pub struct Atom { /* private fields */ }
Expand description

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.

Implementations

Create an atom with the given name, and set the atom type to name.

Example
let atom = Atom::new("He");
assert_eq!(atom.name(), "He");

Get the atom mass, in atomic mass units.

Example
let atom = Atom::new("He");
assert_eq!(atom.mass(), 4.002602);

Set the atom mass to mass, in atomic mass units.

Example
let mut atom = Atom::new("He");

atom.set_mass(34.9);
assert_eq!(atom.mass(), 34.9);

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

Example
let atom = Atom::new("He");
assert_eq!(atom.charge(), 0.0);

Set the atom charge to charge, in number of the electron charge e.

Example
let mut atom = Atom::new("He");

atom.set_charge(-2.0);
assert_eq!(atom.charge(), -2.0);

Get the atom name.

Example
let atom = Atom::new("He");
assert_eq!(atom.name(), "He");

Get the atom type.

Example
let atom = Atom::new("He");
assert_eq!(atom.atomic_type(), "He");

Set the atom name to name.

Example
let mut atom = Atom::new("He");

atom.set_name("Zn3");
assert_eq!(atom.name(), "Zn3");

Set the atom type to atomic_type.

Example
let mut atom = Atom::new("He");

atom.set_atomic_type("F");
assert_eq!(atom.atomic_type(), "F");

Try to get the full name of the atom from the atomic type. For example, the full name of “He” is “Helium”, and so on. If the name can not be found, this function returns the empty string.

Example
let atom = Atom::new("Zn");
assert_eq!(atom.full_name(), "Zinc");

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

Example
assert_eq!(Atom::new("He").vdw_radius(), 1.4);
assert_eq!(Atom::new("Xxx").vdw_radius(), 0.0);

Try to get the covalent radius of the atom from the atomic type. If the radius can not be found, returns 0.

Example
assert_eq!(Atom::new("He").covalent_radius(), 0.32);
assert_eq!(Atom::new("Xxx").covalent_radius(), 0.0);

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

Example
assert_eq!(Atom::new("He").atomic_number(), 2);
assert_eq!(Atom::new("Xxx").atomic_number(), 0);

Add a new property with the given name to this atom.

If a property with the same name already exists, this function override the existing property with the new one.

Examples
let mut atom = Atom::new("He");
atom.set("a bool", true);
atom.set("a string", "test");

assert_eq!(atom.get("a bool"), Some(Property::Bool(true)));
assert_eq!(atom.get("a string"), Some(Property::String("test".into())));

Get a property with the given name in this atom, if it exist.

Examples
let mut atom = Atom::new("He");
atom.set("foo", Property::Double(22.2));

assert_eq!(atom.get("foo"), Some(Property::Double(22.2)));
assert_eq!(atom.get("Bar"), None);

Get an iterator over all (name, property) pairs for this atom

Examples
let mut atom = Atom::new("He");
atom.set("foo", Property::Double(22.2));
atom.set("bar", Property::Bool(false));

for (name, property) in atom.properties() {
    if name == "foo" {
        assert_eq!(property, Property::Double(22.2));
    } else if name == "bar" {
        assert_eq!(property, Property::Bool(false));
    }
}

Trait Implementations

Returns a copy of the value. Read more

Performs copy-assignment from source. Read more

Executes the destructor for this type. Read more

Auto Trait Implementations

Blanket Implementations

Gets the TypeId of self. Read more

Immutably borrows from an owned value. Read more

Mutably borrows from an owned value. Read more

Returns the argument unchanged.

Calls U::from(self).

That is, this conversion is whatever the implementation of From<T> for U chooses to do.

The resulting type after obtaining ownership.

Creates owned data from borrowed data, usually by cloning. Read more

🔬 This is a nightly-only experimental API. (toowned_clone_into)

Uses borrowed data to replace owned data, usually by cloning. Read more

The type returned in the event of a conversion error.

Performs the conversion.

The type returned in the event of a conversion error.

Performs the conversion.