The BuriedUnsatPenaltyGraph consists of nodes representing resiudues (or rotamers in packing mode) and edges representing hydrogen-bonding interactions. Each node stores a list of hydrogen bond donor and acceptor atoms that we're seeking to satisfy; each edge stores the donors and acceptors that are connected by hydrogen bonds when two residues (or rotamers) interact. More...

#include <BuriedUnsatPenaltyGraph.hh>

Inheritance diagram for core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph:

[legend]

Public Types
typedef utility::graph::Graph	parent

Public Member Functions
	BuriedUnsatPenaltyGraph ()=delete
	Default constructor – explicitly deleted. More...

	BuriedUnsatPenaltyGraph (BuriedUnsatPenaltyGraphOptionsCOP options, core::scoring::hbonds::HBondOptionsCOP hbond_options)
	Options constructor. More...

	BuriedUnsatPenaltyGraph (platform::Size const num_nodes, BuriedUnsatPenaltyGraphOptionsCOP options, core::scoring::hbonds::HBondOptionsCOP hbond_options)
	Nodecount constructor with options. More...

	BuriedUnsatPenaltyGraph (BuriedUnsatPenaltyGraph const &src)
	Copy constructor. More...

	~BuriedUnsatPenaltyGraph () override
	Destructor. More...

void	delete_edge (utility::graph::Edge *edge) override
	Needed override from base class. More...

void	delete_node (utility::graph::Node *node) override
	Needed override from base class. More...

void	set_always_rotamer_one (bool const setting)
	Set whether this is a graph that just stores one rotamer per position. More...

void	provide_pymol_commands_to_show_groups (std::ostream &out, core::pose::Pose const &pose) const
	Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor and donor groups orange. Useful for debugging degree of burial. More...

void	initialize_graph_for_scoring (core::pose::Pose const &pose)
	Initialize a BuriedUnsatPenaltyGraph from a pose, for scoring. More...

void	initialize_graph_for_packing (core::pose::Pose const &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, bool const only_scoring=false, bool const prevent_pruning=false)
	Initialize a BuriedUnsatPenaltyGraph from a pose and a residue set, for packing. More...

void	compute_unsats_all_nodes ()
	Given this BuriedUnsatPenaltyGraph with some number of nodes, iterate through each node and update the internally-stored counts for unsats and oversats based on the edges connected to that node. More...

void	compute_unsats_changed_nodes (utility::vector1< core::Size > const &changed_node_indices, utility::vector1< core::Size > const &changed_node_partners)
	Given two lists (one of changed nodes, one of their partners), update the internally-stored counts for unsats and oversats for those nodes only. More...

void	compute_unsats_for_node (core::Size const node_index)
	Given this BuriedUnsatPenaltyGraph with some number of nodes and the index of a node, update the internally-stored counts for unsats and oversats based on the edges connected to that node. More...

void	copy_node_and_connected_edges (core::Size const node_index_in_this_graph, BuriedUnsatPenaltyGraph const &other_graph, core::Size const node_index_in_other_graph)
	Given an index of a node in this graph, an owning pointer to another graph, and a node index in the other graph, copy the node from the other graph to the node in this graph, flush the edges that were connected to the node in this graph, and copy those edges from the other graph that can be connected to nodes in this graph. More...

core::Size	get_node_index (core::Size const seqpos, core::Size const rotamer_index) const
	Given the sequence position and rotamer index of a residue, get the corresponding node index. More...

bool	has_node_corresponding_to_residue (core::conformation::ResidueCOP residue) const
	Given a const owning pointer to a residue, determine whether a corresponding node exists. More...

core::Size	get_node_index (core::conformation::ResidueCOP residue) const
	Given a const owning pointer to a residue, get the corresponding node index. More...

core::conformation::ResidueCOP	nodeindex_to_residue_memory_address (core::Size const nodeindex) const
	Get the memory address of the residue corresponding to a particular node. More...

Static Public Member Functions
static void	configure_hbond_options (core::scoring::hbonds::HBondOptions &hbondoptions)
	Set up options for hbond detection. More...

Protected Member Functions
utility::graph::Node *	create_new_node (platform::Size node_index) override
	Factory method for node creation, defined by derived graph classes, called by the base class. More...

utility::graph::Edge *	create_new_edge (platform::Size index1, platform::Size index2) override
	Factory method for edge creation, defined by derived graph classes, called by the base class. More...

utility::graph::Edge *	create_new_edge (utility::graph::Edge const *example_edge) override
	This is also needed for edge creation, when copying graphs. More...

