Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
protocols::flexpack::interaction_graph::FlexbbInteractionGraph Class Reference

#include <FlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::FlexbbInteractionGraph:
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Collaboration diagram for protocols::flexpack::interaction_graph::FlexbbInteractionGraph:
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List of all members.

Public Types

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

virtual ~FlexbbInteractionGraph ()
 GRAPH.
 FlexbbInteractionGraph (int num_nodes)
virtual void initialize (core::pack::rotamer_set::RotamerSetsBase const &rot_sets)
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
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
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
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.
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.
void increment_count_nodes_in_flexseg ()
 Owner keeps a count of the number of nodes undergoing a simultaneous rotamer substitution as the backbone moves.
virtual unsigned int count_dynamic_memory () const

Protected Member Functions

FlexbbNode const * get_flexbb_node (int index) const
 Downcasts.
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.
int flexseg_considering_alt_bb () const
 Only allowed to ask for the flexible segment considering an alternate backbone conformation during a backbone-moving substitution.
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.
void set_flexseg_considering_alt_bb (int setting)
 Track the last flexible segment at which a moving-backbone substitution took place.
void set_last_considered_backbone_sub_valid (bool setting)
virtual void update_internal_energy_totals ()

Member Typedef Documentation


Member Enumeration Documentation

Enumerator:
SC_ONLY 
BOTH_SC_AND_BB 

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::FlexbbInteractionGraph::~FlexbbInteractionGraph ( ) [virtual]

GRAPH.

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

Member Function Documentation

FlexbbEdge const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::cast_flexbb_edge ( EdgeBase const *  edge) const [inline, protected]
FlexbbEdge* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::cast_flexbb_edge ( EdgeBase edge) [inline, protected]
virtual PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::commit_considered_backbone_move ( ObjexxFCL::FArray1_int &  rotamer_on_node) [pure virtual]
virtual void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::consider_backbone_move ( int  bb_id,
core::PackerEnergy delta_energy,
core::PackerEnergy prev_flexseg_energy,
bool valid_motion,
int num_nodes_changing_state 
) [pure virtual]
virtual void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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 
) [pure virtual]
unsigned int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::count_dynamic_memory ( ) const [virtual]
FlexbbEdge const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::find_flexbb_edge ( int  node1,
int  node2 
) const [inline, protected]
FlexbbEdge* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::find_flexbb_edge ( int  node1,
int  node2 
) [inline, protected]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_considering_alt_bb ( ) const [inline, protected]

Only allowed to ask for the flexible segment considering an alternate backbone conformation during a backbone-moving substitution.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::complete_deltaE_prediction_for_bbmove(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::resolve_uncommitted_substitution().

int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_for_moltenres ( int  moltenres) const [inline, protected]
utility::vector1< Size > const& protocols::flexpack::interaction_graph::FlexbbInteractionGraph::flexseg_members ( int  flexseg) const [inline]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_accessible_states ( Subsitution  move_mode,
utility::vector1< Size > &  rotlist 
) const
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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.

References protocols::flexpack::interaction_graph::FlexbbNode::get_backbone_for_current_state(), and get_flexbb_node().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_backbone_list ( utility::vector1< Size > &  bblist) const
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_bb_for_state ( int  node,
int  state 
) const
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::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.

FlexbbNode const* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexbb_node ( int  index) const [inline, protected]
FlexbbNode* protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexbb_node ( int  index) [inline, protected]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_bb_offset ( int  flexseg_id) const [inline]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_flexseg_for_bb ( int  bb) const [inline]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_aa_types ( ) const [inline]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_nodes_changing_state ( ) const [protected]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::get_num_states_per_backbone_for_node ( int  node,
int  bb 
) const
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::increment_count_nodes_in_flexseg ( )

Owner keeps a count of the number of nodes undergoing a simultaneous rotamer substitution as the backbone moves.

I don't remember what this is for... prev: increment_count_nodes_in_moving_fragment.

Referenced by protocols::flexpack::interaction_graph::FlexbbNode::inform_edges_of_alt_state_before_bbjump().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::initialize ( core::pack::rotamer_set::RotamerSetsBase const &  rot_sets) [virtual]

Implements core::pack::interaction_graph::InteractionGraphBase.

Reimplemented in protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph, and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph.

References protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegid_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_start_moltenresid(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::flexsegment_stop_moltenresid(), get_flexbb_node(), core::pack::interaction_graph::InteractionGraphBase::get_num_nodes(), protocols::flexpack::interaction_graph::FlexbbNode::get_num_states_for_bb(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::local_rotid_start_for_moltenres_in_bbconf(), core::conformation::Residue::name(), core::conformation::Residue::natoms(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbackbone_conformations(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nbbconfs_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nflexible_segments(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nmoltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::nrotamers_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::num_states_per_backbone_for_moltenres(), protocols::flexpack::rotamer_set::FlexbbRotamerSets::rotset_for_moltenres(), protocols::flexpack::interaction_graph::FlexbbNode::set_closest_states_on_other_bbs(), protocols::flexpack::interaction_graph::FlexbbNode::set_num_distinct_backbones(), core::pack::interaction_graph::InteractionGraphBase::set_num_states_for_node(), protocols::flexpack::interaction_graph::FlexbbNode::set_num_states_per_backbone(), and core::conformation::Residue::xyz().

Referenced by protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::initialize().

bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_unresolved ( ) const [inline, protected]
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_backbone_sub_valid ( ) const [inline, protected]
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_kept_backbone_fixed ( ) const [inline, protected]
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_moved_the_backbone ( ) const [inline, protected]
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::last_considered_substitution_unresolved ( ) const [inline, protected]
int protocols::flexpack::interaction_graph::FlexbbInteractionGraph::node_considering_alt_state ( ) const [inline, protected]
bool protocols::flexpack::interaction_graph::FlexbbInteractionGraph::nodes_from_same_flexseg ( int  node1,
int  node2 
) const
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_bbjump_substitution ( ) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_fixedbb_substitution ( ) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::note_last_considered_substitution_resolved ( ) [protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::reset_node_in_moving_flexseg_count ( ) [protected]

at the beginning of backbone-changing substitutions, derived classes must invoke this function to get a proper count of the number of nodes undergoing a simultaneous rotamer substitution

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_backbone_move(), and protocols::flexpack::interaction_graph::MinimalistFlexbbInteractionGraph::consider_bbmove_w_state_substitution().

void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_enforce_bb_contiguity ( bool  setting) [protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_flexseg_considering_alt_bb ( int  setting) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_last_considered_backbone_sub_valid ( bool  setting) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_node_considering_alt_state ( int  setting) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_alternate_state_assignment ( PackerEnergy  setting) [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::set_total_energy_current_state_assignment ( PackerEnergy  setting) [protected]
PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_alternate_state_assignment ( ) const [inline, protected]
PackerEnergy protocols::flexpack::interaction_graph::FlexbbInteractionGraph::total_energy_current_state_assignment ( ) const [inline, protected]
void protocols::flexpack::interaction_graph::FlexbbInteractionGraph::update_internal_energy_totals ( ) [protected, virtual]

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