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protocols::flexpack::interaction_graph::OTFFlexbbEdge Class Reference

#include <OTFFlexbbInteractionGraph.hh>

Inheritance diagram for protocols::flexpack::interaction_graph::OTFFlexbbEdge:
Inheritance graph
[legend]

Public Types

typedef FlexbbEdge parent
 
typedef core::conformation::Residue Residue
 
typedef ObjexxFCL::FArray2D
< PackerEnergy
FArray2D_PackerEnergy
 
- Public Types inherited from protocols::flexpack::interaction_graph::FlexbbEdge
typedef
core::pack::interaction_graph::EdgeBase 
parent
 
typedef core::PackerEnergy PackerEnergy
 
typedef core::Real Real
 
typedef core::Size Size
 

Public Member Functions

 OTFFlexbbEdge (OTFFlexbbInteractionGraph *owner, int node1, int node2)
 EDGE. More...
 
 ~OTFFlexbbEdge () override
 
PackerEnergy compute_samebbconf_alternate_state_energy_first_node ()
 
PackerEnergy compute_samebbconf_alternate_state_energy_second_node ()
 
PackerEnergy compute_altbbconf_alternate_state_energy ()
 
void otfedge_note_substitution_accepted ()
 
unsigned int count_dynamic_memory () const override
 
void set_ProCorrection_values (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 (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 prepare_for_simulated_annealing () override
 
void note_long_range_interactions_exist ()
 
void print_alt_energies () const
 
- Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbEdge
 FlexbbEdge (FlexbbInteractionGraph *owner, int first_node_ind, int second_node_ind)
 
 ~FlexbbEdge () override
 
bool get_nodes_from_same_flexseg () const
 
void set_alt_state (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)
 Called by FlexbbNode in prepare_for_bb_jump: Edges must know the alternate states that nodes are considering. Precondition: alt_state_ for a fixed node must match its cur_state_. More...
 
void acknowledge_partial_state_assignment (int node_index, int new_state, FlexbbSparseMatrixIndex const &state_info)
 
void note_state_substitution_accepted ()
 Copy alt data to current data after a state substitution. More...
 
void reset_alternate_states_for_uncommited_substitution ()
 After a rejected state substitution, the FlexbbNode will call this function to reset the alt_state data to establish the invariant that the alternate state held on the flexbb edges reflect the the current state of those nodes not considering a state substitution. More...
 
PackerEnergy cur_energy () const
 
PackerEnergy alt_energy () const
 
- Public Member Functions inherited from core::pack::interaction_graph::EdgeBase
virtual ~EdgeBase ()
 copy constructor, do not use More...
 
 EdgeBase (InteractionGraphBase *owner, int first_node_ind, int second_node_ind)
 main constructor for edge, no default nor copy constructors More...
 
int get_other_ind (int callers_index) const
 returns the index of the other node that the edge is incident upon More...
 
NodeBaseget_other_node (int callers_index) const
 returns a pointer to the other node that the edge is incident upon More...
 
int get_first_node_ind () const
 returns the index of the smaller-indexed node More...
 
int get_second_node_ind () const
 returns the index of the larger-indexed node More...
 
void set_pos_in_owners_list (std::list< EdgeBase * >::iterator edge_iterator)
 edge keeps iterator to its position in it's owner's edge list More...
 
void set_pos_in_node_edgevector (int callers_index, int position)
 edge keeps index it has in node_ind's edge vector More...
 
bool same_edge (int node1, int node2) const
 returns true if this edge connects nodes of index node1 and node2 the order of node1 and node2 is not important More...
 
virtual void declare_energies_final ()=0
 
virtual unsigned int count_static_memory () const =0
 
Real edge_weight () const
 
virtual void set_edge_weight (Real weight)=0
 
bool marked_for_deletion () const
 Has this edge indicated that it can be deleted? More...
 
InteractionGraphBase const * get_owner () const
 
InteractionGraphBaseget_owner ()
 

Protected Member Functions

OTFFlexbbNode const * get_otfflexbb_node (int index) const
 Downcasts. More...
 
OTFFlexbbNodeget_otfflexbb_node (int index)
 
OTFFlexbbInteractionGraph const * get_otfflexbbig_owner () const
 
OTFFlexbbInteractionGraphget_otfflexbbig_owner ()
 
Residue const & alt_rot (int which_node) const
 
void zero_state_on_node (int which_node)
 
- Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbEdge
FlexbbNode const * get_flexbb_node (int index) const
 
FlexbbNodeget_flexbb_node (int index)
 
FlexbbInteractionGraph const * get_flexbbig_owner () const
 
FlexbbInteractionGraphget_flexbbig_owner ()
 
int num_bb (int node)
 
bool nodes_part_of_same_flexseg () const
 
bool nodes_considering_bb_move () const
 
void set_nodes_considering_bb_move (bool status)
 
int nodes_cur_state (int node) const
 
FlexbbSparseMatrixIndex const & nodes_cur_info (int node) const
 
int nodes_alt_state (int node) const
 
FlexbbSparseMatrixIndex const & nodes_alt_info (int node) const
 
bool alt_e_up_to_date () const
 
void set_nodes_cur_state (int node, int setting)
 Set the currently assigned state for a node; node == 0 || 1. More...
 
void set_nodes_cur_info (int node, FlexbbSparseMatrixIndex const &setting)
 
void set_nodes_alt_state (int node, int setting)
 Set the altnernate state being considered for a node; node == 0 || 1. More...
 
