Class Avogadro::Core::AtomTemplate#

template<class Molecule_T>
class Avogadro::Core::AtomTemplate#

Unnamed Group

void setAtomicNumber(unsigned char num)#

The proton count of the atom.

unsigned char atomicNumber() const#

The proton count of the atom.

Unnamed Group

void setPosition2d(const Vector2 &pos)#

The 2D position of this atom.

Note

Not all molecule types support 2D positions. If the current MoleculeType class does not, calling this method will result in a compilation error.

Vector2 position2d() const#

The 2D position of this atom.

Note

Not all molecule types support 2D positions. If the current MoleculeType class does not, calling this method will result in a compilation error.

Unnamed Group

void setPosition3d(const Vector3 &pos)#

The 3D position of this atom.

Vector3 position3d() const#

The 3D position of this atom.

Unnamed Group

void setHybridization(AtomHybridization hyb)#

The hybridization / coordination of this atom

AtomHybridization hybridization() const#

The hybridization / coordination of this atom

Unnamed Group

void setFormalCharge(signed char charge)#

The formal charge of this atom

signed char formalCharge() const#

The formal charge of this atom

Unnamed Group

void setColor(Vector3ub color)#

The color of this atom

Vector3ub color() const#

The color of this atom

Unnamed Group

void setLayer(size_t layer)#

The layer of this atom

size_t layer() const#

The layer of this atom

Public Types

typedef Molecule_T MoleculeType#

Public Functions

AtomTemplate()#

Creates a new, invalid atom object.

AtomTemplate(MoleculeType *m, Index i)#

Creates a new atom object representing the atom at index i in molecule m.

bool operator==(const AtomTemplate<MoleculeType> &other) const#
Returns

True if this and other share the same index and molecule.

bool operator!=(const AtomTemplate<MoleculeType> &other) const#
Returns

True if this and other do not share the same index or molecule.

AtomTemplate<MoleculeType> &operator++()#

Prefix increment operator. Increment this Atom’s index by 1 and return a self-reference. Check isValid() before calling any other methods.

AtomTemplate<MoleculeType> operator++(int)#

Postfix increment operator. Increment this Atom’s index by 1 and return a copy of the current Atom. Check isValid() before calling any other methods.

AtomTemplate<MoleculeType> &operator--()#

Prefix decrement operator. Decrement this Atom’s index by 1 and return a self-reference. Check isValid() before calling any other methods.

AtomTemplate<MoleculeType> operator--(int)#

Postfix decrement operator. Decrement this Atom’s index by 1 and return a copy of the current Atom. Check isValid() before calling any other methods.

bool isValid() const#
Returns

True if the molecule is set and the index is less than the number of atoms.

MoleculeType *molecule() const#
Returns

The molecule that contains this Atom.

Index index() const#
Returns

The index of this atom in molecule().

void setSelected(bool selected)#

Is the atom selected. {@

bool selected() const#
void setForceVector(const Vector3 &force)#

The force on this atom. {@

Vector3 forceVector() const#
void setLabel(const std::string &label)#
std::string label() const#