Private Member Functions
BuriedUnsatPenaltyEdge *	add_edge (core::Size const seqpos1, core::Size const rotamer_index1, core::Size const seqpos2, core::Size const rotamer_index2)
	Add an edge, representing an interresidue hydrogen bonded interaction (consisting of one or more interresidue hydrogen bonds), to the graph. More...

BuriedUnsatPenaltyEdge *	add_edge (core::Size const node_index1, core::Size const node_index2, BuriedUnsatPenaltyEdge const &other_edge)
	Add an edge, representing an interresidue hydrogen bonded interaction (consisting of one or more interresidue hydrogen bonds), to the graph. More...

bool	get_edge_exists (core::Size const seqpos1, core::Size const rotamer_index1, core::Size const seqpos2, core::Size const rotamer_index2) const
	Determine whether an edge exists in the graph, by seqpos and rotamer index. More...

BuriedUnsatPenaltyEdge *	find_edge (core::Size const seqpos1, core::Size const rotamer_index1, core::Size const seqpos2, core::Size const rotamer_index2)
	Retrieve an edge by seqpos and rotamer index. More...

BuriedUnsatPenaltyEdge const *	find_edge (core::Size const seqpos1, core::Size const rotamer_index1, core::Size const seqpos2, core::Size const rotamer_index2) const
	Retrieve an edge by seqpos and rotamer index. More...

void	initialize_node (core::Size const node_index, core::Size const residue_position, core::Size const rotamer_index, core::conformation::ResidueCOP residue, core::pose::Pose const &pose, core::scoring::hbonds::HBondDatabase const &hb_data, bool const is_symmetric)
	Initialize a node to represent a given residue position and rotamer index, and store in it all of the relevant hydrogen bond donors and acceptors. More...

Private Attributes
bool	always_rotamer_one_
	In some cases, the graph should only store one rotamer per position. More...

std::map< std::pair< core::Size, core::Size >, core::Size >	residuepos_rotamerindex_to_nodeindex_
	A map of (residue position, rotamer index)-->(node index). More...

std::map< core::conformation::ResidueCOP, core::Size >	residue_memory_address_to_nodeindex_
	A map of (Residue memory address)-->(node index). More...

std::map< core::Size, core::conformation::ResidueCOP >	nodeindex_to_residue_memory_address_
	A map of (node index)-->(Residue memory address). More...

BuriedUnsatPenaltyGraphOptionsCOP	options_
	A const owning pointer to an options container, containing settings for the BuriedUnsatPenaltyGraph. More...

core::scoring::hbonds::HBondOptionsCOP	hbond_options_
	A const owning pointer to an options container for hydrogen bonds. More...

boost::unordered_object_pool< BuriedUnsatPenaltyEdge > *	bunsat_edge_pool_
	Storage for the edges of this graph. More...

Friends
class	::BuriedUnsatPenaltyGraphTests

class	::BuriedUnsatPenaltyGraphSymmetricTests

class	::BuriedUnsatPenaltyTests

class	::BuriedUnsatPenaltySymmetricTests

Detailed Description

The BuriedUnsatPenaltyGraph consists of nodes representing resiudues (or rotamers in packing mode) and edges representing hydrogen-bonding interactions. Each node stores a list of hydrogen bond donor and acceptor atoms that we're seeking to satisfy; each edge stores the donors and acceptors that are connected by hydrogen bonds when two residues (or rotamers) interact.

Member Typedef Documentation

◆ parent

typedef utility::graph::Graph core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::parent

Constructor & Destructor Documentation

◆ BuriedUnsatPenaltyGraph() [1/4]

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::BuriedUnsatPenaltyGraph ( )

delete

Default constructor – explicitly deleted.

◆ BuriedUnsatPenaltyGraph() [2/4]

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::BuriedUnsatPenaltyGraph	(	BuriedUnsatPenaltyGraphOptionsCOP	options,
		core::scoring::hbonds::HBondOptionsCOP	hbond_options
	)

Options constructor.

Note: this stores the owning pointer to the options; it doesn't clone them. The hbond options are cloned and modified, though.

References configure_hbond_options(), hbond_options_, and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().

