Atom class

class chemfiles.Atom(name, type=None)

An Atom is a particle in the current Frame. It stores the following atomic properties:

• atom name;

• atom type;

• atom mass;

• atom charge.

The atom name is usually an unique identifier ("H1", "C_a") while the atom type will be shared between all particles of the same type: "H", "Ow", "CH3".

Create a new Atom with the given name. If type is present, use it as the atom type. Else the atom name is used as atom type.

property atomic_number

Try to get the atomic number of this Atom from its type. If the atomic number can not be found, returns 0.

property charge

Get this Atom charge, in number of the electron charge e.

property covalent_radius

Try to get the covalent radius of this Atom from its type. If the radius can not be found, returns 0.

property full_name

Try to get the full name of this Atom from its type. For example, the full name of “He” is “Helium”. If the name can not be found, returns the empty string.

list_properties()

Get the name of all properties in this atom.

property mass

Get this Atom mass, in atomic mass units.

property name

Get this Atom name.

properties_count()

Get the number of properties in this atom.

property type

Get this Atom type.

property vdw_radius

Try to get the Van der Waals radius of this Atom from its type. If the radius can not be found, returns 0.