A class for a hydrogen bond donor group or acceptor group. More...

#include <BuriedUnsatPenaltyGraph.hh>

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

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

	BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup (bool const is_acceptor, bool const is_counted, core::Size const heavyatom_index, core::conformation::Residue const &residue)
	Options constructor. More...

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

	~BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup () override
	Destructor. More...

BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup &	operator= (BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup const &src)
	Assignment operator. More...

bool	is_donor () const
	Is this group a donor? More...

bool	is_acceptor () const
	Is this group an acceptor? More...

bool	is_counted () const
	Is this group a group to count (e.g. a buried group)? More...

void	set_counted (bool const setting)
	Set whether this is a group to count. More...

core::Size	heavyatom_index () const
	Get the atom index in the relevant residue of the heavyatom for this group. More...

utility::vector1< core::Size > const &	proton_indices () const
	Get the vector of atom indices in the relevant residue of the protons attached to the heavyatom. More...

core::Size	n_protons () const
	Get the number of protons in this group. Synonymous with max_donated_hbond_count(). More...

void	add_proton_index (core::Size const index_in)
	Add a proton to the list of protons in this group. More...

core::Size	max_donated_hbond_count () const
	Get the maximum donated hydrogen bond count. More...

core::Size	max_accepted_hbond_count () const
	Get the maximum accepted hydrogen bond count. More...

Static Public Member Functions
static core::Size	determine_max_accepted_hbond_count (bool const is_acceptor, core::Size const heavyatom_index, core::conformation::Residue const &residue)
	Determine the maximum number of hydrogen bonds that a group can accept, based on the identity of the heavyatom. More...

Private Attributes
bool	is_acceptor_
	Is this group an acceptor? More...

bool	is_counted_
	Is this a group to count (e.g. a buried group)? More...

core::Size	heavyatom_index_
	The atom index in the relevant residue of the heavyatom for this group. More...

utility::vector1< core::Size >	proton_indices_
	The atom indices in the relevant residue of the protons attached to the heavyatom. More...

core::Size	max_accepted_hbond_count_
	The maximum number of hbonds that this group can accept. More...

Friends
class	::BuriedUnsatPenaltyGraphTests

class	::BuriedUnsatPenaltyGraphSymmetricTests

class	::BuriedUnsatPenaltyTests

class	::BuriedUnsatPenaltySymmetricTests

Detailed Description

A class for a hydrogen bond donor group or acceptor group.

An "acceptor group" is (usually) just an acceptor atom (with the exception noted below). A "donor group" is a donor proton and its parent heavyatom, plus any other protons on that parent.

Note: In rare cases (e.g. a hydroxyl), a group can be both donor and acceptor.

Constructor & Destructor Documentation

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

delete

Default constructor – explicitly deleted.

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup	(	bool const	is_acceptor,
		bool const	is_counted,
		core::Size const	heavyatom_index,
		core::conformation::Residue const &	residue
	)

Options constructor.

Note that protons are initialized to an empty list, and must be added later.

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup ( BuriedUnsatPenaltyGraphHbond const & src )

delete

Copy constructor – explicitly deleted.

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

override

Destructor.

Member Function Documentation

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::add_proton_index ( core::Size const index_in )

Add a proton to the list of protons in this group.

References proton_indices_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::determine_max_accepted_hbond_count	(	bool const	is_acceptor,
		core::Size const	heavyatom_index,
		core::conformation::Residue const &	residue
	)

static

Determine the maximum number of hydrogen bonds that a group can accept, based on the identity of the heavyatom.

Oxygens can accept 2; nitrogens can accept 1. For now, the rule is that simple. At some point, we might look up the information from a database lookup table based on the details of the oxygen type or nitrogen type or whatnot.

Note: Returns 0 if "is_acceptor" is false. This is a static function.

References core::chemical::ResidueType::element(), core::chemical::element::O, and core::conformation::Residue::type().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::heavyatom_index ( ) const

inline

Get the atom index in the relevant residue of the heavyatom for this group.

References heavyatom_index_.

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_acceptor ( ) const

inline

Is this group an acceptor?

References is_acceptor_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted ( ) const

inline

Is this group a group to count (e.g. a buried group)?

References is_counted_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_donor ( ) const

inline

Is this group a donor?

References proton_indices().

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count ( ) const

inline

Get the maximum accepted hydrogen bond count.

References max_accepted_hbond_count_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_donated_hbond_count ( ) const

inline

Get the maximum donated hydrogen bond count.

Synonym for n_protons().

References proton_indices_.

Referenced by core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::decrement_counts(), and core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyNode::increment_counts().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::n_protons ( ) const

inline

Get the number of protons in this group. Synonymous with max_donated_hbond_count().

References proton_indices_.

BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup & core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::operator= ( BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup const & src )

Assignment operator.

References heavyatom_index_, is_acceptor_, is_counted_, max_accepted_hbond_count_, and proton_indices_.

utility::vector1< core::Size > const& core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::proton_indices ( ) const

inline

Get the vector of atom indices in the relevant residue of the protons attached to the heavyatom.

References proton_indices_.

Referenced by is_donor().

void core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::set_counted ( bool const setting )

inline

Set whether this is a group to count.

References is_counted_.

Friends And Related Function Documentation

friend class ::BuriedUnsatPenaltyGraphSymmetricTests

friend

friend class ::BuriedUnsatPenaltyGraphTests

friend

friend class ::BuriedUnsatPenaltySymmetricTests

friend

friend class ::BuriedUnsatPenaltyTests

friend

Member Data Documentation

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::heavyatom_index_

private

The atom index in the relevant residue of the heavyatom for this group.

Referenced by heavyatom_index(), and operator=().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_acceptor_

private

Is this group an acceptor?

Referenced by is_acceptor(), and operator=().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted_

private

Is this a group to count (e.g. a buried group)?

Referenced by is_counted(), operator=(), and set_counted().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count_

private

The maximum number of hbonds that this group can accept.

Referenced by max_accepted_hbond_count(), and operator=().

utility::vector1< core::Size > core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::proton_indices_

private

The atom indices in the relevant residue of the protons attached to the heavyatom.

Referenced by add_proton_index(), max_donated_hbond_count(), n_protons(), operator=(), and proton_indices().

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

Static Public Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Friends And Related Function Documentation

Member Data Documentation