Struct gchemol::Atom

pub struct Atom {
    pub properties: PropertyStore,
    // some fields omitted
}

Atom is the smallest particle still characterizing a chemical element.

Reference

https://goldbook.iupac.org/html/A/A00493.html

Fields

properties: PropertyStore

Arbitrary property stored in key-value pair. Key is a string type, but it is the responsibility of the user to correctly interpret the value.

Methods

impl Atom

pub fn new<S, P>(s: S, p: P) -> Atom where
    P: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>,
    S: Into<AtomKind>, 

pub fn symbol(&self) -> &str

Return element symbol

pub fn number(&self) -> usize

Return atomic number

pub fn position(&self) -> [f64; 3]

Return atom position in 3D Cartesian coordinates

pub fn set_position<P>(&mut self, p: P) where
    P: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

Set atom position in 3D Cartesian coordinates

pub fn kind(&self) -> &AtomKind

Return atom kind.

pub fn momentum(&self) -> [f64; 3]

Vector quantity equal to the product of mass and velocity.

pub fn set_momentum<P>(&mut self, m: P) where
    P: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>, 

TODO: momentum, momenta

pub fn set_label<S>(&mut self, lbl: S) where
    S: Into<String>, 

Set atom label

pub fn label(&self) -> &str

Return the user defined atom label, if not return the elment symbol.

pub fn set_symbol<S>(&mut self, symbol: S) where
    S: Into<AtomKind>, 

Set atom symbol.

pub fn set_partial_charge(&mut self, c: f64)

Assign atom partial charge, usually for molecular mechanical calculations.

pub fn is_dummy(&self) -> bool

Return true if atom is dummy.

pub fn is_element(&self) -> bool

Return true if atom is an element.

impl Atom

pub fn get_cov_radius(&self) -> Option<f64>

Access covalent radius of atom. Return None if no data available or atom is dummy.

pub fn get_vdw_radius(&self) -> Option<f64>

Access Van der Waals radius of atom. Return None if no data available

pub fn cov_radius(&self) -> Option<f64>

Deprecated:

use get_cov_radius instead

Access covalent radius of atom. Return None if no data available or atom is dummy.

pub fn get_mass(&self) -> Option<f64>

Get mass in atomic mass unit. Return None if atom is dummy.

pub fn vdw_radius(&self) -> Option<f64>

Deprecated:

Use get_vdw_radius instead

Access Van der Waals radius of atom. Return None if no data available

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<(), Error>

Formats the value using the given formatter.

impl Default for Atom

fn default() -> Atom

Returns the "default value" for a type.

impl<'de> Deserialize<'de> for Atom

fn deserialize<__D>(
    __deserializer: __D
) -> Result<Atom, <__D as Deserializer<'de>>::Error> where
    __D: Deserializer<'de>, 

Deserialize this value from the given Serde deserializer.

impl Display for Atom

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

Formats the value using the given formatter.

impl<S, P> From<(S, P)> for Atom where
    P: Into<Matrix<f64, U3, U1, <DefaultAllocator as Allocator<f64, U3, U1>>::Buffer>>,
    S: Into<AtomKind>, 

fn from(item: (S, P)) -> Atom

Performs the conversion.

impl FromStr for Atom

type Err = Error

The associated error which can be returned from parsing.

fn from_str(line: &str) -> Result<Atom, Error>

Parses a string s to return a value of this type.

impl Serialize for Atom

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

Serialize this value into the given Serde serializer.