Residue Class Reference

#include <indigox/classes/residue.hpp>

Classes
struct	Impl

Public Types
using	ResidueAtoms = eastl::vector_set< Atom >
enum	Type

Public Member Functions
	Residue ()=default
	Residue (const Residue &)=default
	Residue (Residue &&)=default
	~ Residue ()=default
const ResidueAtoms &	GetAtoms () const
Type	GetType ()
	Determine the type of the residue. More...
bool	HasAtom (const Atom &atom) const
bool	IsAlphaAminoAcid ()
bool	IsAminoAcid ()
	Determine if the residue is an amino acid. More...
bool	IsBetaAminoAcid ()
bool	IsDeltaAminoAcid ()
bool	IsGammaAminoAcid ()
bool	IsLipid ()
bool	IsNucleicAcid ()
bool	IsSugar ()
	operator bool () const
bool	operator!= (const Residue &res) const
bool	operator< (const Residue &res) const
bool	operator<= (const Residue &res) const
Residue &	operator= (const Residue &)=default
Residue &	operator= (Residue &&)=default
bool	operator== (const Residue &res) const
bool	operator> (const Residue &res) const
bool	operator>= (const Residue &res) const

Friends
class	cereal::access
class	Molecule
std::ostream &	operator<< (std::ostream &os, const Residue &res)

Member Typedef Documentation

ResidueAtoms

using ResidueAtoms = eastl::vector_set<Atom>

Member Enumeration Documentation

Type

enum Type

strong

Enumerator
Unspecified
AminoAcid
NucleicAcid
Sugar
Lipid
NonSpecific

Constructor & Destructor Documentation

Residue() [1/3]

Residue ( )

default

Residue() [2/3]

Residue ( const Residue &  )

default

Residue() [3/3]

Residue ( Residue &&  )

default

~ Residue()

~ Residue ( )

default

Member Function Documentation

GetAtoms()

const ResidueAtoms& GetAtoms

(

)

const

GetType()

Type GetType

(

)

Determine the type of the residue.

Checks if the residue matches each of the specific residue types, in order. The first type which matches is the returned type. If you want to check if a residue is also another type, use the IsType methods directly.

HasAtom()

bool HasAtom

(

const Atom &

atom

)

const

IsAlphaAminoAcid()

bool IsAlphaAminoAcid

(

)

IsAminoAcid()

bool IsAminoAcid

(

)

Determine if the residue is an amino acid.

The algorithm for determining if a residue is an amino acid is as follows. First, all potential carboxylic acid and amine atoms are identified. For carbon atoms, they are classed as potential carboxylic acid atoms if they are 3 co-ordinate, have a carbonyl bond and another neighbouring oxygen atom. The additional neighbouring oxygen atom can also be accounted for by a bond between this residue and the next. For nitrogen atoms, they are classed as potential amine atoms if they have a hydrogen bond or a bond to the next residue. This allows for proline to be identified as an amino acid even though it technically is not.

Once all potential carboxylic and amine atoms are identified, shortest paths between all pairs of them are checked. If one of these paths consists of only carbon atoms, the residue is regarded as being an amino acid.

IsBetaAminoAcid()

bool IsBetaAminoAcid

(

)

IsDeltaAminoAcid()

bool IsDeltaAminoAcid

(

)

IsGammaAminoAcid()

bool IsGammaAminoAcid

(

)

IsLipid()

bool IsLipid

(

)

IsNucleicAcid()

bool IsNucleicAcid

(

)

IsSugar()

bool IsSugar

(

)

operator bool()

operator bool ( ) const

inline

operator!=()

bool operator!= ( const Residue &  res ) const

inline

operator<()

bool operator<

(

const Residue &

res

)

const

operator<=()

bool operator<= ( const Residue &  res ) const

inline

operator=() [1/2]

Residue& operator= ( const Residue &  )

default

operator=() [2/2]

Residue& operator= ( Residue &&  )

default

operator==()

bool operator==

(

const Residue &

res

)

const

operator>()

bool operator>

(

const Residue &

res

)

const

operator>=()

bool operator>= ( const Residue &  res ) const

inline

Friends And Related Function Documentation

cereal::access

friend class cereal::access

friend

Molecule

friend class Molecule

friend

operator<<

std::ostream& operator<< ( std::ostream &  os, const Residue &  res  )

friend

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

• include/indigox/classes/residue.hpp