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

#include <OTFFlexbbInteractionGraph.hh>

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...
 
virtual ~OTFFlexbbEdge ()
 
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 ()
 
virtual unsigned int count_dynamic_memory () const
 
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)
 
virtual void prepare_for_simulated_annealing ()
 
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)
 
virtual ~FlexbbEdge ()
 
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 void declare_energies_final ()=0
 
virtual unsigned int count_static_memory () const =0
 
virtual void set_edge_weight (Real weight)=0
 

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)
 

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

bool compute_bbbb_and_scbb_otf_
 
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 ( )
virtual

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
virtual
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

Referenced by OTFFlexbbEdge().

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 ( )
virtual
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
bool protocols::flexpack::interaction_graph::OTFFlexbbEdge::compute_bbbb_and_scbb_otf_
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.

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: