- Protected Member Functions inherited from protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph
OTFFlexbbNode const * get_otfflexbb_node (int index) const
 Downcasts. More...
 
OTFFlexbbNodeget_otfflexbb_node (int index)
 
OTFFlexbbEdge const * find_otfflexbb_edge (int node1, int node2) const
 
OTFFlexbbEdgefind_otfflexbb_edge (int node1, int node2)
 
OTFFlexbbEdge const * cast_otfflexbb_edge (EdgeBase const *edge) const
 
OTFFlexbbEdgecast_otfflexbb_edge (EdgeBase *edge)
 
- Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbInteractionGraph
FlexbbNode const * get_flexbb_node (int index) const
 Downcasts. More...
 
FlexbbNodeget_flexbb_node (int index)
 
FlexbbEdge const * find_flexbb_edge (int node1, int node2) const
 
FlexbbEdgefind_flexbb_edge (int node1, int node2)
 
FlexbbEdge const * cast_flexbb_edge (EdgeBase const *edge) const
 
FlexbbEdgecast_flexbb_edge (EdgeBase *edge)
 
void set_enforce_bb_contiguity (bool)
 
void note_bbjump_substitution ()
 
void note_fixedbb_substitution ()
 
bool last_considered_substitution_kept_backbone_fixed () const
 
bool last_considered_substitution_moved_the_backbone () const
 
bool last_considered_backbone_sub_unresolved () const
 
bool last_considered_substitution_unresolved () const
 
void note_last_considered_substitution_resolved ()
 
void reset_node_in_moving_flexseg_count ()
 
int get_num_nodes_changing_state () const
 
PackerEnergy total_energy_current_state_assignment () const
 
PackerEnergy total_energy_alternate_state_assignment () const
 
int node_considering_alt_state () const
 Only allowed to ask for the node considering an alternate state during a fixed-backbone substitution. More...
 
int flexseg_considering_alt_bb () const
 Only allowed to ask for the flexible segment considering an alternate backbone conformation during a backbone-moving substitution. More...
 
bool last_considered_backbone_sub_valid () const
 
int flexseg_for_moltenres (int moltenres) const
 
void set_total_energy_current_state_assignment (PackerEnergy setting)
 
void set_total_energy_alternate_state_assignment (PackerEnergy setting)
 
void set_node_considering_alt_state (int setting)
 Track the last node at which a fixed-backbone substitution took place. More...
 
void set_flexseg_considering_alt_bb (int setting)
 Track the last flexible segment at which a moving-backbone substitution took place. More...
 
void set_last_considered_backbone_sub_valid (bool setting)
 
virtual void update_internal_energy_totals ()
 

Private Member Functions

virtual PackerEnergy commit_considered_backbone_move (ObjexxFCL::FArray1_int &rotamer_on_node)
 
PackerEnergy project_deltaE_for_substitution (int alternate_state, PackerEnergy &prev_energy_for_node)
 Virtual functions from OTFFlexbbInteractionGraph. More...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::MinimalistFlexbbInteractionGraph ( int  num_nodes)

GRAPH.

Referenced by count_static_memory().

protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::~MinimalistFlexbbInteractionGraph ( )
virtual

Member Function Documentation

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::blanket_assign_state_0 ( )
virtual
MinimalistFlexbbEdge const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::cast_minimalist_flexbb_edge ( EdgeBase const *  edge) const
inlineprotected
MinimalistFlexbbEdge * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::cast_minimalist_flexbb_edge ( EdgeBase edge)
inlineprotected
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_backbone_move ( ObjexxFCL::FArray1_int &  rotamer_on_node)
privatevirtual
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::commit_considered_substitution ( )
virtual
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove ( core::PackerEnergy delta_energy,
core::PackerEnergy prev_energy_for_flexseg,
bool valid_motion,
int num_nodes_changing_state 
)
protected
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move ( int  bb_id,
core::PackerEnergy delta_energy,
core::PackerEnergy prev_flexseg_energy,
bool valid_motion,
int num_nodes_changing_state 
)
virtual
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::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 
)
virtual
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_substitution ( int  node_ind,
int  new_state,
PackerEnergy delta_energy,
PackerEnergy prev_energy_for_node 
)
virtual
unsigned int protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::count_dynamic_memory ( ) const
protectedvirtual
unsigned int protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::count_static_memory ( ) const
protectedvirtual

Virtual functions from InteractionGraphBase.

References MinimalistFlexbbInteractionGraph().

core::pack::interaction_graph::EdgeBase * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::create_new_edge ( int  index1,
int  index2 
)
protectedvirtual
core::pack::interaction_graph::NodeBase * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::create_new_node ( int  node_index,
int  num_states 
)
protectedvirtual
MinimalistFlexbbEdge const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::find_minimalist_flexbb_edge ( int  node1,
int  node2 
) const
inlineprotected
MinimalistFlexbbEdge * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::find_minimalist_flexbb_edge ( int  node1,
int  node2 
)
inlineprotected
int protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_edge_memory_usage ( ) const
virtual
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_current_state_assignment ( )
virtual
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_energy_sum_for_vertex_group ( int  group_id)
virtual
MinimalistFlexbbNode const * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_minimalistflexbb_node ( int  index) const
inlineprotected
MinimalistFlexbbNode * protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_minimalistflexbb_node ( int  index)
inlineprotected
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::get_one_body_energy_for_node_state ( int  node,
int  state 
)
virtual
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::initialize ( core::pack::rotamer_set::RotamerSetsBase const &  rot_sets)
virtual
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::print_current_state_assignment ( ) const
virtual
PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::project_deltaE_for_substitution ( int  alternate_state,
PackerEnergy prev_energy_for_node 
)
private

Virtual functions from OTFFlexbbInteractionGraph.

returns the change in energy that would be induced by switching this node from its current state into another state on the same backbone

Referenced by consider_substitution().

void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution ( )
protected
void protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_errorfull_deltaE_threshold ( PackerEnergy  deltaE)
virtual

noop. This IG does not allow for inaccuracies in its energy function.

MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_network_state ( ObjexxFCL::FArray1_int &  node_states)
virtual
MinimalistFlexbbInteractionGraph::PackerEnergy protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::set_state_for_node ( int  node_ind,
int  new_state 
)
virtual

The documentation for this class was generated from the following files: