Avogadro::Core::Residue#

class Residue#

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

Public Types

enum SecondaryStructure#

Values:

enumerator piHelix#

enumerator bend#

enumerator alphaHelix#

enumerator betaSheet#

enumerator helix310#

enumerator betaBridge#

enumerator turn#

enumerator coil#

enumerator maybeBeta#

enumerator undefined#

using AtomNameMap = std::map<std::string, Atom>#: Type for atom name map.

Public Functions

Residue() = default#: Creates a new, empty residue.

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)#

virtual ~Residue() = default#

inline std::string residueName() const#

inline void setResidueName(std::string &name)#

inline Index residueId() const#

inline void setResidueId(Index &number)#

inline char chainId() const#

inline void setChainId(const char &id)#

inline SecondaryStructure secondaryStructure() const#

inline void setSecondaryStructure(const SecondaryStructure &ss)#

void addResidueAtom(const std::string &name, const Atom &atom)#: Adds an atom to the residue class

std::vector<Atom> residueAtoms() const#

Returns:: a vector containing the atoms added to the residue

inline AtomNameMap &atomNameMap()#

Returns:: the atom map for the residue

void resolveResidueBonds(Molecule &mol)#: Sets bonds to atoms in the residue based on data from residuedata header

Atom getAtomByName(std::string name) const#

Returns:: the atom with the name specified (e.g., “CA”)

int getAtomicNumber(std::string name) const#

Returns:: the atomic number of the atom with the name specified (e.g., “CA” = “C”)

std::string getAtomName(const Atom atom) const#

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

std::string getAtomName(const Index index) const#

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

bool hasAtomByIndex(Index index) const#

inline void setHeterogen(bool heterogen)#: Set whether this residue is a “HET” / “HETATOM” ligand

inline bool isHeterogen() const#

Returns:: is this residue a heterogen (HET / HETATM)

void setColor(const Vector3ub color)#: Set a custom color for this residue

Vector3ub color() const#

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

Protected Attributes

std::string m_residueName#

Index m_residueId = std::numeric_limits<Index>::max()#

char m_chainId#

AtomNameMap m_atomNameMap#

bool m_heterogen#

Vector3ub m_color#

bool m_customColorSet#

SecondaryStructure m_secondaryStructure#