Struct Atom 

pub struct Atom {
    pub name: AtomStr,
    pub resname: AtomStr,
    pub resid: i32,
    pub resindex: usize,
    pub atomic_number: u8,
    pub mass: f32,
    pub charge: f32,
    pub type_name: AtomStr,
    pub type_id: u32,
    pub chain: char,
    pub bfactor: f32,
    pub occupancy: f32,
}

Information about the atom except its coordinates.

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: f32

Mass in atomic units

charge: f32

Charge in electroc charges.

type_name: AtomStr

Name of the atom type.

type_id: u32

Unique id of the atom type.

chain: char

bfactor: f32

occupancy: f32

PDB occupancy.

Implementations

impl Atom

pub fn new() -> Self

pub fn guess_element_from_name(&mut self)

pub fn guess_element_and_mass_from_name(&mut self)

pub fn vdw(&self) -> f32

Naive guessing of the mass and element from the atom name. Returns atom’s Van der Waals radius based on its atomic number. If the element is not recognized returns a default value of 0.15 nm (atomnum ‘0’).

Trait Implementations

impl AtomLike for Atom

fn get_name(&self) -> &str

Atom name.

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

fn get_resname(&self) -> &str

Residue name.

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

fn get_resid(&self) -> isize

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

fn set_resid(&mut self, resid: isize)

fn get_resindex(&self) -> usize

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

fn set_resindex(&mut self, resindex: usize)

fn get_atomic_number(&self) -> u8

Atomic number in the periodic table.

fn set_atomic_number(&mut self, atomic_number: u8)

fn get_mass(&self) -> f32

Mass in atomic units

fn set_mass(&mut self, mass: f32)

fn get_charge(&self) -> f32

Charge in electric charges.

fn set_charge(&mut self, charge: f32)

fn get_type_name(&self) -> &str

Name of the atom type.

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

fn get_type_id(&self) -> u32

Unique id of the atom type.

fn set_type_id(&mut self, type_id: u32)

fn get_chain(&self) -> char

PDB chain identifier.

fn set_chain(&mut self, chain: char)

fn get_bfactor(&self) -> f32

PDB B-factor.

fn set_bfactor(&mut self, bfactor: f32)

fn get_occupancy(&self) -> f32

PDB occupancy.

fn set_occupancy(&mut self, occupancy: f32)

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.