Each HBondNode represents a rotamer from the RotamerSets object. More...

#include <HBondGraph.hh>

Inheritance diagram for core::scoring::hbonds::graph::HBondNode:

Public Member Functions
	HBondNode ()

	HBondNode (const HBondNode &)

	HBondNode (Size node_id)

	HBondNode (NodeIDSize node_id, MResIDSize mres_id, RotamerIDSize rotamer_id)

	~HBondNode ()

void	print () const

Size	count_static_memory () const

Size	count_dynamic_memory () const

unsigned int	moltenres () const
	get molten residue id for this rotamer More...

void	set_moltenres (MResIDSize mres)
	set molten residue id for this rotamer. More...

unsigned int	local_rotamer_id () const
	get local rotamer id (local to the residue position) More...

void	set_local_rotamer_id (RotamerIDSize rot_id)
	set local rotamer id (local to the residue position). More...

Size	global_rotamer_id () const
	duplicate interface for getting the global rotamer id. Identical to this->get_node_index() details this is equivalent to pack_basic::RotamerSetsBase::nrotamer_offset_for_moltenres( this->moltenres() ) + this->local_rotamer_id() More...

void	register_clash (NodeIDSize node_id)
	keep track of another node (rotamer) that this clashes with. You do not need to call this for all of the rotamers that share a residue position. More...

bool	clashes (NodeIDSize node_id) const
	does this node clash with another node (at another residue position)? More...

AtomInfoSet &	polar_sc_atoms_not_satisfied_by_background ()

AtomInfoSet const &	polar_sc_atoms_not_satisfied_by_background () const

void	add_polar_atom (unsigned short int local_atom_id, numeric::xyzVector< float > const &atom_position, bool is_hydrogen, bool is_donor, bool is_acceptor, bool is_hydroxyl, bool is_backbone)

void	add_polar_atom_if_doesnt_exist (AtomInfo const &info)
	The polar atoms are sorted, so we have to cleverly insert and maintain the order. More...

void	remove_atom_info (unsigned short int local_atom_id)

void	merge_data (HBondNode const &other, utility::vector1< Size > const &other_node_to_my_node, bool merge_with_OR_logic)
	Only merges new data added by this class. Does not merge edges!!! There are two ways to merge the atoms. OR_logic - Take the union of the atoms at each node AND_logic - Take the intersection of the atoms at each node. More...

HBondNode &	operator= (HBondNode const &src)

Private Attributes
unsigned int	mres_id_

unsigned int	rotamer_id_

boost::container::flat_set < unsigned int >	ids_of_clashing_nodes_

AtomInfoSet	polar_sc_atoms_not_satisfied_by_background_

Detailed Description

Each HBondNode represents a rotamer from the RotamerSets object.

Constructor & Destructor Documentation

core::scoring::hbonds::graph::HBondNode::HBondNode ( )

Referenced by count_static_memory().

core::scoring::hbonds::graph::HBondNode::HBondNode ( const HBondNode & )

core::scoring::hbonds::graph::HBondNode::HBondNode ( Size node_id )

core::scoring::hbonds::graph::HBondNode::HBondNode	(	NodeIDSize	node_id,
		MResIDSize	mres_id,
		RotamerIDSize	rotamer_id
	)

core::scoring::hbonds::graph::HBondNode::~HBondNode ( )

default

Member Function Documentation

void core::scoring::hbonds::graph::HBondNode::add_polar_atom	(	unsigned short int	local_atom_id,
		numeric::xyzVector< float > const &	atom_position,
		bool	is_hydrogen,
		bool	is_donor,
		bool	is_acceptor,
		bool	is_hydroxyl,
		bool	is_backbone
	)

inline

References polar_sc_atoms_not_satisfied_by_background_.

Referenced by core::pack::hbonds::determine_atom_level_node_info().

void core::scoring::hbonds::graph::HBondNode::add_polar_atom_if_doesnt_exist ( AtomInfo const & info )

inline

The polar atoms are sorted, so we have to cleverly insert and maintain the order.

Used by merge

References polar_sc_atoms_not_satisfied_by_background_.

Referenced by merge_data().

bool core::scoring::hbonds::graph::HBondNode::clashes ( NodeIDSize node_id ) const

inline

does this node clash with another node (at another residue position)?

References ids_of_clashing_nodes_.

Referenced by merge_data(), protocols::hbnet::HBNet::monte_carlo_net_clash(), protocols::hbnet::HBNet::monte_carlo_seed_is_dead_end(), and protocols::hbnet::HBNet::node_is_compatible().

Size core::scoring::hbonds::graph::HBondNode::count_dynamic_memory ( ) const

References ids_of_clashing_nodes_, and polar_sc_atoms_not_satisfied_by_background_.

Size core::scoring::hbonds::graph::HBondNode::count_static_memory ( ) const

References HBondNode().

Size core::scoring::hbonds::graph::HBondNode::global_rotamer_id ( ) const

inline

duplicate interface for getting the global rotamer id. Identical to this->get_node_index() details this is equivalent to pack_basic::RotamerSetsBase::nrotamer_offset_for_moltenres( this->moltenres() ) + this->local_rotamer_id()

Referenced by core::pack::hbonds::determine_atom_level_node_info(), core::pack::hbonds::find_satisfying_interactions_with_background(), protocols::hbnet::HBNet::get_next_node(), and protocols::hbnet::HBNet::monte_carlo_seed_is_dead_end().

unsigned int core::scoring::hbonds::graph::HBondNode::local_rotamer_id ( ) const

inline

get local rotamer id (local to the residue position)

this is equivalent to pack_basic::RotamerSetsBase::rotid_on_moltenresidue( this->get_node_index() )

References rotamer_id_.

