Struct chemfiles::Atom

pub struct Atom { /* fields omitted */ }

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.

Methods

impl Atom

fn new<'a, S>(name: S) -> Result<Atom> where
    S: Into<&'a str>, 

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

Example

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

fn mass(&self) -> Result<f64>

Get the atom mass, in atomic mass units.

Example

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

fn set_mass(&mut self, mass: f64) -> Result<()>

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

Example

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

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

fn charge(&self) -> Result<f64>

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

Example

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

fn set_charge(&mut self, charge: f64) -> Result<()>

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

Example

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

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

fn name(&self) -> Result<String>

Get the atom name.

Example

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

fn atomic_type(&self) -> Result<String>

Get the atom type.

Example

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

fn set_name<'a, S>(&mut self, name: S) -> Result<()> where
    S: Into<&'a str>, 

Set the atom name to name.

Example

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

atom.set_name("Zn3").unwrap();
assert_eq!(atom.name(), Ok(String::from("Zn3")));

fn set_atomic_type<'a, S>(&mut self, atomic_type: S) -> Result<()> where
    S: Into<&'a str>, 

Set the atom type to atomic_type.

Example

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

atom.set_atomic_type("F").unwrap();
assert_eq!(atom.atomic_type(), Ok(String::from("F")));

fn full_name(&self) -> Result<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").unwrap();
assert_eq!(atom.full_name(), Ok(String::from("Zinc")));

fn vdw_radius(&self) -> Result<f64>

Try to get the Van der Waals radius of the atom from the atomic type. If the radius can not be found, returns -1.

Example

let atom = Atom::new("He").unwrap();
assert_eq!(atom.vdw_radius(), Ok(1.4));

fn covalent_radius(&self) -> Result<f64>

Try to get the covalent radius of the atom from the atomic type. If the radius can not be found, returns -1.

Example

let atom = Atom::new("He").unwrap();
assert_eq!(atom.covalent_radius(), Ok(0.32));

fn atomic_number(&self) -> Result<i64>

Try to get the atomic number of the atom from the atomic type. If the number can not be found, returns -1.

Example

let atom = Atom::new("He").unwrap();
assert_eq!(atom.atomic_number(), Ok(2));

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 Drop for Atom

fn drop(&mut self)

A method called when the value goes out of scope.