Residue Class Reference

The Residue class represents a chemical residue, used commonly in the PDB format.

#include <avogadro/core/residue.h>

Public Types
enum	SecondaryStructure {   piHelix = 0 ,   bend = 1 ,   alphaHelix = 2 ,   betaSheet = 3 ,   helix310 = 4 ,   betaBridge = 5 ,   turn = 6 ,   coil = 7 ,   maybeBeta = -3 ,   undefined = -1 }
using	AtomNameMap = std::map<std::string, Atom>

Public Member Functions
	Residue ()=default
	Residue (std::string &name)
	Residue (std::string &name, Index &number)
	Residue (std::string &name, Index &number, char &id)
	Residue (const Residue &other)
Residue &	operator= (Residue other)
std::string	residueName () const
void	setResidueName (std::string &name)
Index	residueId () const
void	setResidueId (Index &number)
char	chainId () const
void	setChainId (const char &id)
SecondaryStructure	secondaryStructure () const
void	setSecondaryStructure (const SecondaryStructure &ss)
void	addResidueAtom (const std::string &name, const Atom &atom)
std::vector< Atom >	residueAtoms () const
AtomNameMap &	atomNameMap ()
void	resolveResidueBonds (Molecule &mol)
Atom	atomByName (std::string name) const
int	atomicNumber (std::string name) const
std::string	atomName (const Atom atom) const
std::string	atomName (const Index index) const
bool	hasAtomByIndex (Index index) const
void	setHeterogen (bool heterogen)
bool	isHeterogen () const
void	setColor (const Vector3ub color)
Vector3ub	color () const

Static Public Member Functions
static int	atomicNumberFromResidueData (const std::string &residueName, const std::string &atomName)

Protected Attributes
std::string	m_residueName
Index	m_residueId = std::numeric_limits<Index>::max()
char	m_chainId = 'A'
AtomNameMap	m_atomNameMap
bool	m_heterogen = false
Vector3ub	m_color = Vector3ub(0, 0, 0)
bool	m_customColorSet = false
SecondaryStructure	m_secondaryStructure = undefined

Member Typedef Documentation

AtomNameMap

using AtomNameMap = std::map<std::string, Atom>

Type for atom name map.

Constructor & Destructor Documentation

Residue()

Residue ( )

default

Creates a new, empty residue.

Member Function Documentation

addResidueAtom()

void addResidueAtom	(	const std::string &	name,
		const Atom &	atom )

Adds an atom to the residue class

residueAtoms()

std::vector< Atom > residueAtoms

(

)

const

Returns

a vector containing the atoms added to the residue

atomNameMap()

AtomNameMap & atomNameMap

(

)

Returns

the atom map for the residue

resolveResidueBonds()

void resolveResidueBonds

(

Molecule &

mol

)

Sets bonds to atoms in the residue based on data from residuedata header

atomByName()

Atom atomByName

(

std::string

name

)

const

Returns

the atom with the name specified (e.g., "CA")

atomicNumber()

int atomicNumber

(

std::string

name

)

const

Returns

the atomic number of the atom with the name specified (e.g., "CA" = "C")

atomicNumberFromResidueData()

int atomicNumberFromResidueData ( const std::string & residueName, const std::string & atomName )

static

Look up an atom name in the residue dictionary, without needing a Residue instance.

Returns

the atomic number of atom atomName in residue type residueName (e.g., "CYS", "SG" = 16), or 0 if either is unknown.

atomName() [1/2]

std::string atomName

(

const Atom

atom

)

const

Returns

the name of atom or an empty string if not in this residue

atomName() [2/2]

std::string atomName

(

const Index

index

)

const

Returns

the name of atom index or an empty string if not in this residue

setHeterogen()

void setHeterogen

(

bool

heterogen

)

Set whether this residue is a "HET" / "HETATOM" ligand

isHeterogen()

bool isHeterogen

(

)

const

Returns

is this residue a heterogen (HET / HETATM)

setColor()

void setColor

(

const Vector3ub

color

)

Set a custom color for this residue

color()

Vector3ub color

(

)

const

Returns

the color set for this residue, or a default from the chain id

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

• residue.h