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core::pack::interaction_graph::NPDHBondNode< V, E, G > Class Template Reference

Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph. More...

#include <NPDHBondInteractionGraph.hh>

Inheritance diagram for core::pack::interaction_graph::NPDHBondNode< V, E, G >:
Inheritance graph
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Public Types

typedef FirstClassNode< V, E, Gparent
 
typedef V grandparent
 
- Public Types inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
typedef std::list
< BackgroundToFirstClassEdge
< V, E, G > * > 
BackgroundEdgeList
 
typedef std::list
< BackgroundToFirstClassEdge
< V, E, G > * >::iterator 
BackgroundEdgeListIter
 
typedef std::vector
< BackgroundNode< V, E, G > * > 
BackgroundNodeVector
 
typedef std::vector
< BackgroundToFirstClassEdge
< V, E, G > * > 
BackgroundEdgeVector
 
typedef std::vector
< BackgroundToFirstClassEdge
< V, E, G > * >::iterator 
BackgroundEdgeVectorIter
 

Public Member Functions

 NPDHBondNode (G *owner, int node_index, int num_states)
 NPDHBondNode constructor. More...
 
 ~NPDHBondNode () override
 
void set_rotamers (rotamer_set::RotamerSetCOP rotamers)
 
conformation::Residue const & get_rotamer (int state) const
 
conformation::ResidueCOP get_rotamer_op (int state) const
 
conformation::Residue const & curr_state_rotamer () const
 
conformation::ResidueOP curr_state_rotamer_op () const
 
conformation::Residue const & alt_state_rotamer () const
 
conformation::ResidueCOP alt_state_rotamer_op () const
 
Size seqpos () const
 
void prepare_for_simulated_annealing () override
 invokes V's prep_for_simA method More...
 
void assign_zero_state () override
 
void acknowledge_neighbors_substitution ()
 bookkeeping to follow a neighbors state substitution. this method gets called when a NPDHBondNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident NPDHBondEdges. More...
 
void acknowledge_neighbors_state_zeroed (Size seqpos)
 
core::PackerEnergy calculate_PD_deltaE_for_substitution (int alternate_state, core::PackerEnergy &prev_PDenergies_for_node)
 Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only. More...
 
core::PackerEnergy get_pd_energy_delta ()
 Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub(). More...
 
Real consider_alternate_state ()
 Return the change in energy induced by substituting an alternate rotamer at this position. More...
 
void prepare_for_neighbors_substitution (Size nbrs_seqpos)
 
void compute_alt_weights_for_hbonds (bool curr_state)
 
utility::vector1< NPDHBondOP > & current_hbs ()
 
utility::vector1< NPDHBondOP > & alternate_hbs ()
 
utility::vector1
< utility::vector1< NPDHBondOP > > & 
alternate_hbs_for_atoms ()
 
utility::vector1< NPDHBondOP > & alternate_hbs_for_atom (Size atom_index)
 
Real get_upper_npd_hbond_energy_totals () const
 
void commit_considered_substitution ()
 Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering. More...
 
void reset_after_rejected_substitution ()
 
virtual unsigned int getMemoryUsageInBytes () const
 Not implemented, but needs to be! More...
 
unsigned int count_static_memory () const override
 Returns the amount of static memory used by this Node object. More...
 
unsigned int count_dynamic_memory () const override
 Returns the amount of dynamic memory used by this Node object. More...
 
void print () const override
 useful for debugging More...
 
- Public Member Functions inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
 ~FirstClassNode () override
 FirstClassNode destructor. More...
 
 FirstClassNode (G *owner, int node_id, int num_states)
 FirstClassNode constructor. More...
 
BackgroundEdgeListIter add_background_edge (BackgroundToFirstClassEdge< V, E, G > *edge)
 Adds a BackgroundToFirstClassEdge to the node's list of such edges and returns an iterator to that list position. More...
 
void drop_background_edge (BackgroundEdgeListIter edge)
 Removes an edge from the node's BackgroundToFirstClassEdge list. More...
 
unsigned int count_dynamic_memory () const override
 Returns an int representing the amount of memory in bytes used by this node. More...
 

Protected Member Functions

NPDHBondEdge< V, E, G > const * get_incident_npd_hbond_edge (int index) const
 
NPDHBondEdge< V, E, G > * get_incident_npd_hbond_edge (int index)
 
NPDHBondNode< V, E, G > const * get_adjacent_npd_hbond_node (int index) const
 
NPDHBondNode< V, E, G > * get_adjacent_npd_hbond_node (int index)
 
NPDHBondBackgroundEdge< V, E,
G > const * 
get_edge_to_npd_hbond_bg_node (int index) const
 
NPDHBondBackgroundEdge< V, E, G > * get_edge_to_npd_hbond_bg_node (int index)
 
NPDHBondBackgroundNode< V, E,
G > const * 
get_adjacent_npd_hbond_bg_node (int index) const
 
NPDHBondBackgroundNode< V, E, G > * get_adjacent_npd_hbond_bg_node (int index)
 
