Each BuriedUnsatPenaltyNode represents a rotamer from the RotamerSets object, or a residue (if we're doing a simple scoring pass). More...

#include <BuriedUnsatPenaltyGraph.hh>

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

[legend]

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

	BuriedUnsatPenaltyNode (utility::graph::Graph *owner, platform::Size const node_id)
	Node constructor. More...

	BuriedUnsatPenaltyNode (BuriedUnsatPenaltyNode const &src)=delete
	Copy constructor – explicitly deleted. More...

	~BuriedUnsatPenaltyNode () override
	Destructor. More...

void	initialize_node (core::Size const residue_position, core::Size const rotamer_index, core::conformation::ResidueCOP residue, core::pose::Pose const &pose, BuriedUnsatPenaltyGraphOptionsCOP options, core::scoring::hbonds::HBondOptionsCOP hbond_options, core::scoring::hbonds::HBondDatabase const &hbond_database, bool const is_symmetric)
	Initialize this node, setting its residue_position, rotamer_index,. More...

void	copy_from (utility::graph::Node const *other_node) override
	Given another node, set this node to copy that one. More...

core::Size	get_donor_acceptor_group_from_heavyatom_index (core::Size const heavyatom_index) const
	Given the index of a donor or acceptor heavyatom, get the donor/acceptor group index. More...

BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup const &	donor_acceptor_group (core::Size const donor_acceptor_group_index) const
	Get a donor or acceptor group, by donor or acceptor group index. More...

void	clear_hbond_counts ()
	For every donor/acceptor group, reset the counts of hydrogen bonds to/from that group. More...

void	increment_accepted_hbond_count_for_group (core::Size const group_index)
	Add one to the number of accepted hydrogen bonds for the Nth donor/acceptor group in this node. More...

void	increment_donated_hbond_count_for_group (core::Size const group_index)
	Add one to the number of donated hydrogen bonds for the Nth donor/acceptor group in this node. More...

void	increment_counts (core::Size &unsat_acceptor_count, core::Size &unsat_donor_count, core::Size &unsat_acceptor_and_donor_count, core::Size &oversat_acceptor_count, core::Size &oversat_donor_count, core::Size &oversat_acceptor_and_donor_count) const
	After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories. More...

void	decrement_counts (core::Size &unsat_acceptor_count, core::Size &unsat_donor_count, core::Size &unsat_acceptor_and_donor_count, core::Size &oversat_acceptor_count, core::Size &oversat_donor_count, core::Size &oversat_acceptor_and_donor_count, graph::BuriedUnsatPenaltyNodeDataCOP data) const
	After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories. More...

void	prune_donor_acceptor_groups_lacking_hbonds_to_packable (core::pack::rotamer_set::RotamerSets const &rotsets)
	Iterate through each donor and acceptor group in this node, and set to "do not count" if the group forms no hydrogen bonds to any packable residue's groups. More...

core::Size	residue_position () const
	Get the residue index (position in the pose) for this node. More...

core::Size	rotamer_index () const
	Get the rotamer index for this node. More...

core::Size	num_donor_acceptor_groups () const
	Get the number of donor/acceptor groups. More...

BuriedUnsatPenaltyNodeDataCOP	stored_data () const
	Const access to the stored data. More...

Private Member Functions
bool	is_buried (core::Size const atom_index, core::conformation::Residue const &residue, core::pose::Pose const &pose) const
	Determine whether an atom is buried by the method of sidechain neighbors. More...

void	detect_intra_residue_hydrogen_bonds (core::conformation::Residue const &residue, core::scoring::hbonds::HBondDatabase const &hbond_database, BuriedUnsatPenaltyNodeDataOP new_stored_data)
	Given a residue, detect intramolecular hydrogen bonds. More...

void	detect_intra_residue_hydrogen_bonds_symmetric (core::Size const res_index, core::conformation::ResidueCOP rotamer, core::pose::Pose const &pose, core::conformation::symmetry::SymmetryInfoCOP const symminfo, core::scoring::hbonds::HBondDatabase const &hbond_database, core::scoring::hbonds::HBondOptions const &hbond_options, BuriedUnsatPenaltyNodeDataOP new_stored_data)
	Given a residue, detect intramolecular hydrogen bonds. More...

Private Attributes
BuriedUnsatPenaltyNodeDataOP	stored_data_
	Owning pointer to the data object. More...

utility::vector1< core::Size >	donated_hbond_count_
	The number of hbonds that each group is donating. More...

utility::vector1< core::Size >	accepted_hbond_count_
	The number of hbonds that each group is accepting. More...

