Rosetta 3.4
Public Member Functions | Protected Member Functions
core::pack::interaction_graph::LinearMemNode Class Reference

#include <LinearMemoryInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::LinearMemNode:
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Collaboration diagram for core::pack::interaction_graph::LinearMemNode:
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List of all members.

Public Member Functions

 LinearMemNode (InteractionGraphBase *owner, int node_id, int num_states)
 main constructor, no default ctor, uncopyable
virtual ~LinearMemNode ()
 virtual dstor
virtual void prepare_for_simulated_annealing ()
 linmem ig does not have to do anything before sim annealing begins
virtual void print () const
 write internal energy and bookkeeping data to standard out
virtual bool state_unassigned () const
 state 0 represents the unasigned state
virtual core::PackerEnergy get_totalE () const
 return the total energy for this node; includes full energies to neighboring residues
void assign_zero_state ()
 set to state 0
void assign_state (int new_state)
 set to a particular state -- updates the energies internally
void partial_assign_state (int new_state)
 first half of an entire-graph state assignment that avoids unnecessary energy updates as produced in assign_state. Adjust all node's states first, then update all energies.
void complete_state_assignment ()
 second half of the entire-graph state assignment.
int get_current_state () const
 return the index of the currently assigned state
int get_curr_state_recent_state_id () const
 return the "recent state id" for the currently assigned state
core::PackerEnergy get_one_body_energy_current_state () const
 return the one-body energy for the currently assigned state
core::PackerEnergy project_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_node_energy)
 compute the change in energy induced by substituting the currently assigned state with some alternative state
void commit_considered_substitution ()
 proceed to change the currently assigned state to the alternative state considered in the last call to project_deltaE_for_substitution
void acknowledge_last_substititon_not_committed ()
 update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state.
core::PackerEnergy compute_pair_energy_for_current_state (int edge_making_energy_request)
 comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two
core::PackerEnergy compute_pair_energy_for_alternate_state (int edge_making_energy_request)
 comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two
void acknowledge_neighbors_state_substitution (int edge_to_altered_neighbor, core::PackerEnergy new_edge_energy, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info, int other_node_recent_history_index)
void acknowledge_neighbors_partial_state_substitution (int edge_to_altered_neighbor, int other_node_new_state, SparseMatrixIndex const &other_node_new_state_sparse_info, int other_state_recent_history_index)
SparseMatrixIndex const & get_sparse_mat_info_for_curr_state () const
void set_recent_history_size (int num_states_to_maintain_in_recent_history)
int get_recent_history_size () const
void print_internal_energies () const
void update_internal_energy_sums ()
virtual unsigned int count_static_memory () const
virtual unsigned int count_dynamic_memory () const

Protected Member Functions

conformation::Residue const & get_current_rotamer ()
core::PackerEnergy get_curr_pd_energy_total () const
core::PackerEnergy get_alt_pd_energy_total () const
void set_alternate_state (int alt)
int get_alternate_state () const
void calc_deltaEpd (int alternate_state)
bool considering_alternate_state () const

Constructor & Destructor Documentation

core::pack::interaction_graph::LinearMemNode::LinearMemNode ( InteractionGraphBase owner,
int  node_id,
int  num_states 
)

main constructor, no default ctor, uncopyable

main constructor, no default or copy constructors

Referenced by count_static_memory().

core::pack::interaction_graph::LinearMemNode::~LinearMemNode ( ) [virtual]

virtual dstor


Member Function Documentation

void core::pack::interaction_graph::LinearMemNode::acknowledge_last_substititon_not_committed ( )

update bookkeeping info to acknolwedge that the last alternative state considered was not in fact chosen for the currently assigned state.

