Atom
type¶
- type
Atom
¶ An
Atom
is a particle in the currentFrame
.- 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”.
- function
Atom
(name::String)¶ - Create an atom with the given
name
and set the atomtype
to be the same asname
.
- function
Atom
(frame::Frame, index::Integer)¶ - Get a copy of the
atom
at the givenindex
from aframe
.
- function
Atom
(topology::Topology, index::Integer)¶ - Get a copy of the
atom
at the givenindex
from atopology
.
- function
deepcopy
(atom::Atom)¶ - Make a deep copy of an
atom
.
- function
mass
(atom::Atom)¶ - Get the mass of an
atom
in atomic mass units.
- function
set_mass!
(atom::Atom, mass)¶ Set the mass of an
atom
tomass
.The mass must be in atomic mass units.
- function
charge
(atom::Atom)¶ - Get the charge of an
atom
in number of the electron charge e.
- function
set_charge!
(atom::Atom, charge)¶ Set the charge of an
atom
tocharge
.The charge must be in number of the electron charge e.
- function
name
(atom::Atom)¶ - Get the name of an
atom
.
- function
set_name!
(atom::Atom, name::String)¶ - Set the name of an
atom
toname
.
- function
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”.
- function
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.
- function
covalent_radius
(atom::Atom)¶ Get the covalent radius of an
atom
from the atom type.If the radius can not be found, returns 0.
- function
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.
- function
type
(atom::Atom)¶ - Get the type of an
atom
.
- function
set_type!
(atom::Atom, type::String)¶ - Set the type of an
atom
totype
.
- function
property
(atom::Atom, name::String)¶ - Get a named property for the given atom.
- function
set_property!
(atom::Atom, name::String, value)¶ - Set a named property for the given atom.
- function
properties_count
(atom::Atom)¶ - Get the number of properties associated with an atom.
- function
list_properties
(atom::Atom)¶ - Get the names of all properties associated with an atom.