Friends
class	::BuriedUnsatPenaltyGraphTests

class	::BuriedUnsatPenaltyGraphSymmetricTests

class	::BuriedUnsatPenaltyTests

class	::BuriedUnsatPenaltySymmetricTests

Detailed Description

Each BuriedUnsatPenaltyNode represents a rotamer from the RotamerSets object, or a residue (if we're doing a simple scoring pass).

Internally, this stores a list of hydrogen bond donor and acceptor atoms that must be satisfied.

Constructor & Destructor Documentation

◆ BuriedUnsatPenaltyNode() [1/3]

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

delete

Default constructor – explicitly deleted.

◆ BuriedUnsatPenaltyNode() [2/3]

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::BuriedUnsatPenaltyNode	(	utility::graph::Graph *	owner,
		platform::Size const	node_id
	)

Node constructor.

◆ BuriedUnsatPenaltyNode() [3/3]

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

delete

Copy constructor – explicitly deleted.

◆ ~BuriedUnsatPenaltyNode()

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

overridedefault

Destructor.

Member Function Documentation

◆ clear_hbond_counts()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::clear_hbond_counts ( )

For every donor/acceptor group, reset the counts of hydrogen bonds to/from that group.

The donated_hbond_count_ and accepted_hbond_count_ vars are initialized to the intra-residue donated and intra-residue accepted counts, respectively (i.e. inter-residue donated and inter-residue accepted counts have not yet been added in).

References accepted_hbond_count_, donated_hbond_count_, and stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node().

◆ copy_from()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::copy_from ( utility::graph::Node const * other_node )

override

Given another node, set this node to copy that one.

Note: this does NOT copy the rotamer index, but instead sets it to 1. The donated_hbond_count_ and accepted_hbond_count_ vars are initialized to the intra-residue donated and intra-residue accepted counts, respectively (i.e. inter-residue donated and inter-residue accepted counts have not yet been added in).

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges().

◆ decrement_counts()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts	(	core::Size &	unsat_acceptor_count,
		core::Size &	unsat_donor_count,
		core::Size &	unsat_acceptor_and_donor_count,
		core::Size &	oversat_acceptor_count,
		core::Size &	oversat_donor_count,
		core::Size &	oversat_acceptor_and_donor_count,
		graph::BuriedUnsatPenaltyNodeDataCOP	data
	)		const

After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories.

The integer instances passed in are DECREMENTED appropriately by this function. (So if there is an incoming count of 5 unsaturated acceptors, and the current node accounts for 3 unsaturated acceptors, the unsat_acceptor_count will drop to 2).

Parameters

[out]	unsat_acceptor_count	The number of acceptor (and not donor) groups that are unsatisfied.
[out]	unsat_donor_count	The number of donor (and not acceptor) groups that are unsatisfied.
[out]	unsat_acceptor_and_donor_count	The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. lack either a donated hbond or an accepted hbond).
[out]	oversat_acceptor_count	The number of acceptor (and not donor) groups that are oversatisfied.
[out]	oversat_donor_count	The number of donor (and not acceptor) groups that are oversatisfied. (This generally doesn't happen).
[out]	oversat_acceptor_and_donor_count	The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. have either too many donated hbonds or too many accepted hbonds).
[in]	data	The BuriedUnsatPenaltyNodeData to use. Since this has often been replaced by the time this function is called, we need to pass it in separately.

References accepted_hbond_count_, donated_hbond_count_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_acceptor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_donor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_donated_hbond_count().

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

◆ detect_intra_residue_hydrogen_bonds()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds	(	core::conformation::Residue const &	residue,
		core::scoring::hbonds::HBondDatabase const &	hbond_database,
		BuriedUnsatPenaltyNodeDataOP	new_stored_data
	)

private

Given a residue, detect intramolecular hydrogen bonds.

Populates the donor_acceptor_groups_intrares_hbonds_donated_ and donor_acceptor_groups_intrares_hbonds_accepted_ lists.

Note: This version is for the ASYMMETRIC and SYMMETRIC cases. It only detects the intraresidue hbonds. In the symmetric case, the detect_intra_residue_hydrogen_bonds_symmetric() function should be called immediately after this to detect the interresidue hbonds between this residue and its symmetry mates.

References core::scoring::hbonds::HBond::acc_atm(), core::chemical::ICoorAtomID::atomno(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::HBondSet::hbond(), core::conformation::Residue::icoor(), core::scoring::hbonds::identify_intra_res_hbonds(), core::scoring::hbonds::HBondSet::nhbonds(), and core::chemical::AtomICoor::stub_atom1().

Referenced by initialize_node().

◆ detect_intra_residue_hydrogen_bonds_symmetric()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::detect_intra_residue_hydrogen_bonds_symmetric	(	core::Size const	res_index,
		core::conformation::ResidueCOP	rotamer,
		core::pose::Pose const &	pose,
		core::conformation::symmetry::SymmetryInfoCOP const	symminfo,
		core::scoring::hbonds::HBondDatabase const &	hbond_database,
		core::scoring::hbonds::HBondOptions const &	hbond_options,
		BuriedUnsatPenaltyNodeDataOP	new_stored_data
	)

private

Given a residue, detect intramolecular hydrogen bonds.

Populates the donor_acceptor_groups_intrares_hbonds_donated_ and donor_acceptor_groups_intrares_hbonds_accepted_ lists.

Note: This version is for the SYMMETRIC case. It detects interresidue hbonds between this residue and its symmetry mates. This should be called after detect_intra_residue_hydrogen_bonds().

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::pose::Pose::conformation(), core::pose::Pose::conformation_ptr(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::scoring::hbonds::HBondSet::hbond(), core::scoring::hbonds::HBondSet::nhbonds(), and core::conformation::Conformation::residue_cop().

Referenced by initialize_node().

◆ donor_acceptor_group()

BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup const& core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::donor_acceptor_group ( core::Size const donor_acceptor_group_index ) const

inline

Get a donor or acceptor group, by donor or acceptor group index.

This version provides const access.

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups().

◆ get_donor_acceptor_group_from_heavyatom_index()

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::get_donor_acceptor_group_from_heavyatom_index ( core::Size const heavyatom_index ) const

inline

Given the index of a donor or acceptor heavyatom, get the donor/acceptor group index.

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing().

◆ increment_accepted_hbond_count_for_group()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_accepted_hbond_count_for_group ( core::Size const group_index )

Add one to the number of accepted hydrogen bonds for the Nth donor/acceptor group in this node.

References accepted_hbond_count_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node().

◆ increment_counts()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts	(	core::Size &	unsat_acceptor_count,
		core::Size &	unsat_donor_count,
		core::Size &	unsat_acceptor_and_donor_count,
		core::Size &	oversat_acceptor_count,
		core::Size &	oversat_donor_count,
		core::Size &	oversat_acceptor_and_donor_count
	)		const

After hydrogen bonds from edges have been counted, report the number of donor/acceptor groups in each of several categories.

The integer instances passed in are incremented appropriately by this function. (So if there is an incoming count of 5 unsaturated acceptors, and the current node has 3 more, the unsat_acceptor_count will end up being 8).

Parameters

[out]	unsat_acceptor_count	The number of acceptor (and not donor) groups that are unsatisfied.
[out]	unsat_donor_count	The number of donor (and not acceptor) groups that are unsatisfied.
[out]	unsat_acceptor_and_donor_count	The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. lack either a donated hbond or an accepted hbond).
[out]	oversat_acceptor_count	The number of acceptor (and not donor) groups that are oversatisfied.
[out]	oversat_donor_count	The number of donor (and not acceptor) groups that are oversatisfied. (This generally doesn't happen).
[out]	oversat_acceptor_and_donor_count	The number of groups that are both donors and acceptors (e.g. hydroxyls) that are unsatisfied (i.e. have either too many donated hbonds or too many accepted hbonds).

References accepted_hbond_count_, donated_hbond_count_, core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_acceptor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_donor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_donated_hbond_count(), and stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::calculate_penalty_once_from_scratch(), and core::pack::guidance_scoreterms::buried_unsat_penalty::BuriedUnsatPenalty::increment_counts().

◆ increment_donated_hbond_count_for_group()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_donated_hbond_count_for_group ( core::Size const group_index )

Add one to the number of donated hydrogen bonds for the Nth donor/acceptor group in this node.

References donated_hbond_count_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::compute_unsats_for_node().

◆ initialize_node()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::initialize_node	(	core::Size const	residue_position,
		core::Size const	rotamer_index,
		core::conformation::ResidueCOP	residue,
		core::pose::Pose const &	pose,
		BuriedUnsatPenaltyGraphOptionsCOP	options,
		core::scoring::hbonds::HBondOptionsCOP	hbond_options,
		core::scoring::hbonds::HBondDatabase const &	hbond_database,
		bool const	is_symmetric
	)

Initialize this node, setting its residue_position, rotamer_index,.

The options owning pointer is stored directly; the options are not cloned.

References accepted_hbond_count_, core::pose::Pose::conformation_ptr(), detect_intra_residue_hydrogen_bonds(), detect_intra_residue_hydrogen_bonds_symmetric(), donated_hbond_count_, core::chemical::AtomType::is_acceptor(), is_buried(), core::chemical::AtomType::is_hydrogen(), core::chemical::AtomType::is_polar_hydrogen(), core::conformation::symmetry::is_symmetric(), residue_position(), rotamer_index(), stored_data_, core::pose::Pose::total_residue(), and core::pack::guidance_scoreterms::buried_unsat_penalty::TR().

