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

Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable. More...

#include <HPatchInteractionGraph.hh>

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List of all members.

Public Types

typedef BackgroundNode< V, E, Gparent

Public Member Functions

 HPatchBackgroundNode (AdditionalBackgroundNodesInteractionGraph< V, E, G > *owner, int node_index)
 main constructor. No default constructor, copy constructor or assignment operator
virtual ~HPatchBackgroundNode ()
void set_rotamer (conformation::ResidueOP const &rotamer)
 inits the RotamerOP held by a background node. called in the HPatchIG::initialize method.
conformation::ResidueCOP get_rotamer () const
 returns a const reference to the ResidueOP object held by this background Node. needed by the initialize_bg_bg_overlap call in this class so that one BGNode can get at the residue/rotamer information on another BGNode instance.
void set_rotamer_dots (RotamerDots const &bg_rd)
 inits the RotamerDots object held by a background node. called in the HPatchIG::initialize method.
bool detect_overlap (HPatchNode< V, E, G > *node) const
 returns true if this background residue overlaps with any atom on any rotamer of a HPatchNode.
virtual void prepare_for_simulated_annealing ()
 detects self overlap and asks its incident HPatchBackgroundEdges to compute and cache the overlaps of this residue with all states on the neighboring HPatchNode.
void initialize_bg_bg_overlap (HPatchBackgroundNode< V, E, G > &other)
 stores the sphere overlap for a pair of background nodes
Real update_state_for_substitution (HPatchNode< V, E, G > *fc_node_changing, RotamerDotsCache const &nodes_curr_overlap_with_bg_res, RotamerDotsCache const &nodes_alt_overlap_with_bg_res)
 returns the change in sasa induced by a HPatchNode undergoing a state substitution. The overlap between the HPatchNode and this HPatchBackgroundNode has been precomputed and stored in the HPatchBackgroundEdge that connects them. There is little work to do in this subroutine.
void reset_alt_state_dots ()
 Sets the alt state dots to the current state dots. See comments in HIG and commit_considered_substitution for more information about why this method exists.
void acknowledge_substitution ()
 bookkeeping to reflect a HPatchNode's state substitution. uses the RotamerDots class method operator=.
Real get_current_sasa () const
 returns the total SASA under the current state assignment
Real get_current_sasa (Size atom_index) const
 Returns the current state SASA for the passed in atom index.
Real get_alternate_sasa () const
 returns the total SASA under the alternate state assignment
Real get_alternate_sasa (Size atom_index) const
 Returns the alternate state SASA for the passed in atom index.
utility::vector1
< utility::vector1< bool >
> const & 
get_atom_atom_self_overlaps () const
 Returns a const reference to the atom x atom pair vector of vectors of bools that specifies which atoms are overlapping.
utility::vector1< Size > const & get_hphobes () const
Size n_hphobes () const
virtual unsigned int count_static_memory () const
virtual unsigned int count_dynamic_memory () const
virtual void print () const
 used only for debugging
RotamerDots const & get_current_state_rotamer_dots ()
 Returns current state. Only used by the unit tests.
RotamerDots const & get_alt_state_rotamer_dots ()
 Returns current state. Only used by the unit tests.
InvRotamerDots const & curr_state_inv_dots () const
InvRotamerDots const & alt_state_inv_dots () const
utility::vector1< Size > const & curr_state_exp_hphobes () const
utility::vector1< Size > const & alt_state_exp_hphobes () const
Size n_curr_state_exp_hphobes () const
Size n_alt_state_exp_hphobes () const

Protected Member Functions

HPatchBackgroundEdge< V, E, G > * get_hpatch_bg_edge (int index)
HPatchInteractionGraph< V, E, G > * get_hpatch_owner () const

Detailed Description

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

Defines a Background Node which will contribute to changes in SASA/hpatchE due to state changes on neighboring nodes, and not because of state changes to it. No default constructor makes this class uncopyable.

HPatchBackgroundNode


Member Typedef Documentation

template<typename V, typename E, typename G>
typedef BackgroundNode< V, E, G > core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::parent

Constructor & Destructor Documentation

template<typename V , typename E , typename G >
core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::HPatchBackgroundNode ( AdditionalBackgroundNodesInteractionGraph< V, E, G > *  owner,
int  node_index 
)

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

HPatchBackgroundNode::HPatchBackgroundNode

template<typename V , typename E , typename G >
core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::~HPatchBackgroundNode ( ) [virtual]

Member Function Documentation

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::acknowledge_substitution ( )

bookkeeping to reflect a HPatchNode's state substitution. uses the RotamerDots class method operator=.

HPatchBackgroundNode::acknowledge_substitution

template<typename V, typename E, typename G>
utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_exp_hphobes ( ) const [inline]
template<typename V, typename E, typename G>
InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_inv_dots ( ) const [inline]
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_dynamic_memory ( ) const [virtual]
template<typename V , typename E , typename G >
unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_static_memory ( ) const [virtual]
template<typename V, typename E, typename G>
utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_exp_hphobes ( ) const [inline]
template<typename V, typename E, typename G>
InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots ( ) const [inline]
template<typename V , typename E , typename G >
bool core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::detect_overlap ( HPatchNode< V, E, G > *  node) const

returns true if this background residue overlaps with any atom on any rotamer of a HPatchNode.