Referenced by protocols::hbnet::HBNet::MC_traverse_IG(), core::scoring::hbonds::graph::HBondGraph::merge(), and merge_data().

void core::scoring::hbonds::graph::HBondNode::merge_data	(	HBondNode const &	other,
		utility::vector1< Size > const &	other_node_to_my_node,
		bool	merge_with_OR_logic
	)

Only merges new data added by this class. Does not merge edges!!! There are two ways to merge the atoms. OR_logic - Take the union of the atoms at each node AND_logic - Take the intersection of the atoms at each node.

other_node_to_my_node is a map of node indices from the other graph to node indices in this graph. other_node_to_my_node.size() == other_graph.num_nodes()

References add_polar_atom_if_doesnt_exist(), clashes(), ids_of_clashing_nodes_, local_rotamer_id(), moltenres(), polar_sc_atoms_not_satisfied_by_background(), polar_sc_atoms_not_satisfied_by_background_, and register_clash().

Referenced by core::scoring::hbonds::graph::HBondGraph::merge().

unsigned int core::scoring::hbonds::graph::HBondNode::moltenres ( ) const

inline

get molten residue id for this rotamer

References mres_id_.

Referenced by protocols::hbnet::NetworkState::add_polar_atoms(), protocols::hbnet::HBNet::add_residue_to_network_state(), protocols::hbnet::edge_satisfies_heavy_unsat_for_node(), core::pack::hbonds::find_satisfying_interactions_with_background(), protocols::hbnet::HBNet::MC_traverse_IG(), core::scoring::hbonds::graph::HBondGraph::merge(), merge_data(), protocols::hbnet::HBNet::monte_carlo_seed_is_dead_end(), and protocols::hbnet::HBNet::node_is_compatible().

HBondNode& core::scoring::hbonds::graph::HBondNode::operator= ( HBondNode const & src )

inline

References ids_of_clashing_nodes_, mres_id_, polar_sc_atoms_not_satisfied_by_background_, and rotamer_id_.

AtomInfoSet& core::scoring::hbonds::graph::HBondNode::polar_sc_atoms_not_satisfied_by_background ( )

inline

References polar_sc_atoms_not_satisfied_by_background_.

Referenced by protocols::hbnet::NetworkState::add_polar_atoms(), protocols::task_operations::PruneBuriedUnsats_RotamerSetsOperation::alter_rotamer_sets(), merge_data(), and core::pack::guidance_scoreterms::approximate_buried_unsat_penalty::three_body_approximate_buried_unsat_calculation().

AtomInfoSet const& core::scoring::hbonds::graph::HBondNode::polar_sc_atoms_not_satisfied_by_background ( ) const

inline

References polar_sc_atoms_not_satisfied_by_background_.

void core::scoring::hbonds::graph::HBondNode::print ( ) const

References mres_id_, rotamer_id_, and core::scoring::hbonds::TR().

void core::scoring::hbonds::graph::HBondNode::register_clash ( NodeIDSize node_id )

inline

keep track of another node (rotamer) that this clashes with. You do not need to call this for all of the rotamers that share a residue position.

References ids_of_clashing_nodes_.

Referenced by core::pack::hbonds::HBondGraphInitializerIG::eval_rot_pair(), and merge_data().

void core::scoring::hbonds::graph::HBondNode::remove_atom_info ( unsigned short int local_atom_id )

inline

O( N )

References polar_sc_atoms_not_satisfied_by_background_, and core::scoring::hbonds::graph::AtomInfoSet::remove().

Referenced by core::pack::hbonds::find_satisfying_interactions_with_background().

void core::scoring::hbonds::graph::HBondNode::set_local_rotamer_id ( RotamerIDSize rot_id )

inline

set local rotamer id (local to the residue position).

References rotamer_id_.

Referenced by core::pack::hbonds::init_node_info().

void core::scoring::hbonds::graph::HBondNode::set_moltenres ( MResIDSize mres )

inline

set molten residue id for this rotamer.

References mres_id_.

Referenced by core::pack::hbonds::init_node_info().

Member Data Documentation

boost::container::flat_set< unsigned int > core::scoring::hbonds::graph::HBondNode::ids_of_clashing_nodes_

private

Referenced by clashes(), count_dynamic_memory(), merge_data(), operator=(), and register_clash().

unsigned int core::scoring::hbonds::graph::HBondNode::mres_id_

private

Referenced by moltenres(), operator=(), print(), and set_moltenres().

AtomInfoSet core::scoring::hbonds::graph::HBondNode::polar_sc_atoms_not_satisfied_by_background_

private

Referenced by add_polar_atom(), add_polar_atom_if_doesnt_exist(), count_dynamic_memory(), merge_data(), operator=(), polar_sc_atoms_not_satisfied_by_background(), and remove_atom_info().

unsigned int core::scoring::hbonds::graph::HBondNode::rotamer_id_

private

Referenced by local_rotamer_id(), operator=(), print(), and set_local_rotamer_id().

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

src/core/scoring/hbonds/graph/HBondGraph.hh
src/core/scoring/hbonds/graph/HBondGraph.cc

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation