Struct Atom 

pub struct Atom {

    pub name: AtomStr,
    pub resname: AtomStr,
    pub resid: i32,
    pub resindex: usize,
    pub atomic_number: u8,
    pub mass: Float,
    pub charge: Float,
    pub chain: char,
    pub bfactor: Float,
    pub occupancy: Float,
    pub type_name: Option<AtomStr>,
    pub type_id: Option<u32>,
    pub formal_charge: Option<i32>,
    pub flags: Option<AtomFlags>,
}

Information about the atom except its coordinates.

Retained as the detached, densely-packed construction/interchange row even though Topology stores atoms column-wise (Struct-of-Arrays). The four optional force-field/chemistry fields are Option — None means “never assigned”.

Fields

name: AtomStr

Atom name.

resname: AtomStr

Residue name.

resid: i32

Residue id (aka residue number). This could be negative!

resindex: usize

Residue index. Assigned when reading the topology. Unique for each contigous span of resid. Starts from zero.

atomic_number: u8

Atomic number in the periodic table.

mass: Float

Mass in atomic units

charge: Float

Partial (working) charge in electron charges. The integer formal charge is stored separately in formal_charge.

chain: char

bfactor: Float

occupancy: Float

PDB occupancy.

type_name: Option<AtomStr>

Name of the atom type (force field).

type_id: Option<u32>

Unique id of the atom type.

formal_charge: Option<i32>

Integer formal charge (e.g. from an SDF M CHG record).

flags: Option<AtomFlags>

Perceived-chemistry flags (ring membership, aromaticity, …).

Implementations

impl Atom

pub fn new() -> Self

pub fn with_name(self, name: &str) -> Self

pub fn with_resname(self, resname: &str) -> Self

pub fn with_resid(self, resid: i32) -> Self

pub fn with_resindex(self, resindex: usize) -> Self

pub fn with_atomic_number(self, n: u8) -> Self

pub fn with_mass(self, mass: Float) -> Self

pub fn with_charge(self, charge: Float) -> Self

pub fn with_chain(self, chain: char) -> Self

pub fn with_bfactor(self, bfactor: Float) -> Self

pub fn with_occupancy(self, occupancy: Float) -> Self

pub fn with_type_name(self, type_name: &str) -> Self

pub fn with_type_id(self, type_id: u32) -> Self

pub fn with_formal_charge(self, formal_charge: i32) -> Self

pub fn with_flags(self, flags: AtomFlags) -> Self

pub fn guess(self) -> Self

Chainable version of guess_element_and_mass_from_name().

pub fn hydrogen() -> Self

pub fn carbon() -> Self

pub fn nitrogen() -> Self

pub fn oxygen() -> Self

pub fn phosphorus() -> Self

pub fn sulfur() -> Self

pub fn guess_element_from_name(&mut self)

pub fn guess_element_and_mass_from_name(&mut self)

Trait Implementations

impl AtomLike for Atom

fn get_name(&self) -> &str

Atom name.

fn get_resname(&self) -> &str

Residue name.

fn get_resid(&self) -> isize

Residue id (aka residue number). This could be negative!

fn get_resindex(&self) -> usize

Residue index. Unique for each contiguous span of resid. Starts from zero.

fn get_atomic_number(&self) -> u8

Atomic number in the periodic table.

fn get_mass(&self) -> Float

Mass in atomic units.

fn get_charge(&self) -> Float

Partial (working) charge in electron charges.

fn get_chain(&self) -> char

PDB chain identifier.

fn get_bfactor(&self) -> Float

PDB B-factor.

fn get_occupancy(&self) -> Float

PDB occupancy.

fn get_type_name(&self) -> Option<&str>

Name of the atom type (force field).

fn get_type_id(&self) -> Option<u32>

Unique id of the atom type.

fn get_formal_charge(&self) -> Option<i32>

Integer formal charge (e.g. from an SDF M CHG record).

fn get_flags(&self) -> Option<AtomFlags>

Perceived-chemistry flags.

fn is_in_ring(&self) -> bool

Whether the atom is a member of some ring (false when flags are unset).

fn is_aromatic(&self) -> bool

Whether the atom belongs to an aromatic ring (false when flags are unset).

fn vdw(&self) -> Float

Van der Waals radius (nm) from the atomic number; 0.15 nm for unknown (Z=0).

impl AtomLikeMut for Atom

fn set_name(&mut self, name: &str)

fn set_resname(&mut self, resname: &str)

fn set_resid(&mut self, resid: isize)

fn set_resindex(&mut self, resindex: usize)

fn set_atomic_number(&mut self, atomic_number: u8)

fn set_mass(&mut self, mass: Float)

fn set_charge(&mut self, charge: Float)

fn set_chain(&mut self, chain: char)

fn set_bfactor(&mut self, bfactor: Float)

fn set_occupancy(&mut self, occupancy: Float)

fn set_type_name(&mut self, type_name: &str)

fn set_type_id(&mut self, type_id: u32)

fn set_formal_charge(&mut self, formal_charge: i32)

fn set_flags(&mut self, flags: AtomFlags)

fn set_in_ring(&mut self, v: bool)

fn set_aromatic(&mut self, v: bool)

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 Default for Atom

fn default() -> Self

Returns the “default value” for a type.

impl<'a> Extend<&'a Atom> for AtomStorage

fn extend<I: IntoIterator<Item = &'a Atom>>(&mut self, iter: I)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl Extend<Atom> for AtomStorage

fn extend<I: IntoIterator<Item = Atom>>(&mut self, iter: I)

Extends a collection with the contents of an iterator.

fn extend_one(&mut self, item: A)

🔬This is a nightly-only experimental API. (extend_one)

Extends a collection with exactly one element.

fn extend_reserve(&mut self, additional: usize)

🔬This is a nightly-only experimental API. (extend_one)

Reserves capacity in a collection for the given number of additional elements.

impl<T: AtomLike> From<&T> for Atom

fn from(a: &T) -> Self

Converts to this type from the input type.

impl FromIterator<Atom> for AtomStorage

fn from_iter<I: IntoIterator<Item = Atom>>(iter: I) -> Self

Creates a value from an iterator.