Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Private Attributes | Friends | List of all members
core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup Class Reference

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:
Inheritance graph
[legend]

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...
 
BuriedUnsatPenaltyGraphHbondDonorAcceptorGroupoperator= (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::Sizeproton_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
bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_counted ( ) const
inline
bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::is_donor ( ) const
inline
core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_accepted_hbond_count ( ) const
inline
core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbondDonorAcceptorGroup::max_donated_hbond_count ( ) const
inline
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)
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: