Atom
type¶Atom
¶An Atom
is a particle in the current Frame
.
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
(name::String)¶name
and set the atom type
to be the same
as name
.Atom
(frame::Frame, index::Integer)¶atom
at the given index
from a frame
.Atom
(topology::Topology, index::Integer)¶atom
at the given index
from a topology
.deepcopy
(atom::Atom)¶atom
.mass
(atom::Atom)¶atom
in atomic mass units.set_mass!
(atom::Atom, mass)¶Set the mass of an atom
to mass
.
The mass must be in atomic mass units.
charge
(atom::Atom)¶atom
in number of the electron charge e.set_charge!
(atom::Atom, charge)¶Set the charge of an atom
to charge
.
The charge must be in number of the electron charge e.
name
(atom::Atom)¶atom
.set_name!
(atom::Atom, name::String)¶atom
to name
.fullname
(atom::Atom)¶Get the full name of an atom
from the atom type.
For example, the full name of an atom with type “He” is “Helium”.
vdw_radius
(atom::Atom)¶Get the van der Waals radius of an atom
from the atom type.
If the radius can not be found, this function returns 0.
covalent_radius
(atom::Atom)¶Get the covalent radius of an atom
from the atom type.
If the radius can not be found, returns 0.
atomic_number
(atom::Atom)¶Get the atomic number of an atom
from the atom type.
If the atomic number can not be found, returns 0.
type
(atom::Atom)¶atom
.set_type!
(atom::Atom, type::String)¶atom
to type
.property
(atom::Atom, name::String)¶set_property!
(atom::Atom, name::String, value)¶properties_count
(atom::Atom)¶list_properties
(atom::Atom)¶