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

#include <OTFFlexbbInteractionGraph.hh>

Public Types

typedef FlexbbNode parent
 
typedef core::conformation::Residue Residue
 
typedef
core::conformation::ResidueCOP 
ResidueCOP
 
typedef core::Size Size
 
typedef core::PackerEnergy PackerEnergy
 
typedef core::Real Real
 
typedef core::Vector Vector
 
typedef core::DistanceSquared DistanceSquared
 
- Public Types inherited from protocols::flexpack::interaction_graph::FlexbbNode
typedef
core::pack::interaction_graph::NodeBase 
parent
 
typedef core::PackerEnergy PackerEnergy
 
typedef core::Size Size
 

Public Member Functions

 OTFFlexbbNode (OTFFlexbbInteractionGraph *, int node_id, int num_states)
 
virtual ~OTFFlexbbNode ()
 
virtual void print () const
 
virtual unsigned int count_dynamic_memory () const
 
Residue const & rotamer (int index) const
 
void set_rotamer (int state, ResidueCOP rotamer)
 
void declare_all_rotamers_initialized ()
 
Real bounding_radius_for_rotamers (int aatype, int bb) const
 
bool rotamer_is_proline (int state) const
 
bool rotamer_is_glycine (int state) const
 
- Public Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbNode
 FlexbbNode (FlexbbInteractionGraph *owner, int node_id, int num_states)
 
virtual ~FlexbbNode ()
 
void set_num_distinct_backbones (int nbbconfs)
 
int get_num_distinct_backbones () const
 
void set_num_states_per_backbone (utility::vector1< int > const &)
 
int get_bb_for_state (int state) const
 
int get_num_states_for_bb (int bbconf) const
 
int get_state_offset_for_bb (int bbconf) const
 
void get_states_on_curr_bb (utility::vector1< Size > &state_list, int offset) const
 
void get_all_states (utility::vector1< Size > &rotlist, int offset) const
 
void set_closest_states_on_other_bbs (ObjexxFCL::FArray2D_int const &)
 
void set_amino_acid_types (utility::vector1< int > const &)
 
ObjexxFCL::FArray1A_int getNumStatesPerAAPerBB (int aa)
 
virtual void add_to_one_body_energies (ObjexxFCL::FArray1< PackerEnergy > &energies)
 
virtual void add_to_one_body_energy (int state, PackerEnergy energy)
 
virtual void update_one_body_energy (int state, PackerEnergy energy)
 
virtual void zero_one_body_energies ()
 
virtual bool state_unassigned () const
 
PackerEnergy get_one_body_energy (int state) const
 
virtual void prepare_for_simulated_annealing ()
 
int get_current_state () const
 
int get_backbone_for_current_state () const
 
void write_current_state_to_state_array (ObjexxFCL::FArray1_int &nodes_states)
 
bool inform_edges_of_alt_state_before_bbjump ()
 Preliminatry bookkeeping for the node the Graph contacted about a backbone move. This node is the "root" of the DFS traversal. More...
 
bool state_has_same_backbone_as_current (int state) const
 Did the alterenate state assigned during a flexbb move actually preserve the currently assigned bb? More...
 
int get_num_states_for_aa_type_for_bb (int aa_type, int bb) const
 
void print_internal_energies ()
 
void update_internal_energy_sums ()
 
int num_aa_types () const
 Read access to private data to both derived classes and the world. More...
 
int num_bbconfs () const
 
utility::vector1< int > const & num_states_for_bb ()
 
utility::vector1< int > const & state_offsets_for_bb ()
 
ObjexxFCL::FArray2D_int const & num_states_for_aa_for_bb ()
 
ObjexxFCL::FArray2D_int const & state_offsets_for_aa_for_bb ()
 
ObjexxFCL::FArray2D_int const & closest_state_on_alt_bb () const
 
FlexbbSparseMatrixIndex const & state_info (int state) const
 
utility::vector1< PackerEnergy >
const & 
one_body_energies () const
 
int current_state () const
 
FlexbbSparseMatrixIndex const & current_state_info () const
 
int curr_bb () const
 
PackerEnergy curr_state_one_body_energy () const
 
PackerEnergy curr_state_total_energy () const
 
utility::vector1< PackerEnergy >
const & 
curr_state_two_body_energies ()
 
int alternate_state () const
 
FlexbbSparseMatrixIndex const & alternate_state_info () const
 
int alt_bb () const
 
PackerEnergy alternate_state_one_body_energy () const
 
PackerEnergy alternate_state_total_energy () const
 
utility::vector1< PackerEnergy >
const & 
alternate_state_two_body_energies () const
 
PackerEnergy alternate_state_two_body_energies (int ind) const
 
utility::vector1< bool > const & edge_connects_flexsegmate () const
 
bool count_energy_to_node_in_my_fragtotalE (int edge_index) const
 Convention for acumulating energies between flexsegmates during a backbone move: The smaller-indexed node counts the interaction, the larger-indexed node does not. More...
 
bool alternate_state_is_being_considered () const
 

Protected Member Functions

OTFFlexbbEdge const * get_incident_otfflexbb_edge (int index) const
 Downcast pointers to incident edges, adjacent nodes, and the owning graph. More...
 
