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

#include <OTFFlexbbInteractionGraph.hh>

Public Types

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

 OTFFlexbbInteractionGraph (int num_nodes)
 GRAPH. More...
 
virtual ~OTFFlexbbInteractionGraph ()
 
virtual void initialize (core::pack::rotamer_set::RotamerSetsBase const &)
 
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 unsigned int count_dynamic_memory () const
 
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
 
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. 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

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 Attributes

PoseOP pose_
 
ScoreFunctionOP sfxn_
 
OtherContextScoreFunctionOP oc_sfxn_
 
PoseOP current_pose_
 For debugging purposes. More...
 
Real current_pose_energy_
 
PoseOP alternate_pose_
 
Real alternate_pose_energy_
 
utility::vector1< Sizechanging_seqpos_
 
utility::vector1
< core::conformation::ResidueOP
alt_rots_
 
utility::vector1< intalt_rot_inds_
 
utility::vector1< Sizeresid_2_moltenres_
 
utility::vector1< Sizemoltenres_2_resid_
 

Member Typedef Documentation

Constructor & Destructor Documentation

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

GRAPH.

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

Member Function Documentation

OTFFlexbbEdge const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::cast_otfflexbb_edge ( EdgeBase const *  edge) const
inlineprotected
OTFFlexbbEdge* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::cast_otfflexbb_edge ( EdgeBase edge)
inlineprotected
unsigned int protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::count_dynamic_memory ( ) const
virtual
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_accepted_substitution ( )
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_considered_substitution ( core::conformation::Residue const &  alt_rotamer,
int  index 
)
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution ( PackerEnergy  deltaE,
PackerEnergy  node_alt_total,
bool  require_match = true 
)
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_rejected_substitution ( )
OTFFlexbbEdge const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::find_otfflexbb_edge ( int  node1,
int  node2 
) const
inlineprotected
OTFFlexbbEdge* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::find_otfflexbb_edge ( int  node1,
int  node2 
)
inlineprotected
OTFFlexbbNode const* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_otfflexbb_node ( int  index) const
inlineprotected
OTFFlexbbNode* protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_otfflexbb_node ( int  index)
inlineprotected
OTFFlexbbInteractionGraph::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_pose ( ) const

Edges request the pose and the score function at the time of their creation.

References pose_.

OTFFlexbbInteractionGraph::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::get_scorefxn ( ) const

References sfxn_.

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::initialize ( core::pack::rotamer_set::RotamerSetsBase const &  rot_sets)
virtual
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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.

References find_otfflexbb_edge(), and protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_one_body_energies_for_otf_ig().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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 
)
void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_pose ( Pose const &  pose)
virtual

Pose must be set before any edges are added to the graph.

References alternate_pose_, current_pose_, moltenres_2_resid_, pose_, resid_2_moltenres_, and core::pose::Pose::total_residue().

void protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::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 protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::set_scorefxn ( ScoreFunction const &  sfxn)
virtual

Score function must be set before any edges are added to the graph.

References core::scoring::ScoreFunction::clone(), n_score_types, oc_sfxn_, pose_, and sfxn_.

Member Data Documentation

utility::vector1< int > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alt_rot_inds_
private
utility::vector1< core::conformation::ResidueOP > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alt_rots_
private
PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alternate_pose_
private
Real protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::alternate_pose_energy_
private
utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::changing_seqpos_
private
PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::current_pose_
private

For debugging purposes.

Referenced by debug_note_projected_deltaE_of_considered_substitution(), and set_pose().

Real protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::current_pose_energy_
private
utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::moltenres_2_resid_
private

Referenced by initialize(), and set_pose().

OtherContextScoreFunctionOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::oc_sfxn_
private
PoseOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::pose_
private

Referenced by get_pose(), set_pose(), and set_scorefxn().

utility::vector1< Size > protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::resid_2_moltenres_
private
ScoreFunctionOP protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::sfxn_
private

Referenced by get_scorefxn(), and set_scorefxn().


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