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_node().

◆ is_buried()

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::is_buried	(	core::Size const	atom_index,
		core::conformation::Residue const &	residue,
		core::pose::Pose const &	pose
	)		const

private

Determine whether an atom is buried by the method of sidechain neighbors.

References core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::angle_exponent(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::angle_shift_factor(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::burial_threshold(), core::select::util::determine_whether_point_is_buried(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::dist_exponent(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphOptions::dist_midpoint(), stored_data_, and core::conformation::Residue::xyz().

Referenced by initialize_node().

◆ num_donor_acceptor_groups()

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::num_donor_acceptor_groups ( ) const

inline

Get the number of donor/acceptor groups.

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::provide_pymol_commands_to_show_groups(), and prune_donor_acceptor_groups_lacking_hbonds_to_packable().

◆ prune_donor_acceptor_groups_lacking_hbonds_to_packable()

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::prune_donor_acceptor_groups_lacking_hbonds_to_packable ( core::pack::rotamer_set::RotamerSets const & rotsets )

Iterate through each donor and acceptor group in this node, and set to "do not count" if the group forms no hydrogen bonds to any packable residue's groups.

This should only be called for nodes corresponding to non-packable positions.

References core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::acceptor_group(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_group(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::first_node_is_the_acceptor(), core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::hbond(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyEdge::n_hbonds(), num_donor_acceptor_groups(), residue_position(), and stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing().

◆ residue_position()

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::residue_position ( ) const

inline

Get the residue index (position in the pose) for this node.

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges(), core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::initialize_graph_for_packing(), initialize_node(), and prune_donor_acceptor_groups_lacking_hbonds_to_packable().

◆ rotamer_index()

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::rotamer_index ( ) const

inline

Get the rotamer index for this node.

References stored_data_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraph::copy_node_and_connected_edges(), and initialize_node().

◆ stored_data()

BuriedUnsatPenaltyNodeDataCOP core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::stored_data ( ) const

inline

Const access to the stored data.

References stored_data_.

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

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

◆ accepted_hbond_count_

utility::vector1< core::Size > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::accepted_hbond_count_

private

The number of hbonds that each group is accepting.

Referenced by clear_hbond_counts(), decrement_counts(), increment_accepted_hbond_count_for_group(), increment_counts(), and initialize_node().

◆ donated_hbond_count_

utility::vector1< core::Size > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::donated_hbond_count_

private

The number of hbonds that each group is donating.

Referenced by clear_hbond_counts(), decrement_counts(), increment_counts(), increment_donated_hbond_count_for_group(), and initialize_node().

◆ stored_data_

BuriedUnsatPenaltyNodeDataOP core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::stored_data_

private

Owning pointer to the data object.

Referenced by clear_hbond_counts(), copy_from(), donor_acceptor_group(), get_donor_acceptor_group_from_heavyatom_index(), increment_counts(), initialize_node(), is_buried(), num_donor_acceptor_groups(), prune_donor_acceptor_groups_lacking_hbonds_to_packable(), residue_position(), rotamer_index(), and stored_data().

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 Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ BuriedUnsatPenaltyNode() [1/3]

◆ BuriedUnsatPenaltyNode() [2/3]

◆ BuriedUnsatPenaltyNode() [3/3]

◆ ~BuriedUnsatPenaltyNode()

Member Function Documentation

◆ clear_hbond_counts()

◆ copy_from()

◆ decrement_counts()

◆ detect_intra_residue_hydrogen_bonds()

◆ detect_intra_residue_hydrogen_bonds_symmetric()

◆ donor_acceptor_group()

◆ get_donor_acceptor_group_from_heavyatom_index()

◆ increment_accepted_hbond_count_for_group()

◆ increment_counts()

◆ increment_donated_hbond_count_for_group()

◆ initialize_node()

◆ is_buried()

◆ num_donor_acceptor_groups()

◆ prune_donor_acceptor_groups_lacking_hbonds_to_packable()

◆ residue_position()

◆ rotamer_index()

◆ stored_data()

Friends And Related Function Documentation

◆ ::BuriedUnsatPenaltyGraphSymmetricTests

◆ ::BuriedUnsatPenaltyGraphTests

◆ ::BuriedUnsatPenaltySymmetricTests

◆ ::BuriedUnsatPenaltyTests

Member Data Documentation

◆ accepted_hbond_count_

◆ donated_hbond_count_

◆ stored_data_