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Rosetta 3.4
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Rosetta 3.4
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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>
Public Types | |
| typedef BackgroundNode< V, E, G > | parent |
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 |
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.
| typedef BackgroundNode< V, E, G > core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::parent |
| 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
| core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::~HPatchBackgroundNode | ( | ) | [virtual] |
| 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=.
| utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_exp_hphobes | ( | ) | const [inline] |
| InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::alt_state_inv_dots | ( | ) | const [inline] |
| unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_dynamic_memory | ( | ) | const [virtual] |
| unsigned int core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::count_static_memory | ( | ) | const [virtual] |
| utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_exp_hphobes | ( | ) | const [inline] |
| InvRotamerDots const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::curr_state_inv_dots | ( | ) | const [inline] |
| 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
References core::pack::interaction_graph::HPatchNode< V, E, G >::detect_any_overlap_with_rotamer().
| RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alt_state_rotamer_dots | ( | ) |
Returns current state. Only used by the unit tests.
| Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_alternate_sasa | ( | ) | const |
returns the total SASA under the alternate state assignment
| 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.
| 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
| Real core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_sasa | ( | ) | const |
returns the total SASA under the current state assignment
| 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.
| RotamerDots const & core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_current_state_rotamer_dots | ( | ) |
Returns current state. Only used by the unit tests.
| HPatchBackgroundEdge< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_bg_edge | ( | int | index | ) | [inline, protected] |
| HPatchInteractionGraph< V, E, G >* core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hpatch_owner | ( | ) | const [inline, protected] |
| utility::vector1< Size > const& core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::get_hphobes | ( | ) | const [inline] |
| 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.
| 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
| Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_alt_state_exp_hphobes | ( | ) | const [inline] |
| Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_curr_state_exp_hphobes | ( | ) | const [inline] |
| Size core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::n_hphobes | ( | ) | const [inline] |
| 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
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
| void core::pack::interaction_graph::HPatchBackgroundNode< V, E, G >::print | ( | ) | const [virtual] |
used only for debugging
HPatchBackgroundNode::print HPatchBackgroundNode::print
used only for debugging
Implements core::pack::interaction_graph::BackgroundNode< V, E, G >.
References core::pack::interaction_graph::TR_BGNODE().
| 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().
| 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().
| 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.
| 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().
1.7.4
