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core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond Class Reference

A hydrogen bond between two atoms in two residues. Since this is tied to a BuriedUnsatPenaltyEdge (which in turn is associated with two residues), it stores only donor group index and acceptor group index. The group indices match the indexing in the corresponding node. More...

#include <BuriedUnsatPenaltyGraph.hh>

Inheritance diagram for core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond:
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Public Member Functions

 BuriedUnsatPenaltyGraphHbond ()
 Default constructor. More...
 
 BuriedUnsatPenaltyGraphHbond (bool const first_node_is_the_acceptor, core::Size const donor_group_index, core::Size const acceptor_group_index, core::Real const energy, core::Size const lower_numbered_node_symmetry_copy_index, core::Size const higher_numbered_node_symmetry_copy_index)
 Initialization constructor. More...
 
 BuriedUnsatPenaltyGraphHbond (BuriedUnsatPenaltyGraphHbond const &src)
 Copy constructor. More...
 
 ~BuriedUnsatPenaltyGraphHbond () override
 Destructor. More...
 
BuriedUnsatPenaltyGraphHbondoperator= (BuriedUnsatPenaltyGraphHbond const &src)
 Assignment operator. More...
 
core::Size donor_group () const
 Get the index of the Hbond donor group in the donor residue. More...
 
core::Size acceptor_group () const
 Get the index of the Hbond acceptor group in the donor residue. More...
 
bool first_node_is_the_acceptor () const
 Is the first node the acceptor? More...
 
core::Size lower_numbered_node_symmetry_copy_index () const
 Get the symmetry copy index of the lower-numbered node. More...
 
core::Size higher_numbered_node_symmetry_copy_index () const
 Get the symmetry copy index of the higher-numbered node. More...
 
core::Size acceptor_symmetry_copy_index () const
 Get the symmetry copy index of the node that's the acceptor. More...
 
core::Size donor_symmetry_copy_index () const
 Get the symmetry copy index of the node that's the donor. More...
 

Private Attributes

bool first_node_is_the_acceptor_
 Is the first node the acceptor? More...
 
core::Size donor_group_index_
 The index of the Hbond donor group in the donor residue. More...
 
core::Size acceptor_group_index_
 The index of the Hbond acceptor group in the acceptor residue. More...
 
core::Real energy_
 The energy of the hydrogen bond. More...
 
core::Size lower_numbered_node_symmetry_copy_index_
 The symmetry copy index of the lower-numbered node. More...
 
core::Size higher_numbered_node_symmetry_copy_index_
 The symmetry copy index of the higher-numbered node. More...
 

Friends

class ::BuriedUnsatPenaltyGraphTests
 
class ::BuriedUnsatPenaltyGraphSymmetricTests
 
class ::BuriedUnsatPenaltyTests
 
class ::BuriedUnsatPenaltySymmetricTests
 

Detailed Description

A hydrogen bond between two atoms in two residues. Since this is tied to a BuriedUnsatPenaltyEdge (which in turn is associated with two residues), it stores only donor group index and acceptor group index. The group indices match the indexing in the corresponding node.

A "donor group" can be a single atom or a collection of related atoms (e.g. the pair of NH2 protons in an aspartate side-chain). This allows us to impose a little bit of prior knowledge: sometimes, you're satisfied if one of the protons in a group is making a hydrogen bond.

Constructor & Destructor Documentation

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

Default constructor.

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::BuriedUnsatPenaltyGraphHbond ( bool const  first_node_is_the_acceptor,
core::Size const  donor_group_index,
core::Size const  acceptor_group_index,
core::Real const  energy,
core::Size const  lower_numbered_node_symmetry_copy_index,
core::Size const  higher_numbered_node_symmetry_copy_index 
)
core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::BuriedUnsatPenaltyGraphHbond ( BuriedUnsatPenaltyGraphHbond const &  src)

Copy constructor.

core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::~BuriedUnsatPenaltyGraphHbond ( )
overridedefault

Destructor.

Member Function Documentation

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::acceptor_group ( ) const
inline

Get the index of the Hbond acceptor group in the donor residue.

References acceptor_group_index_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::acceptor_symmetry_copy_index ( ) const

Get the symmetry copy index of the node that's the acceptor.

Returns 1 in the asymmetric case.

References first_node_is_the_acceptor_, higher_numbered_node_symmetry_copy_index_, and lower_numbered_node_symmetry_copy_index_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_group ( ) const
inline

Get the index of the Hbond donor group in the donor residue.

References donor_group_index_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_symmetry_copy_index ( ) const

Get the symmetry copy index of the node that's the donor.

Returns 1 in the asymmetric case.

References first_node_is_the_acceptor_, higher_numbered_node_symmetry_copy_index_, and lower_numbered_node_symmetry_copy_index_.

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::first_node_is_the_acceptor ( ) const
inline

Is the first node the acceptor?

References first_node_is_the_acceptor_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::higher_numbered_node_symmetry_copy_index ( ) const
inline

Get the symmetry copy index of the higher-numbered node.

Returns 1 in the asymmetric case.

References higher_numbered_node_symmetry_copy_index_.

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::lower_numbered_node_symmetry_copy_index ( ) const
inline

Get the symmetry copy index of the lower-numbered node.

Returns 1 in the asymmetric case.

References lower_numbered_node_symmetry_copy_index_.

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

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::BuriedUnsatPenaltyGraphHbond::acceptor_group_index_
private

The index of the Hbond acceptor group in the acceptor residue.

Referenced by acceptor_group(), BuriedUnsatPenaltyGraphHbond(), and operator=().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::donor_group_index_
private

The index of the Hbond donor group in the donor residue.

Referenced by BuriedUnsatPenaltyGraphHbond(), donor_group(), and operator=().

core::Real core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::energy_
private

The energy of the hydrogen bond.

Referenced by operator=().

bool core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::first_node_is_the_acceptor_
private
core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::higher_numbered_node_symmetry_copy_index_
private

The symmetry copy index of the higher-numbered node.

Always 1 in the asymmetric case.

Referenced by acceptor_symmetry_copy_index(), BuriedUnsatPenaltyGraphHbond(), donor_symmetry_copy_index(), higher_numbered_node_symmetry_copy_index(), and operator=().

core::Size core::pack::guidance_scoreterms::buried_unsat_penalty::graph::BuriedUnsatPenaltyGraphHbond::lower_numbered_node_symmetry_copy_index_
private

The symmetry copy index of the lower-numbered node.

Always 1 in the asymmetric case.

Referenced by acceptor_symmetry_copy_index(), BuriedUnsatPenaltyGraphHbond(), donor_symmetry_copy_index(), lower_numbered_node_symmetry_copy_index(), and operator=().


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