◆ BuriedUnsatPenaltyGraph() [3/4]

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::BuriedUnsatPenaltyGraph	(	platform::Size const	num_nodes,
		BuriedUnsatPenaltyGraphOptionsCOP	options,
		core::scoring::hbonds::HBondOptionsCOP	hbond_options
	)

Nodecount constructor with options.

Note: this stores the owning pointer to the options; it doesn't clone them. The hbond options are cloned and modified, though.

References configure_hbond_options(), hbond_options_, and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().

◆ BuriedUnsatPenaltyGraph() [4/4]

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::BuriedUnsatPenaltyGraph ( BuriedUnsatPenaltyGraph const & src )

Copy constructor.

◆ ~BuriedUnsatPenaltyGraph()

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::~BuriedUnsatPenaltyGraph ( )

override

Destructor.

References bunsat_edge_pool_.

Member Function Documentation

◆ add_edge() [1/2]

BuriedUnsatPenaltyEdge * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::add_edge	(	core::Size const	node_index1,
		core::Size const	node_index2,
		BuriedUnsatPenaltyEdge const &	other_edge
	)

private

Add an edge, representing an interresidue hydrogen bonded interaction (consisting of one or more interresidue hydrogen bonds), to the graph.

Returns a pointer to the newly-created edge. This version copies an edge from another graph.

Note: In the graph base class, the first node index is always numbered lower than the second node index for an edge. The swap happens automatically.

References core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::copy_from().

◆ add_edge() [2/2]

BuriedUnsatPenaltyEdge * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::add_edge	(	core::Size const	seqpos1,
		core::Size const	rotamer_index1,
		core::Size const	seqpos2,
		core::Size const	rotamer_index2
	)

private

Add an edge, representing an interresidue hydrogen bonded interaction (consisting of one or more interresidue hydrogen bonds), to the graph.

Returns a pointer to the newly-created edge.

Note: In the graph base class, the first node index is always numbered lower than the second node index for an edge. The swap happens automatically.

References get_node_index().

Referenced by copy_node_and_connected_edges(), and initialize_graph_for_packing().

◆ compute_unsats_all_nodes()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_all_nodes ( )

Given this BuriedUnsatPenaltyGraph with some number of nodes, iterate through each node and update the internally-stored counts for unsats and oversats based on the edges connected to that node.

Calls compute_unsats_for_node().

Calls compute_unsats_for_node();

References compute_unsats_for_node().

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_almost_from_scratch_using_reference_graph().

◆ compute_unsats_changed_nodes()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_changed_nodes	(	utility::vector1< core::Size > const &	changed_node_indices,
		utility::vector1< core::Size > const &	changed_node_partners
	)

Given two lists (one of changed nodes, one of their partners), update the internally-stored counts for unsats and oversats for those nodes only.

calls compute_unsats_for_node().

References compute_unsats_for_node().

◆ compute_unsats_for_node()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node ( core::Size const node_index )

Given this BuriedUnsatPenaltyGraph with some number of nodes and the index of a node, update the internally-stored counts for unsats and oversats based on the edges connected to that node.

Referenced by compute_unsats_all_nodes(), and compute_unsats_changed_nodes().

◆ configure_hbond_options()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::configure_hbond_options ( core::scoring::hbonds::HBondOptions & hbondoptions )

static

Set up options for hbond detection.

References core::scoring::hbonds::HBondOptions::bb_donor_acceptor_check(), core::scoring::hbonds::HBondOptions::exclude_DNA_DNA(), core::scoring::hbonds::HBondOptions::exclude_intra_res_protein(), core::scoring::hbonds::HBondOptions::exclude_intra_res_RNA(), core::scoring::hbonds::HBondOptions::exclude_self_hbonds(), core::scoring::hbonds::HBondOptions::smooth_hb_env_dep(), core::scoring::hbonds::HBondOptions::use_hb_env_dep(), and core::scoring::hbonds::HBondOptions::use_hb_env_dep_DNA().

Referenced by BuriedUnsatPenaltyGraph().

◆ copy_node_and_connected_edges()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges	(	core::Size const	node_index_in_this_graph,
		BuriedUnsatPenaltyGraph const &	other_graph,
		core::Size const	node_index_in_other_graph
	)

Given an index of a node in this graph, an owning pointer to another graph, and a node index in the other graph, copy the node from the other graph to the node in this graph, flush the edges that were connected to the node in this graph, and copy those edges from the other graph that can be connected to nodes in this graph.

Note that the logic for determining whether an edge from the other graph can be related to this graph is based on ResidueCOPs.

References add_edge(), always_rotamer_one_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::copy_from(), nodeindex_to_residue_memory_address(), nodeindex_to_residue_memory_address_, residue_memory_address_to_nodeindex_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::residue_position(), residuepos_rotamerindex_to_nodeindex_, and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::rotamer_index().

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_almost_from_scratch_using_reference_graph().

◆ create_new_edge() [1/2]

utility::graph::Edge * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::create_new_edge	(	platform::Size	index1,
		platform::Size	index2
	)

overrideprotected

Factory method for edge creation, defined by derived graph classes, called by the base class.

factory method for edge creation, defined by derived graph classes, called by the base class

References bunsat_edge_pool_.

◆ create_new_edge() [2/2]

utility::graph::Edge * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::create_new_edge ( utility::graph::Edge const * example_edge )

overrideprotected

This is also needed for edge creation, when copying graphs.

References bunsat_edge_pool_.

◆ create_new_node()

utility::graph::Node * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::create_new_node ( platform::Size node_index )

overrideprotected

Factory method for node creation, defined by derived graph classes, called by the base class.

factory method for node creation, defined by derived graph classes, called by the base class

◆ delete_edge()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::delete_edge ( utility::graph::Edge * edge )

override

Needed override from base class.

References bunsat_edge_pool_.

◆ delete_node()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::delete_node ( utility::graph::Node * node )

override

Needed override from base class.

◆ find_edge() [1/2]

BuriedUnsatPenaltyEdge * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::find_edge	(	core::Size const	seqpos1,
		core::Size const	rotamer_index1,
		core::Size const	seqpos2,
		core::Size const	rotamer_index2
	)

private

Retrieve an edge by seqpos and rotamer index.

Nonconst version.

References get_node_index().

Referenced by initialize_graph_for_packing().

◆ find_edge() [2/2]

BuriedUnsatPenaltyEdge const * core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::find_edge	(	core::Size const	seqpos1,
		core::Size const	rotamer_index1,
		core::Size const	seqpos2,
		core::Size const	rotamer_index2
	)		const

private

Retrieve an edge by seqpos and rotamer index.

Const version.

References get_node_index().

◆ get_edge_exists()

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_edge_exists	(	core::Size const	seqpos1,
		core::Size const	rotamer_index1,
		core::Size const	seqpos2,
		core::Size const	rotamer_index2
	)		const

private

Determine whether an edge exists in the graph, by seqpos and rotamer index.

References get_node_index().

Referenced by initialize_graph_for_packing().

◆ get_node_index() [1/2]

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_node_index ( core::conformation::ResidueCOP residue ) const

inline

Given a const owning pointer to a residue, get the corresponding node index.

Will throw an error if the owning pointer corresponds to no node in this object.

References residue_memory_address_to_nodeindex_.

◆ get_node_index() [2/2]

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::get_node_index	(	core::Size const	seqpos,
		core::Size const	rotamer_index
	)		const

inline

Given the sequence position and rotamer index of a residue, get the corresponding node index.

References always_rotamer_one_, and residuepos_rotamerindex_to_nodeindex_.

Referenced by add_edge(), core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_almost_from_scratch_using_reference_graph(), find_edge(), get_edge_exists(), initialize_graph_for_packing(), and provide_pymol_commands_to_show_groups().

◆ has_node_corresponding_to_residue()

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::has_node_corresponding_to_residue ( core::conformation::ResidueCOP residue ) const

inline

Given a const owning pointer to a residue, determine whether a corresponding node exists.

References residue_memory_address_to_nodeindex_.

Referenced by provide_pymol_commands_to_show_groups().

◆ initialize_graph_for_packing()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing	(	core::pose::Pose const &	pose,
		core::pack::rotamer_set::RotamerSets const &	rotamersets,
		bool const	only_scoring = `false`,
		bool const	prevent_pruning = `false`
	)

Initialize a BuriedUnsatPenaltyGraph from a pose and a residue set, for packing.

If prevent_pruning is true, then we DISABLE pruning of groups that are not packable and not able to hydrogen bond to packable residues.

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), add_edge(), core::chemical::ICoorAtomID::atomno(), core::pose::Pose::conformation(), core::pose::Pose::conformation_ptr(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBond::energy(), find_edge(), core::scoring::hbonds::HBondDatabase::get_database(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::get_donor_acceptor_group_from_heavyatom_index(), get_edge_exists(), get_node_index(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::scoring::hbonds::HBondSet::hbond(), hbond_options_, core::conformation::Residue::icoor(), initialize_node(), core::conformation::symmetry::is_symmetric(), core::pose::symmetry::is_symmetric(), protocols::mean_field::max(), protocols::mean_field::min(), core::conformation::Residue::nbr_atom_xyz(), core::conformation::Residue::nbr_radius(), core::scoring::hbonds::HBondSet::nhbonds(), core::pack::rotamer_set::RotamerSet::num_rotamers(), options_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::prune_donor_acceptor_groups_lacking_hbonds_to_packable(), core::pose::Pose::residue(), core::conformation::Conformation::residue_cop(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::residue_position(), core::pack::rotamer_set::RotamerSet::rotamer(), core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::set_edge_data(), core::chemical::AtomICoor::stub_atom1(), core::pose::Pose::total_residue(), and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().

Referenced by initialize_graph_for_scoring().

◆ initialize_graph_for_scoring()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_scoring ( core::pose::Pose const & pose )

Initialize a BuriedUnsatPenaltyGraph from a pose, for scoring.

References initialize_graph_for_packing().

◆ initialize_node()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_node	(	core::Size const	node_index,
		core::Size const	residue_position,
		core::Size const	rotamer_index,
		core::conformation::ResidueCOP	residue,
		core::pose::Pose const &	pose,
		core::scoring::hbonds::HBondDatabase const &	hb_data,
		bool const	is_symmetric
	)

private

Initialize a node to represent a given residue position and rotamer index, and store in it all of the relevant hydrogen bond donors and acceptors.

Parameters

[in]	node_index	The index of the node to initialize.
[in]	residue_position	The index of the residue that this node represents in the pose.
[in]	rotamer_index	The index of the rotamer for this residue that this node represents.
[in]	residue	The residue object itself, for extracting hbond donor/acceptor information.
[in]	pose	The pose, for context.
[in]	hb_data	The hydrogen bonding database object.
[in]	is_symmetric	Is this a symmetric pose? (We figure this out once and only once, to avoid repeated dynamic_casts.)

References always_rotamer_one_, core::pose::Pose::conformation_ptr(), hbond_options_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::initialize_node(), core::conformation::symmetry::is_symmetric(), nodeindex_to_residue_memory_address_, options_, residue_memory_address_to_nodeindex_, residuepos_rotamerindex_to_nodeindex_, and core::pose::Pose::total_residue().

Referenced by initialize_graph_for_packing().

◆ nodeindex_to_residue_memory_address()

core::conformation::ResidueCOP core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::nodeindex_to_residue_memory_address ( core::Size const nodeindex ) const

inline

Get the memory address of the residue corresponding to a particular node.

References nodeindex_to_residue_memory_address_.

Referenced by copy_node_and_connected_edges().

◆ provide_pymol_commands_to_show_groups()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups	(	std::ostream &	out,
		core::pose::Pose const &	pose
	)		const

Provide Pymol commands to colour the pose grey, non-buried donor and acceptor groups cyan, and buried acceptor and donor groups orange. Useful for debugging degree of burial.

To use, pass in a pose. If this graph contains residues corresponding to those in the pose, commands for colouring them will be written out.

References core::pose::Pose::conformation(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::donor_acceptor_group(), get_node_index(), has_node_corresponding_to_residue(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::heavyatom_index(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::num_donor_acceptor_groups(), core::conformation::membrane::out, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::proton_indices(), core::conformation::Conformation::residue_cop(), and core::pose::Pose::total_residue().

◆ set_always_rotamer_one()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::set_always_rotamer_one ( bool const setting )

Set whether this is a graph that just stores one rotamer per position.

References always_rotamer_one_.

Friends And Related Function Documentation

◆ ::BuriedUnsatPenaltyGraphSymmetricTests

friend class ::BuriedUnsatPenaltyGraphSymmetricTests

friend

◆ ::BuriedUnsatPenaltyGraphTests

friend class ::BuriedUnsatPenaltyGraphTests

friend

◆ ::BuriedUnsatPenaltySymmetricTests

friend class ::BuriedUnsatPenaltySymmetricTests

friend

◆ ::BuriedUnsatPenaltyTests

friend class ::BuriedUnsatPenaltyTests

friend

Member Data Documentation

◆ always_rotamer_one_

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::always_rotamer_one_

private

In some cases, the graph should only store one rotamer per position.

