Struct qsym2::auxiliary::atom::Atom

pub struct Atom {
    pub kind: AtomKind,
    pub atomic_number: u32,
    pub atomic_symbol: String,
    pub atomic_mass: f64,
    pub coordinates: Point3<f64>,
    pub threshold: f64,
}

Structure representing an atom.

Fields

kind: AtomKind

The atom kind.

atomic_number: u32

The atomic number of the atom.

atomic_symbol: String

The atomic symbol of the atom.

atomic_mass: f64

The weighted-average atomic mass for all naturally occuring isotopes.

coordinates: Point3<f64>

The position of the atom.

threshold: f64

A threshold for approximate equality comparisons.

Implementations

impl Atom

pub fn new_ordinary( atomic_symbol: &str, coordinates: Point3<f64>, emap: &ElementMap<'_>, thresh: f64, ) -> Atom

Creates an ordinary atom.

Arguments

• atomic_symbol - The element symbol of the atom.
• coordinates - The coordinates of the atom.
• emap - A hash map between atomic symbols and atomic numbers and masses.
• thresh - The threshold for comparing atoms.

Returns

The required ordinary atom.

pub fn new_special( kind: AtomKind, coordinates: Point3<f64>, thresh: f64, ) -> Option<Atom>

Creates a special atom.

Arguments

• kind - The required special kind.
• coordinates - The coordinates of the special atom.
• thresh - The threshold for comparing atoms.

Returns

None if kind is not one of the special atom kinds, Some(Atom) otherwise.

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<'de> Deserialize<'de> for Atom

fn deserialize<__D>(__deserializer: __D) -> Result<Self, __D::Error>

where __D: Deserializer<'de>,

Deserialize this value from the given Serde deserializer.

impl Display for Atom

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

Formats the value using the given formatter.

impl Hash for Atom

fn hash<H: Hasher>(&self, state: &mut H)

Feeds this value into the given Hasher.

fn hash_slice<H>(data: &[Self], state: &mut H)

where H: Hasher, Self: Sized,

Feeds a slice of this type into the given Hasher.

impl PartialEq for Atom

fn eq(&self, other: &Self) -> bool

The [Self::threshold] value for each atom defines a discrete grid over the real number field. All real numbers (e.g. atomic mass, coordinates) are rounded to take on the values on this discrete grid which are then used for hashing and comparisons.

fn ne(&self, other: &Rhs) -> bool

This method tests for !=. The default implementation is almost always sufficient, and should not be overridden without very good reason.

impl Serialize for Atom

fn serialize<__S>(&self, __serializer: __S) -> Result<__S::Ok, __S::Error>

where __S: Serializer,

Serialize this value into the given Serde serializer.

impl Transform for Atom

fn transform_mut(&mut self, mat: &Matrix3<f64>)

Transforms in-place the coordinates about the origin by a given transformation.

fn rotate_mut(&mut self, angle: f64, axis: &Vector3<f64>)

Rotates in-place the coordinates through angle about axis.

fn improper_rotate_mut( &mut self, angle: f64, axis: &Vector3<f64>, kind: &ImproperRotationKind, )

Improper-rotates in-place the coordinates through angle about axis.

fn translate_mut(&mut self, tvec: &Vector3<f64>)

Translates in-place the coordinates by a specified translation vector in three dimensions.

fn recentre_mut(&mut self)

Recentres in-place to put the centre of mass at the origin.

fn reverse_time_mut(&mut self)

Reverses time by reversing in-place the polarity of any magnetic special atoms.

fn transform(&self, mat: &Matrix3<f64>) -> Self

Clones and transforms the coordinates about the origin by a given transformation.

fn rotate(&self, angle: f64, axis: &Vector3<f64>) -> Self

Clones and rotates the coordinates through angle about axis.

fn improper_rotate( &self, angle: f64, axis: &Vector3<f64>, kind: &ImproperRotationKind, ) -> Self

Clones and improper-rotates the coordinates through angle about axis.

fn translate(&self, tvec: &Vector3<f64>) -> Self

Clones and translates in-place the coordinates by a specified translation in three dimensions.

fn recentre(&self) -> Self

Clones and recentres to put the centre of mass at the origin.

fn reverse_time(&self) -> Self

Clones the molecule and reverses time by reversing the polarity of any magnetic special atoms.

impl Eq for Atom