Atom

An Atom is a particle in the current Frame.

An atom 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 among all particles of the same type: "H", "Ow", "CH3".

Atom(frame::Frame, index::Integer) -> Chemfiles.Atom

Get a copy of the atom at the given index from a frame.

Atom(name::String) -> Chemfiles.Atom

Create an atom with the given name and set the atom type to be the same as name.

Atom(topology::Topology, index::Integer) -> Chemfiles.Atom

Get a copy of the atom at the given index from a topology.

atomic_number(atom::Chemfiles.Atom) -> UInt64

Get the atomic number of an atom from the atom type.

If the atomic number can not be found, returns 0.

deepcopy(atom::Chemfiles.Atom) -> Chemfiles.Atom

Make a deep copy of an atom.

fullname(atom::Chemfiles.Atom) -> String

Get the full name of an atom from the atom type.

For example, the full name of an atom with type "He" is "Helium".

charge(atom::Chemfiles.Atom) -> Float64

Get the charge of an atom in number of the electron charge e.

covalent_radius(atom::Chemfiles.Atom) -> Float64

Get the covalent radius of an atom from the atom type.

If the radius can not be found, returns 0.

list_properties(atom::Chemfiles.Atom) -> Vector{String}

Get the names of all properties associated with an atom.

mass(atom::Chemfiles.Atom) -> Float64

Get the mass of an atom in atomic mass units.

name(atom::Chemfiles.Atom) -> String

Get the name of an atom.

properties_count(atom::Chemfiles.Atom) -> Int64

Get the number of properties associated with an atom.

property(atom::Chemfiles.Atom, name::String) -> Any

Get a named property for the given atom.

set_charge!(atom::Chemfiles.Atom, charge)

Set the charge of an atom to charge.

The charge must be in number of the electron charge e.

set_mass!(atom::Chemfiles.Atom, mass)

Set the mass of an atom to mass.

The mass must be in atomic mass units.

set_name!(atom::Chemfiles.Atom, name::String)

Set the name of an atom to name.

set_property!(
    atom::Chemfiles.Atom,
    name::String,
    value::Union{Bool, Float64, String, Vector{Float64}}
)

Set a named property for the given atom.

set_type!(atom::Chemfiles.Atom, type::String)

Set the type of an atom to type.

type(atom::Chemfiles.Atom) -> String

Get the type of an atom.

vdw_radius(atom::Chemfiles.Atom) -> Float64

Get the van der Waals radius of an atom from the atom type.

If the radius can not be found, this function returns 0.