HPatchBackgroundNode::detect_overlap

Detailed:
Uses the HPatchNode function detect_any_overlap_with_rotamer. It calls the function on the passed in HPatchNode with the RotamerDots object this BGNode keeps in current_state_rotamer_dots_.

References core::pack::interaction_graph::HPatchNode< V, E, G >::detect_any_overlap_with_rotamer().

template<typename V , typename E , typename G >
RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alt_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

HPatchBackgroundNode::get_alt_state_rotamer_dots

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alternate_sasa ( ) const

returns the total SASA under the alternate state assignment

HPatchBackgroundNode< V, E, G >::get_alternate_sasa

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alternate_sasa ( Size  atom_index) const

Returns the alternate state SASA for the passed in atom index.

HPatchBackgroundNode< V, E, G >::get_alternate_sasa

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

Returns a const reference to the atom x atom pair vector of vectors of bools that specifies which atoms are overlapping.

HPatchBackgroundNode< V, E, G >::get_atom_atom_self_overlaps

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_sasa ( ) const

returns the total SASA under the current state assignment

HPatchBackgroundNode< V, E, G >::get_current_sasa

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_sasa ( Size  atom_index) const

Returns the current state SASA for the passed in atom index.

HPatchBackgroundNode< V, E, G >::get_current_sasa

template<typename V , typename E , typename G >
RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_state_rotamer_dots ( )

Returns current state. Only used by the unit tests.

HPatchBackgroundNode::get_current_state_rotamer_dots

template<typename V, typename E, typename G>
HPatchBackgroundEdge< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_bg_edge ( int  index) [inline, protected]
template<typename V, typename E, typename G>
HPatchInteractionGraph< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_owner ( ) const [inline, protected]
template<typename V, typename E, typename G>
utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hphobes ( ) const [inline]
template<typename V , typename E , typename G >
conformation::ResidueCOP core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_rotamer ( ) const

returns a const reference to the ResidueOP object held by this background Node. needed by the initialize_bg_bg_overlap call in this class so that one BGNode can get at the residue/rotamer information on another BGNode instance.

HPatchBackgroundNode::get_rotamer

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::initialize_bg_bg_overlap ( HPatchBackgroundNode< V, E, G > &  other)

stores the sphere overlap for a pair of background nodes

HPatchBackgroundNode::initialize_bg_bg_overlap

template<typename V, typename E, typename G>
Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_alt_state_exp_hphobes ( ) const [inline]
template<typename V, typename E, typename G>
Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_curr_state_exp_hphobes ( ) const [inline]
template<typename V, typename E, typename G>
Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_hphobes ( ) const [inline]
template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::prepare_for_simulated_annealing ( ) [virtual]

detects self overlap and asks its incident HPatchBackgroundEdges to compute and cache the overlaps of this residue with all states on the neighboring HPatchNode.

HPatchBackgroundNode::prepare_for_simulated_annealing

Detailed:
if we've already gone through this method once, then don't update the parent classes edge vectors. but we do need to reinitialize the self overlap on the BGNode as well as the overlap caused by all other bg nodes.

Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::print ( ) const [virtual]
template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::reset_alt_state_dots ( )

Sets the alt state dots to the current state dots. See comments in HIG and commit_considered_substitution for more information about why this method exists.

HPatchBackgroundNode::reset_alt_state_dots

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

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer ( conformation::ResidueOP const &  rotamer)

inits the RotamerOP held by a background node. called in the HPatchIG::initialize method.

HPatchBackgroundNode::set_rotamer

References core::chemical::ResidueType::atom_type(), core::chemical::AtomType::element(), and core::chemical::ResidueType::nheavyatoms().

template<typename V , typename E , typename G >
void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::set_rotamer_dots ( RotamerDots const &  bg_rd)

inits the RotamerDots object held by a background node. called in the HPatchIG::initialize method.

HPatchBackgroundNode::set_rotamer_dots

template<typename V , typename E , typename G >
Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::update_state_for_substitution ( HPatchNode< V, E, G > *  fc_node_changing,
RotamerDotsCache const &  nodes_curr_overlap_with_bg_res,
RotamerDotsCache const &  nodes_alt_overlap_with_bg_res 
)

returns the change in sasa induced by a HPatchNode undergoing a state substitution. The overlap between the HPatchNode and this HPatchBackgroundNode has been precomputed and stored in the HPatchBackgroundEdge that connects them. There is little work to do in this subroutine.

HPatchBackgroundNode::update_state_for_substitution

References core::pack::interaction_graph::TR_BGNODE(), and core::pack::interaction_graph::HPatchNode< V, E, G >::wt_seqpos_for_node().


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