AvogadroLibs  1.96.0
Public Types | Public Member Functions | Protected Attributes | List of all members
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 ,
  undefined = -1
}
 
typedef std::map< std::string, AtomAtomNameMap
 

Public Member Functions

 Residue ()
 
 Residue (std::string &name)
 
 Residue (std::string &name, Index &number)
 
 Residue (std::string &name, Index &number, char &id)
 
 Residue (const Residue &other)
 
Residueoperator= (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< AtomresidueAtoms () const
 
AtomNameMapatomNameMap ()
 
void resolveResidueBonds (Molecule &mol)
 
Atom getAtomByName (std::string name) const
 
int getAtomicNumber (std::string name) const
 
bool hasAtomByIndex (Index index) const
 
void setHeterogen (bool heterogen)
 
bool isHeterogen () const
 
void setColor (const Vector3ub color)
 
const Vector3ub color () const
 

Protected Attributes

std::string m_residueName
 
Index m_residueId
 
char m_chainId
 
AtomNameMap m_atomNameMap
 
bool m_heterogen
 
Vector3ub m_color
 
bool m_customColorSet
 
SecondaryStructure m_secondaryStructure
 

Member Typedef Documentation

◆ AtomNameMap

typedef std::map<std::string, Atom> AtomNameMap

Type for atom name map.

Constructor & Destructor Documentation

◆ Residue()

Residue ( )

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

◆ getAtomByName()

Atom getAtomByName ( std::string  name) const
Returns
the atom with the name specified (e.g., "CA")

◆ getAtomicNumber()

int getAtomicNumber ( std::string  name) const
Returns
the atomic number of the atom with the name specified (e.g., "CA" = "C")

◆ 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()

const Vector3ub color ( ) const
Returns
the color set for this residue, or a default from the chain id

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