Rosetta 3.4
Public Types | Public Member Functions | Protected Member Functions
core::pack::interaction_graph::HPatchEdge< V, E, G > Class Template Reference

Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast. More...

#include <HPatchInteractionGraph.hh>

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List of all members.

Public Types

typedef FirstClassEdge< V, E, Gparent

Public Member Functions

 HPatchEdge (G *owner, int node1, int node2)
 main constructor. No default, or copy constructors, no assignment operator
virtual ~HPatchEdge ()
virtual void prepare_for_simulated_annealing ()
 drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself.
void acknowledge_state_zeroed (int node_index)
 respond to when one of its vertices enters the "unassigned" state.
Real update_state_at_neighbor (int node_considering_substitution, int alt_state, RotamerDots &alt_state_dots)
 returns the change in sasa for the neighbor of a node that is produced by the state substitution it is considering.
void acknowledge_substitution ()
 bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider.
utility::vector1
< utility::vector1< bool >
> const & 
get_current_state_atom_atom_overlaps () const
 Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the current state assignment.
utility::vector1
< utility::vector1< bool >
> const & 
get_alt_state_atom_atom_overlaps () const
 Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the alternate state assignment.
virtual void declare_energies_final ()
 Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter.
virtual unsigned int getMemoryUsageInBytes () const
virtual unsigned int count_static_memory () const
virtual unsigned int count_dynamic_memory () const
Real get_current_two_body_energy () const

Protected Member Functions

HPatchNode< V, E, G > * get_hpatch_node (int index)

Detailed Description

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

Defines a HPatch Edge which connects two first-class HPatch Nodes. Edges have to keep some state so that updates to SASA and the hpatch score can be done fast.

HPatchEdge


Member Typedef Documentation

template<typename V, typename E, typename G>
typedef FirstClassEdge< V, E, G > core::pack::interaction_graph::HPatchEdge< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >
core::pack::interaction_graph::HPatchEdge< V, E, G >::HPatchEdge ( G owner,
int  node1,
int  node2 
)

main constructor. No default, or copy constructors, no assignment operator

HPatchEdge::HPatchEdge

Parameters:
owner- [in] - the owning interaction graph object node1 - [in] - the index of the lower-indexed HPatchNode node2 - [in] - the index of the higher-indexed HPatchNode
template<typename V , typename E , typename G >
core::pack::interaction_graph::HPatchEdge< V, E, G >::~HPatchEdge ( ) [virtual]

Member Function Documentation

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_state_zeroed ( int  node_that_changed)

respond to when one of its vertices enters the "unassigned" state.

HPatchEdge::acknowledge_state_zeroed

Detailed:
called during the HIG::blanket_assign_state_0 -> HPatchNode::assign_zero_state() cascade of calls.
template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchEdge< V, E, G >::acknowledge_substitution ( )

bookkeeping following the decision to substitute a nodes current state with the alternate it was asked to consider.

HPatchEdge::acknowledge_substitution

template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::HPatchEdge< V, E, G >::count_dynamic_memory ( ) const [virtual]
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::HPatchEdge< V, E, G >::count_static_memory ( ) const [virtual]
template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchEdge< V, E, G >::declare_energies_final ( ) [virtual]

Reduces memory usage in the two body energy table after the energy calculating function declares that the energies will not change thereafter.

HPatchEdge::declare_energies_final

Remarks:
(all by apl) In the PDEdge's version of this method, after invoking two_body_energies_.drop_zero_submatrices_where_possible(); the PDEdge checks if the two body energy table it now holds is empty. If the table is empty, the edge deletes itself.

A HPatchEdge should not delete itself if the pair energies are all zero since the Minkowski sum of a water and a van der Waal's sphere extends further out from an atoms center than its (lj_atr, lj_rep, lksolv) interaction sphere. However, if a HPatchEdge holds no pair energies, it's a very good candidate for removal -- it just first needs to check that no (vdw + 1.4 A) spheres overlap between any pair of rotamers on the edges it connects.

template<typename V , typename E , typename G >
utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchEdge< V, E, G >::get_alt_state_atom_atom_overlaps ( ) const

Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the alternate state assignment.

HPatchEdge< V, E, G >::get_alt_state_atom_atom_overlaps

template<typename V , typename E , typename G >
utility::vector1< utility::vector1< bool > > const & core::pack::interaction_graph::HPatchEdge< V, E, G >::get_current_state_atom_atom_overlaps ( ) const

Returns a const reference to the atom-x-atom-pair vector-of-vectors of bools that specifies which atoms are overlapping, assuming the current state assignment.

HPatchEdge< V, E, G >::get_current_state_atom_atom_overlaps

template<typename V, typename E, typename G>
Real core::pack::interaction_graph::HPatchEdge< V, E, G >::get_current_two_body_energy ( ) const
template<typename V, typename E, typename G>
HPatchNode< V, E, G >* core::pack::interaction_graph::HPatchEdge< V, E, G >::get_hpatch_node ( int  index) [inline, protected]
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::HPatchEdge< V, E, G >::getMemoryUsageInBytes ( ) const [virtual]

HPatchEdge::getMemoryUsageInBytes

Remarks:
Not implemented.
template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchEdge< V, E, G >::prepare_for_simulated_annealing ( ) [virtual]

drops zero submatrices of the AminoAcidNeighborSparseMatrix and if the two_body_energies_ member then holds nothing, it checks whether or not its incident nodes have any sphere overlaps. If they don't then the edge deletes itself.

HPatchEdge::prepare_for_simulated_annealing

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

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchEdge< V, E, G >::update_state_at_neighbor ( int  node_considering_substitution,
int  alt_state,
RotamerDots changing_node_alt_state_dots 
)

returns the change in sasa for the neighbor of a node that is produced by the state substitution it is considering.

HPatchEdge::update_state_at_neighbor

Detailed:
Very complicated. See HPatchNode::project_deltaE_for_neighbors_state_sub This edge collects cached sphere overlaps and hands this cached data to the node that is not considering the state substitution. That node computes more sphere overlaps and returns a delta sasa; this method then passes that delta sasa along.

See more comments inline.

Parameters:
changing_node_alt_state_dots- [in] - the RotamerDots object for the alternate state at the changing Node

References core::pack::interaction_graph::RotamerDots::get_num_atoms().


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