Struct chemfiles::Atom

pub struct Atom { /* private fields */ }

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

impl Atom

pub fn new<'a>(name: impl Into<&'a str>) -> Atom

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");

pub fn mass(&self) -> f64

Get the atom mass, in atomic mass units.

Example

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

pub fn set_mass(&mut self, mass: f64)

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);

pub fn charge(&self) -> f64

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

Example

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

pub fn set_charge(&mut self, charge: f64)

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);

pub fn name(&self) -> String

Get the atom name.

Example

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

pub fn atomic_type(&self) -> String

Get the atom type.

Example

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

pub fn set_name<'a>(&mut self, name: impl Into<&'a str>)

Set the atom name to name.

Example

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

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

pub fn set_atomic_type<'a>(&mut self, atomic_type: impl Into<&'a str>)

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");

pub fn full_name(&self) -> String

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");

pub fn vdw_radius(&self) -> f64

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);

pub fn covalent_radius(&self) -> f64

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);

pub fn atomic_number(&self) -> u64

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);

pub fn set(&mut self, name: &str, property: impl Into<Property>)

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())));

pub fn get(&self, name: &str) -> Option<Property>

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);

pub fn properties(&self) -> PropertiesIter<'_>

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

impl Clone for Atom

fn clone(&self) -> Atom

Returns a copy of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for Atom

fn fmt(&self, f: &mut Formatter<'_>) -> Result

Formats the value using the given formatter.

impl Drop for Atom

fn drop(&mut self)

Executes the destructor for this type.