NPDHBondInteractionGraph< V, E,
G > const * 
get_npd_hbond_owner () const
 
NPDHBondInteractionGraph< V, E,
G > * 
get_npd_hbond_owner ()
 
- Protected Member Functions inherited from core::pack::interaction_graph::FirstClassNode< V, E, G >
int get_num_edges_to_background_nodes () const
 
BackgroundToFirstClassEdge< V,
E, G > const * 
get_edge_to_bg_node (int index) const
 
BackgroundToFirstClassEdge< V,
E, G > * 
get_edge_to_bg_node (int index)
 
int get_index_of_adjacent_background_node (int index) const
 
BackgroundNode< V, E, G > const * get_adjacent_background_node (int index) const
 
BackgroundNode< V, E, G > * get_adjacent_background_node (int index)
 
bool get_bg_edge_vector_up_to_date_ () const
 
void update_bg_edge_vector ()
 Syncs the background edge vector with the background edge list. More...
 

Private Member Functions

 NPDHBondNode ()
 
 NPDHBondNode (NPDHBondNode< V, E, G > const &)
 
NPDHBondNode< V, E, G > & operator= (NPDHBondNode< V, E, G > const &)
 

Private Attributes

core::Size seqpos_
 
utility::vector1
< conformation::ResidueCOP
rotamers_vector_
 
utility::vector1< Sizerestype_group_for_rotamers_
 
Size max_natoms_
 
utility::vector1
< utility::vector1< NPDHBondOP > > 
curr_atom_hbonds_
 
utility::vector1
< utility::vector1< NPDHBondOP > > 
alt_atom_hbonds_
 
utility::vector1< NPDHBondOPcurr_hbonds_
 
utility::vector1< NPDHBondOPalt_hbonds_
 
utility::vector1< Realtmp_energies_
 
utility::vector1< Realtmp_weights_
 

Detailed Description

template<typename V, typename E, typename G>
class core::pack::interaction_graph::NPDHBondNode< V, E, G >

Defines a FirstClass node which will keep track of the hydrogen bonds coming in to the residue and the hydrogen bond score. FirstClassNode is defined and implemented in AdditionalBackgroundNodesInteractionGraph.

Remarks
No public default constructor makes this class uncopyable.

Member Typedef Documentation

template<typename V, typename E, typename G>
typedef V core::pack::interaction_graph::NPDHBondNode< V, E, G >::grandparent
template<typename V, typename E, typename G>
typedef FirstClassNode< V, E, G > core::pack::interaction_graph::NPDHBondNode< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >
core::pack::interaction_graph::NPDHBondNode< V, E, G >::NPDHBondNode ( G owner,
int  node_index,
int  num_states 
)
template<typename V , typename E , typename G >
core::pack::interaction_graph::NPDHBondNode< V, E, G >::~NPDHBondNode ( )
override
template<typename V, typename E, typename G>
core::pack::interaction_graph::NPDHBondNode< V, E, G >::NPDHBondNode ( )
private
template<typename V, typename E, typename G>
core::pack::interaction_graph::NPDHBondNode< V, E, G >::NPDHBondNode ( NPDHBondNode< V, E, G > const &  )
private

Member Function Documentation

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::acknowledge_neighbors_state_zeroed ( Size  seqpos)
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::acknowledge_neighbors_substitution ( )

bookkeeping to follow a neighbors state substitution. this method gets called when a NPDHBondNode commits a sub and then broadcasts that change to all its neighboring fc nodes via the incident NPDHBondEdges.

template<typename V , typename E , typename G >
conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_state_rotamer ( ) const
template<typename V , typename E , typename G >
conformation::ResidueCOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_state_rotamer_op ( ) const
template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs ( )
template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs_for_atom ( Size  atom_index)
template<typename V , typename E , typename G >
utility::vector1< utility::vector1< NPDHBondOP > > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::alternate_hbs_for_atoms ( )
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::assign_zero_state ( )
override
template<typename V , typename E , typename G >
core::PackerEnergy core::pack::interaction_graph::NPDHBondNode< V, E, G >::calculate_PD_deltaE_for_substitution ( int  alternate_state,
core::PackerEnergy prev_PDenergies_for_node 
)

Returns the change in energy induced by changing a node from its current state into some alternate state for the PD energy terms only.

This function always gets called for every substitution. Only the consider_alt_state() call can get procrastinated.

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::commit_considered_substitution ( )

Sets the current state to the alternate state this node was asked to consider. Copies appropriate score information. Notifies all of its neighbors that it is going through with the state substitution it had been considering.

