Struct gchemol_core::Atom

pub struct Atom {
    pub properties: PropertyStore,
    /* private fields */
}

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.

Implementations

impl Atom

pub fn new<S: Into<AtomKind>, P: Into<Vector3f>>(s: S, p: P) -> Self

Construct Atom from element symbol and Cartesian coordinates.

pub fn symbol(&self) -> &str

Return element symbol

pub fn number(&self) -> usize

Return atomic number

pub fn position(&self) -> Point3

Return atom position in 3D Cartesian coordinates

pub fn set_position<P: Into<Vector3f>>(&mut self, p: P)

Set atom position in 3D Cartesian coordinates

pub fn kind(&self) -> &AtomKind

Return atom kind.

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

Set atom label

pub fn label(&self) -> &str

👎Deprecated: use get_label instead

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

pub fn get_label(&self) -> Option<&str>

Return the user defined atom label if defined.

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

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.

pub fn is_fixed(&self) -> bool

Return true if atom has freezing masks in all x, y, z coords

pub fn set_freezing(&mut self, freezing: [bool; 3])

Set freezing mask array for Cartesian coordinates

pub fn freezing(&self) -> [bool; 3]

Return freezing mask array for Cartesian coordinates

pub fn update_position<P: Into<Vector3f>>(&mut self, p: P)

Update Cartesian coordinates partially, without changing its freezing coordinate components (xyz).

impl Atom

Core data for 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 get_bonding_radius(&self) -> Option<f64>

Return bonding radius of this element if 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

Formats the value using the given formatter.

impl Default for Atom

fn default() -> Self

Returns the “default value” for a type.

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<S, P> From<(S, P)> for Atom

where S: Into<AtomKind>, P: Into<Vector3f>,

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

Converts to this type from the input type.

impl FromStr for Atom

type Err = Error

The associated error which can be returned from parsing.

fn from_str(line: &str) -> Result<Self>

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

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.