OTFFlexbbEdgeget_incident_otfflexbb_edge (int index)
 
OTFFlexbbNode const * get_adjacent_otfflexbb_node (int index) const
 
OTFFlexbbNodeget_adjacent_otfflexbb_node (int index)
 
OTFFlexbbInteractionGraph const * get_otfflexbbig_owner () const
 
OTFFlexbbInteractionGraphget_otfflexbbig_owner ()
 
- Protected Member Functions inherited from protocols::flexpack::interaction_graph::FlexbbNode
FlexbbEdge const * get_incident_flexbb_edge (int index) const
 
FlexbbEdgeget_incident_flexbb_edge (int index)
 
FlexbbNode const * get_adjacent_flexbb_node (int index) const
 
FlexbbNodeget_adjacent_flexbb_node (int index)
 
FlexbbInteractionGraph const * get_flexbbig_owner () const
 
FlexbbInteractionGraphget_flexbbig_owner ()
 
void update_internal_vectors ()
 
void inform_edges_considered_fixedbb_substition_uncommitted ()
 
void set_considering_alternate_state ()
 Limited write acces to private data. More...
 
void set_current_state (int setting)
 
void set_curr_state_one_body_energy (PackerEnergy setting)
 
void set_curr_state_total_energy (PackerEnergy setting)
 
void inc_curr_state_total_energy (PackerEnergy setting)
 
void set_curr_state_two_body_energies (Size index, PackerEnergy setting)
 
void set_alternate_state (int setting)
 
void set_alternate_state_one_body_energy (PackerEnergy setting)
 
void set_alternate_state_total_energy (PackerEnergy setting)
 
void inc_alternate_state_total_energy (PackerEnergy setting)
 
void set_alternate_state_two_body_energies (Size index, PackerEnergy setting)
 
void reset_all_rotamer_substitution_bookkeeping_data ()
 
void partial_state_assignment (int new_state)
 
void inform_incident_edges_about_partial_state_assignment ()
 
void copy_alternate_to_current ()
 bookkeeping for DFS traversal. Derived classes should consult this at the beginning of node "get_energies" traversals. Calling this function for a node effectively declares that the code which follows will project the delta energy: after the first time this functio is called, it will return true. Must be proceeded by a call to prepare_for_bb_jump(). Depricated. bool energies_already_projected() const; More...
 
void have_edges_copy_alternate_to_current ()
 Have all incident edges copy their data from "alternate_*" to "current_*". More...
 
void have_edges_copy_alternate_to_current_following_flexbb_accept ()
 Have a subset of the incident edges copy their data from "alternate_*" to "current_*" where this subset includes all edges to non-flexsegmates as well as all all upper edges to flexsegmates. Threadsafe if it can be fruitfully parallelized. More...
 

Private Attributes

utility::vector1< ResidueCOProtamers_
 
utility::vector1
< utility::vector1< Real > > 
bounding_volumes_for_bb_for_aa_
 
utility::vector1< unsigned char > rotamer_is_proline_
 
utility::vector1< unsigned char > rotamer_is_glycine_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::flexpack::interaction_graph::OTFFlexbbNode::OTFFlexbbNode ( OTFFlexbbInteractionGraph owner,
int  node_id,
int  num_states 
)
protocols::flexpack::interaction_graph::OTFFlexbbNode::~OTFFlexbbNode ( )
virtual

Member Function Documentation

OTFFlexbbNode::Real protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_radius_for_rotamers ( int  aatype,
int  bb 
) const
unsigned int protocols::flexpack::interaction_graph::OTFFlexbbNode::count_dynamic_memory ( ) const
virtual
void protocols::flexpack::interaction_graph::OTFFlexbbNode::declare_all_rotamers_initialized ( )
OTFFlexbbNode const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int  index) const
inlineprotected
OTFFlexbbNode * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_adjacent_otfflexbb_node ( int  index)
inlineprotected
OTFFlexbbEdge const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_incident_otfflexbb_edge ( int  index) const
inlineprotected

Downcast pointers to incident edges, adjacent nodes, and the owning graph.

Referenced by protocols::flexpack::interaction_graph::MinimalistFlexbbNode::project_deltaE_for_substitution().

OTFFlexbbEdge * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_incident_otfflexbb_edge ( int  index)
inlineprotected
OTFFlexbbInteractionGraph const * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner ( ) const
inlineprotected
OTFFlexbbInteractionGraph * protocols::flexpack::interaction_graph::OTFFlexbbNode::get_otfflexbbig_owner ( )
inlineprotected
void protocols::flexpack::interaction_graph::OTFFlexbbNode::print ( ) const
virtual
Residue const& protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer ( int  index) const
inline
bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine ( int  state) const
inline
bool protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline ( int  state) const
inline
void protocols::flexpack::interaction_graph::OTFFlexbbNode::set_rotamer ( int  state,
ResidueCOP  rotamer 
)

Member Data Documentation

utility::vector1< utility::vector1< Real > > protocols::flexpack::interaction_graph::OTFFlexbbNode::bounding_volumes_for_bb_for_aa_
private
utility::vector1< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_glycine_
private

Referenced by rotamer_is_glycine(), and set_rotamer().

utility::vector1< unsigned char > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamer_is_proline_
private

Referenced by rotamer_is_proline(), and set_rotamer().

utility::vector1< ResidueCOP > protocols::flexpack::interaction_graph::OTFFlexbbNode::rotamers_
private

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