void core::pack::interaction_graph::LinearMemNode::acknowledge_neighbors_partial_state_substitution ( int  edge_to_altered_neighbor,
int  other_node_new_state,
SparseMatrixIndex const &  other_node_new_state_sparse_info,
int  other_state_recent_history_index 
)
void core::pack::interaction_graph::LinearMemNode::acknowledge_neighbors_state_substitution ( int  edge_to_altered_neighbor,
core::PackerEnergy  new_edge_energy,
int  other_node_new_state,
SparseMatrixIndex const &  other_node_new_state_sparse_info,
int  other_node_recent_history_index 
) [inline]
void core::pack::interaction_graph::LinearMemNode::assign_state ( int  new_state)
void core::pack::interaction_graph::LinearMemNode::assign_zero_state ( ) [virtual]
void core::pack::interaction_graph::LinearMemNode::calc_deltaEpd ( int  alternate_state) [protected]
void core::pack::interaction_graph::LinearMemNode::commit_considered_substitution ( )
void core::pack::interaction_graph::LinearMemNode::complete_state_assignment ( )
core::PackerEnergy core::pack::interaction_graph::LinearMemNode::compute_pair_energy_for_alternate_state ( int  edge_making_energy_request)

comupute the interaction energy between the alternate state being considered on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy().

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::compute_pair_energy_for_current_state ( int  edge_making_energy_request)

comupute the interaction energy between the currently assigned state on this residue and the currently assigned state on a neighboring residue, identified by the index of the edge connecting the two

References core::pack::interaction_graph::OnTheFlyNode::compute_rotamer_pair_energy(), and core::pack::interaction_graph::SparseMatrixIndex::get_aa_type().

bool core::pack::interaction_graph::LinearMemNode::considering_alternate_state ( ) const [inline, protected]
unsigned int core::pack::interaction_graph::LinearMemNode::count_dynamic_memory ( ) const [virtual]

reports the amount of dynamic memory this node allocates recursing to its base class

Reimplemented from core::pack::interaction_graph::OnTheFlyNode.

unsigned int core::pack::interaction_graph::LinearMemNode::count_static_memory ( ) const [virtual]
core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_alt_pd_energy_total ( ) const [inline, protected]
int core::pack::interaction_graph::LinearMemNode::get_alternate_state ( ) const [inline, protected]
core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_curr_pd_energy_total ( ) const [inline, protected]
int core::pack::interaction_graph::LinearMemNode::get_curr_state_recent_state_id ( ) const [inline]

return the "recent state id" for the currently assigned state

conformation::Residue const& core::pack::interaction_graph::LinearMemNode::get_current_rotamer ( ) [inline, protected]
int core::pack::interaction_graph::LinearMemNode::get_current_state ( ) const [inline]

return the index of the currently assigned state

Referenced by core::pack::interaction_graph::LinearMemoryInteractionGraph::print_current_state_assignment().

core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_one_body_energy_current_state ( ) const [inline]

return the one-body energy for the currently assigned state

Referenced by core::pack::interaction_graph::LinearMemoryInteractionGraph::get_energy_sum_for_vertex_group().

int core::pack::interaction_graph::LinearMemNode::get_recent_history_size ( ) const
SparseMatrixIndex const & core::pack::interaction_graph::LinearMemNode::get_sparse_mat_info_for_curr_state ( ) const [inline]
virtual core::PackerEnergy core::pack::interaction_graph::LinearMemNode::get_totalE ( ) const [inline, virtual]

return the total energy for this node; includes full energies to neighboring residues

void core::pack::interaction_graph::LinearMemNode::partial_assign_state ( int  new_state)
void core::pack::interaction_graph::LinearMemNode::prepare_for_simulated_annealing ( ) [virtual]
void core::pack::interaction_graph::LinearMemNode::print ( ) const [virtual]
void core::pack::interaction_graph::LinearMemNode::print_internal_energies ( ) const
core::PackerEnergy core::pack::interaction_graph::LinearMemNode::project_deltaE_for_substitution ( int  alternate_state,
core::PackerEnergy prev_node_energy 
)
void core::pack::interaction_graph::LinearMemNode::set_alternate_state ( int  alt) [inline, protected]
void core::pack::interaction_graph::LinearMemNode::set_recent_history_size ( int  num_states_to_maintain_in_recent_history)
virtual bool core::pack::interaction_graph::LinearMemNode::state_unassigned ( ) const [inline, virtual]

state 0 represents the unasigned state

Implements core::pack::interaction_graph::NodeBase.

void core::pack::interaction_graph::LinearMemNode::update_internal_energy_sums ( )

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