void set_nodes_alt_info (int node, FlexbbSparseMatrixIndex const &setting)
 
void set_cur_energy (PackerEnergy setting)
 
void set_alt_energy (PackerEnergy setting)
 
void copy_alternate_to_current ()
 
void set_node_state_to_zero (int which_node)
 
- Protected Member Functions inherited from core::pack::interaction_graph::EdgeBase
void mark_edge_for_deletion ()
 Mark this edge so that it can be deleted. More...
 
int get_node_index (int index) const
 
int get_num_states_for_node (int index) const
 
NodeBase const * get_node (int index) const
 
NodeBaseget_node (int index)
 
int get_edges_position_in_nodes_edge_vector (int index) const
 
int which_node (int node_index) const
 is a node the first or second node this edge is incident upon? More...
 
void edge_weight (Real)
 protected setter of the edge weight. To be called by derived classes after they have completed the conversion from the previous edge weighting to the new edge weighting. More...
 

Private Member Functions

bool state_is_proline (int which_node, int state) const
 
bool state_is_glycine (int which_node, int state) const
 
int compact_bbindex (int index) const
 

Private Attributes

PackerEnergy all_vs_bb_energy_curr_conf_ [2]
 
PackerEnergy procorr_curr_conf_ [2]
 
PackerEnergy glycorr_curr_conf_ [2]
 
PackerEnergy scsc_energy_curr_conf_
 
PackerEnergy all_vs_bb_energy_alt_conf_ [2]
 
PackerEnergy procorr_alt_conf_ [2]
 
PackerEnergy glycorr_alt_conf_ [2]
 
PackerEnergy scsc_energy_alt_conf_
 
FArray2D_PackerEnergy all_vs_bb_energies_ [2]
 
FArray2D_PackerEnergy procorr_energies_ [2]
 Farray indexed ( state_this, compact bb_other ) More...
 
FArray2D_PackerEnergy glycorr_energies_ [2]
 Farray indexed ( state_this, compact bb_other ) More...
 
ObjexxFCL::FArray4D< unsigned
char > 
sr_aa_neighbors_
 
bool lr_energies_exist_
 
core::pose::PoseCOP pose_
 
core::scoring::ScoreFunctionCOP sfxn_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::OTFFlexbbEdge::OTFFlexbbEdge ( OTFFlexbbInteractionGraph owner,
int  node1,
int  node2 
)
protocols::flexpack::interaction_graph::OTFFlexbbEdge::~OTFFlexbbEdge ( )
overridedefault

Member Function Documentation

Residue const& protocols::flexpack::interaction_graph::OTFFlexbbEdge::alt_rot ( int  which_node) const
inlineprotected
int protocols::flexpack::interaction_graph::OTFFlexbbEdge::compact_bbindex ( int  index) const
inlineprivate
OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_altbbconf_alternate_state_energy ( )
OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_first_node ( )
OTFFlexbbEdge::PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_samebbconf_alternate_state_energy_second_node ( )
unsigned int protocols::flexpack::interaction_graph::OTFFlexbbEdge::count_dynamic_memory ( ) const
overridevirtual
OTFFlexbbNode const * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbb_node ( int  index) const
inlineprotected
OTFFlexbbNode * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbb_node ( int  index)
inlineprotected
OTFFlexbbInteractionGraph const * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbbig_owner ( ) const
inlineprotected
OTFFlexbbInteractionGraph * protocols::flexpack::interaction_graph::OTFFlexbbEdge::get_otfflexbbig_owner ( )
inlineprotected
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::note_long_range_interactions_exist ( )
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::otfedge_note_substitution_accepted ( )
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::prepare_for_simulated_annealing ( )
overridevirtual
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::print_alt_energies ( ) const
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::set_GlyCorrection_values ( 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::OTFFlexbbEdge::set_ProCorrection_values ( 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 
)
bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_glycine ( int  which_node,
int  state 
) const
inlineprivate
bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::state_is_proline ( int  which_node,
int  state 
) const
inlineprivate
void protocols::flexpack::interaction_graph::OTFFlexbbEdge::zero_state_on_node ( int  which_node)
protected

Member Data Documentation

FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energies_[2]
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energy_alt_conf_[2]
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::all_vs_bb_energy_curr_conf_[2]
private

If this flag is "true" then the two tables below are not allocated, and instead sc/bb and bb/bb energies are calculated alongside sc/sc energies in the OTF calculations. Slower, but uses less memory.

Referenced by compute_altbbconf_alternate_state_energy(), compute_samebbconf_alternate_state_energy_first_node(), compute_samebbconf_alternate_state_energy_second_node(), otfedge_note_substitution_accepted(), OTFFlexbbEdge(), print_alt_energies(), and zero_state_on_node().

PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_alt_conf_[2]
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_curr_conf_[2]
private
FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::glycorr_energies_[2]
private
bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::lr_energies_exist_
private
core::pose::PoseCOP protocols::flexpack::interaction_graph::OTFFlexbbEdge::pose_
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_alt_conf_[2]
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_curr_conf_[2]
private
FArray2D_PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::procorr_energies_[2]
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::scsc_energy_alt_conf_
private
PackerEnergy protocols::flexpack::interaction_graph::OTFFlexbbEdge::scsc_energy_curr_conf_
private
core::scoring::ScoreFunctionCOP protocols::flexpack::interaction_graph::OTFFlexbbEdge::sfxn_
private
ObjexxFCL::FArray4D< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbEdge::sr_aa_neighbors_
private

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