Struct Atom 

pub struct Atom {
    pub element: Element,
    pub isotope: Option<u16>,
    pub charge: i8,
    pub hydrogen_count: Option<u8>,
    pub aromatic: bool,
    pub chirality: Chirality,
    pub wildcard: bool,
    pub atom_map: Option<u16>,
    pub cip_code: Option<CipCode>,
}

A single atom in a molecular graph.

• isotope: mass number (e.g. 13 for ¹³C). None = natural isotope abundance.
• charge: formal charge.
• hydrogen_count: explicit H count from a bracket atom [...]. None for organic-subset atoms whose H count is inferred from valence.
• aromatic: set when the atom is written as a lowercase letter (c, n, …) or connected via : bonds.
• wildcard: true for the SMILES * atom (any element, query context).
• atom_map: atom-mapping number used in reaction SMILES.
• cip_code: CIP stereodescriptor (R/S/E/Z). Populated by chematic_chem::assign_cip; None until then.

Fields

element: Element

isotope: Option<u16>

charge: i8

hydrogen_count: Option<u8>

Explicit H count (bracket atoms only). None for organic-subset atoms.

aromatic: bool

chirality: Chirality

wildcard: bool

True for the wildcard atom * or [*].

atom_map: Option<u16>

cip_code: Option<CipCode>

CIP stereodescriptor assigned by chematic_chem::assign_cip. None until explicitly computed.

Implementations

impl Atom

pub fn new(element: Element) -> Self

Create a plain, neutral, non-aromatic atom.

pub fn organic(element: Element) -> Self

Organic-subset atom (charge=0, non-aromatic, implicit H from valence).

pub fn aromatic(element: Element) -> Self

Aromatic organic atom (lowercase SMILES notation).

pub fn bracket( element: Element, isotope: Option<u16>, chirality: Chirality, hydrogen_count: u8, charge: i8, atom_map: Option<u16>, ) -> Self

Bracket atom with explicit properties.

pub fn wildcard() -> Self

Wildcard atom * / [*] (matches any element in query contexts).

pub fn explicit_hcount(&self) -> Option<u8>

Return the explicit H count for bracket atoms; None for organic-subset atoms.

Trait Implementations

impl Clone for Atom

fn clone(&self) -> Atom

Returns a duplicate 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 Display for Atom

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

Formats the value using the given formatter.

impl PartialEq for Atom

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

Tests for self and other values to be equal, and is used by ==.

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

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

impl Eq for Atom

impl StructuralPartialEq for Atom