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::compute_alt_weights_for_hbonds ( bool  curr_state)
template<typename V , typename E , typename G >
Real core::pack::interaction_graph::NPDHBondNode< V, E, G >::consider_alternate_state ( )

Return the change in energy induced by substituting an alternate rotamer at this position.

compute the non-pairwise-decomposable portion of the deltaE

This node must have already been informed what the alternate state is.

template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::NPDHBondNode< V, E, G >::count_dynamic_memory ( ) const
override

Returns the amount of dynamic memory used by this Node object.

template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::NPDHBondNode< V, E, G >::count_static_memory ( ) const
override

Returns the amount of static memory used by this Node object.

template<typename V , typename E , typename G >
conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_state_rotamer ( ) const
template<typename V , typename E , typename G >
conformation::ResidueOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_state_rotamer_op ( ) const
template<typename V , typename E , typename G >
utility::vector1< NPDHBondOP > & core::pack::interaction_graph::NPDHBondNode< V, E, G >::current_hbs ( )
template<typename V, typename E, typename G>
NPDHBondBackgroundNode< V, E, G > const* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_adjacent_npd_hbond_bg_node ( int  index) const
inlineprotected
template<typename V, typename E, typename G>
NPDHBondBackgroundNode< V, E, G >* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_adjacent_npd_hbond_bg_node ( int  index)
inlineprotected
template<typename V, typename E, typename G>
NPDHBondNode< V, E, G > const* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_adjacent_npd_hbond_node ( int  index) const
inlineprotected
template<typename V, typename E, typename G>
NPDHBondNode< V, E, G >* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_adjacent_npd_hbond_node ( int  index)
inlineprotected
template<typename V, typename E, typename G>
NPDHBondBackgroundEdge< V, E, G > const* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_edge_to_npd_hbond_bg_node ( int  index) const
inlineprotected
template<typename V, typename E, typename G>
NPDHBondBackgroundEdge< V, E, G >* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_edge_to_npd_hbond_bg_node ( int  index)
inlineprotected
template<typename V, typename E, typename G>
NPDHBondEdge< V, E, G > const* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_incident_npd_hbond_edge ( int  index) const
inlineprotected
template<typename V, typename E, typename G>
NPDHBondEdge< V, E, G >* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_incident_npd_hbond_edge ( int  index)
inlineprotected
template<typename V, typename E, typename G>
NPDHBondInteractionGraph< V, E, G > const* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_npd_hbond_owner ( ) const
inlineprotected
template<typename V, typename E, typename G>
NPDHBondInteractionGraph< V, E, G >* core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_npd_hbond_owner ( )
inlineprotected
template<typename V , typename E , typename G >
core::PackerEnergy core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_pd_energy_delta ( )

Returns the deltaE for just the PD terms. Separate method from the one above because this one can be called from within a commit_sub call that didn't go through consider_sub().

template<typename V , typename E , typename G >
conformation::Residue const & core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_rotamer ( int  state) const
template<typename V , typename E , typename G >
conformation::ResidueCOP core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_rotamer_op ( int  state) const
template<typename V , typename E , typename G >
Real core::pack::interaction_graph::NPDHBondNode< V, E, G >::get_upper_npd_hbond_energy_totals ( ) const
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::NPDHBondNode< V, E, G >::getMemoryUsageInBytes ( ) const
virtual

Not implemented, but needs to be!

template<typename V, typename E, typename G>
NPDHBondNode< V, E, G >& core::pack::interaction_graph::NPDHBondNode< V, E, G >::operator= ( NPDHBondNode< V, E, G > const &  )
private
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::prepare_for_neighbors_substitution ( Size  nbrs_seqpos)
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::prepare_for_simulated_annealing ( )
override

invokes V's prep_for_simA method

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::print ( ) const
override

useful for debugging

useful for debugging - writes information about a node to the tracer

References core::pack::interaction_graph::TR().

template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::reset_after_rejected_substitution ( )
template<typename V, typename E, typename G>
Size core::pack::interaction_graph::NPDHBondNode< V, E, G >::seqpos ( ) const
inline
template<typename V , typename E , typename G >
void core::pack::interaction_graph::NPDHBondNode< V, E, G >::set_rotamers ( rotamer_set::RotamerSetCOP  rotamers)

Need to save a reference to the rotamer_set so that we can determine what a particular state change will do to the score

Member Data Documentation

template<typename V, typename E, typename G>
utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_atom_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondNode< V, E, G >::alt_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< utility::vector1< NPDHBondOP > > core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_atom_hbonds_
private
template<typename V, typename E, typename G>
utility::vector1< NPDHBondOP > core::pack::interaction_graph::NPDHBondNode< V, E, G >::curr_hbonds_
private
template<typename V, typename E, typename G>
Size core::pack::interaction_graph::NPDHBondNode< V, E, G >::max_natoms_
private
template<typename V, typename E, typename G>
utility::vector1< Size > core::pack::interaction_graph::NPDHBondNode< V, E, G >::restype_group_for_rotamers_
private
template<typename V, typename E, typename G>
utility::vector1< conformation::ResidueCOP > core::pack::interaction_graph::NPDHBondNode< V, E, G >::rotamers_vector_
private
template<typename V, typename E, typename G>
core::Size core::pack::interaction_graph::NPDHBondNode< V, E, G >::seqpos_
private
template<typename V, typename E, typename G>
utility::vector1< Real > core::pack::interaction_graph::NPDHBondNode< V, E, G >::tmp_energies_
private
template<typename V, typename E, typename G>
utility::vector1< Real > core::pack::interaction_graph::NPDHBondNode< V, E, G >::tmp_weights_
private

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