Class Avogadro::Core::AtomTyper

template<typename OutputType>
class AtomTyper

The AtomTyper class provides a base interface for generating a list of type identifiers describing the atoms in a molecule.

Public Types

typedef OutputType ValueType

Public Functions

explicit AtomTyper(const Molecule *mol = nullptr)

virtual ~AtomTyper()

void setMolecule(const Molecule *mol)

Parameters:

mol – The molecule with atoms to type.

virtual void run()

Iterate through the molecule and generate type descriptions for each atom. The results can be obtained by calling types().

virtual OutputType atomType(const Atom &atom)

Perform a type lookup on the specified atom. If run() has been called previously, a cached result is returned.

Returns:

The type of atom.

Array<OutputType> types() const

Returns:

An Array of OutputType objects. There will be one object for each atom of the input Molecule, and they are ordered by the corresponding atom’s index.

virtual void reset()

Reset the typer’s internal state. This is called when the molecule is changed. The base implementation clears the m_types Array.

Protected Functions

virtual void initialize()

Perform any setup needed that needs to be done prior to calling type(). The base implementation of this function reserves enough room in the m_types Array for the current Molecule.

virtual OutputType type(const Atom &atom) = 0

Determines the type of the atom.

Parameters:

atom – The atom to type.

Returns:

The type of atom.

Protected Attributes

const Molecule *m_molecule

The molecule on which to operate.

Array<OutputType> m_types

The array of types to be populated.