AvogadroLibs  1.96.0
Public Types | Public Member Functions | Protected Member Functions | Protected Attributes | List of all members
AtomTyper< OutputType > Class Template Referenceabstract

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

#include <avogadro/core/atomtyper.h>

Public Types

typedef OutputType ValueType
 

Public Member Functions

 AtomTyper (const Molecule *mol=nullptr)
 
void setMolecule (const Molecule *mol)
 
virtual void run ()
 
virtual OutputType atomType (const Atom &atom)
 
Array< OutputType > types () const
 
virtual void reset ()
 

Protected Member Functions

virtual void initialize ()
 
virtual OutputType type (const Atom &atom)=0
 

Protected Attributes

const Moleculem_molecule
 
Array< OutputType > m_types
 

Member Function Documentation

◆ setMolecule()

void setMolecule ( const Molecule mol)
Parameters
molThe molecule with atoms to type.

◆ run()

void run
virtual

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

◆ atomType()

OutputType atomType ( const Atom atom)
virtual

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

Returns
The type of atom.

◆ types()

Array< OutputType > types
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.

◆ reset()

void reset
virtual

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

◆ initialize()

void initialize
protectedvirtual

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.

◆ type()

virtual OutputType type ( const Atom atom)
protectedpure virtual

Determines the type of the atom.

Parameters
atomThe atom to type.
Returns
The type of atom.

Implemented in SymbolAtomTyper, and NameAtomTyper.

Member Data Documentation

◆ m_molecule

const Molecule* m_molecule
protected

The molecule on which to operate.

◆ m_types

Array<OutputType> m_types
protected

The array of types to be populated.


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