Referenced by copy_node_and_connected_edges(), get_node_index(), initialize_node(), and set_always_rotamer_one().

◆ bunsat_edge_pool_

boost::unordered_object_pool< BuriedUnsatPenaltyEdge >* core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::bunsat_edge_pool_

private

Storage for the edges of this graph.

The Graph base class is weird and nasty. If your derived edge class differs from the base edge class, the Graph base clas fails to manage the edges correctly on destruction, and this creates a memory leak. The workaround is to manage edges yourself in the derived Graph class, which is silly.

Referenced by create_new_edge(), delete_edge(), and ~BuriedUnsatPenaltyGraph().

◆ hbond_options_

core::scoring::hbonds::HBondOptionsCOP core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::hbond_options_

private

A const owning pointer to an options container for hydrogen bonds.

Referenced by BuriedUnsatPenaltyGraph(), initialize_graph_for_packing(), and initialize_node().

◆ nodeindex_to_residue_memory_address_

std::map< core::Size, core::conformation::ResidueCOP > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::nodeindex_to_residue_memory_address_

private

A map of (node index)-->(Residue memory address).

Referenced by copy_node_and_connected_edges(), initialize_node(), and nodeindex_to_residue_memory_address().

◆ options_

BuriedUnsatPenaltyGraphOptionsCOP core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::options_

private

A const owning pointer to an options container, containing settings for the BuriedUnsatPenaltyGraph.

Referenced by initialize_graph_for_packing(), and initialize_node().

◆ residue_memory_address_to_nodeindex_

std::map< core::conformation::ResidueCOP, core::Size > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::residue_memory_address_to_nodeindex_

private

A map of (Residue memory address)-->(node index).

Referenced by copy_node_and_connected_edges(), get_node_index(), has_node_corresponding_to_residue(), and initialize_node().

◆ residuepos_rotamerindex_to_nodeindex_

std::map< std::pair< core::Size, core::Size >, core::Size > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::residuepos_rotamerindex_to_nodeindex_

private

A map of (residue position, rotamer index)-->(node index).

Referenced by copy_node_and_connected_edges(), get_node_index(), and initialize_node().

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

src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.hh
src/core/pack/guidance_scoreterms/buried_unsat_penalty/graph/BuriedUnsatPenaltyGraph.cc

Public Types

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Member Typedef Documentation

◆ parent

Constructor & Destructor Documentation

◆ BuriedUnsatPenaltyGraph() [1/4]

◆ BuriedUnsatPenaltyGraph() [2/4]

◆ BuriedUnsatPenaltyGraph() [3/4]

◆ BuriedUnsatPenaltyGraph() [4/4]

◆ ~BuriedUnsatPenaltyGraph()

Member Function Documentation

◆ add_edge() [1/2]

◆ add_edge() [2/2]

◆ compute_unsats_all_nodes()

◆ compute_unsats_changed_nodes()

◆ compute_unsats_for_node()

◆ configure_hbond_options()

◆ copy_node_and_connected_edges()

◆ create_new_edge() [1/2]

◆ create_new_edge() [2/2]

◆ create_new_node()

◆ delete_edge()

◆ delete_node()

◆ find_edge() [1/2]

◆ find_edge() [2/2]

◆ get_edge_exists()

◆ get_node_index() [1/2]

◆ get_node_index() [2/2]

◆ has_node_corresponding_to_residue()

◆ initialize_graph_for_packing()

◆ initialize_graph_for_scoring()

◆ initialize_node()

◆ nodeindex_to_residue_memory_address()

◆ provide_pymol_commands_to_show_groups()

◆ set_always_rotamer_one()

Friends And Related Function Documentation

◆ ::BuriedUnsatPenaltyGraphSymmetricTests

◆ ::BuriedUnsatPenaltyGraphTests

◆ ::BuriedUnsatPenaltySymmetricTests

◆ ::BuriedUnsatPenaltyTests

Member Data Documentation

◆ always_rotamer_one_

◆ bunsat_edge_pool_

◆ hbond_options_

◆ nodeindex_to_residue_memory_address_

◆ options_

◆ residue_memory_address_to_nodeindex_

◆ residuepos_rotamerindex_to_nodeindex_