Struct lib3dmol::structures::atom::Atom

pub struct Atom {
    pub name: String,
    pub a_type: AtomType,
    pub number: u64,
    pub coord: [f32; 3],
    pub is_backbone: bool,
    pub occupancy: Option<f32>,
    pub temp_factor: Option<f32>,
    pub element: Option<String>,
    pub charge: Option<String>,
}

An Atom is a sub-structure linked to a [Residue]. It stores the following properties

• atom name;
• a_type, the type of the Atom according to the AtomType enum
• atom number (atomid);
• Coordinates x, y and z
• if the atom is a constituant of the backbone of the protein
• occupancy
• temp_factor
• element
• charge

Parameters occupancy, temp_factor, element and charge are often not taken into account in softwares. They are store in an Option structure: None if missing and Ok if present. If a PDB is written using the write_pdb function with missing elements, they will be replaced with blank spaces.

Fields

name: String

a_type: AtomType

number: u64

coord: [f32; 3]

is_backbone: bool

occupancy: Option<f32>

temp_factor: Option<f32>

element: Option<String>

charge: Option<String>

Methods

impl Atom

pub fn new(
    name: String,
    atom_type: AtomType,
    number: u64,
    coord: [f32; 3]
) -> Atom

Create a new structure Atom. An atom have a name, a type, a number and x, y, z coordinates If the atom name is "C", "CA", "N", "O", "OT1" or "OT2", it will be consider as backbone This function set to None the parameters for occupancy, tempFactor, element and charge. If these informations are needed, use the Atom structure directly or use the Atom::new_complete function. This function should not be used for real usage and just for tests

Examples

use lib3dmol::structures::atom;

let hydrogen = atom::Atom::new(String::from("HT1"), atom::AtomType::Hydrogen, 1, [0.0, 0.0, 0.0]);
assert_eq!(hydrogen.occupancy, None);

pub fn new_complete(
    name: String,
    number: u64,
    coord: [f32; 3],
    a_type: AtomType,
    occupancy: Option<f32>,
    temp_factor: Option<f32>,
    element: Option<String>,
    charge: Option<String>
) -> Atom

Create a new complete structure Atom with all parameters

pub fn name(&self) -> String

Get the name of the Atom

pub fn compute_distance(&self, a: &Atom) -> f32

Compute the distance between 2 Atom

Examples

use lib3dmol::structures::atom;

let h1 = atom::Atom::new(String::from("HT1"), atom::AtomType::Hydrogen, 1, [1.0, 5.0, 2.0]);
let h2 = atom::Atom::new(String::from("HT1"), atom::AtomType::Hydrogen, 1, [11.0, 17.0, 5.0]);

assert_eq!(15.905973, h1.compute_distance(&h2));

pub fn get_weight(&self) -> f32

Get the weight of the Atom in g/mol based on its AtomType

Examples

use lib3dmol::structures::atom::{Atom, AtomType};

let hydrogen = Atom::new(String::from("H"), AtomType::Hydrogen, 1, [0., 0., 0.]);

assert_eq!(1.008, hydrogen.get_weight());

pub fn get_symbol(&self) -> &str

Get the 1 or 2 letters code of the Atom based on its AtomType

Examples

use lib3dmol::structures::atom::{Atom, AtomType};

let alpha_carbon = Atom::new(String::from("CA"), AtomType::Carbon, 1, [0., 0., 0.]);

assert_eq!("C", alpha_carbon.get_symbol());

pub fn get_fullname(&self) -> &str

Get the fullname of the Atom based on its AtomType

Examples

use lib3dmol::structures::atom::{Atom, AtomType};

let hydrogen = Atom::new(String::from("HG21"), AtomType::Hydrogen, 1, [0., 0., 0.]);

assert_eq!("HYDROGEN", hydrogen.get_fullname());

Trait Implementations

impl Debug for Atom

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

Formats the value using the given formatter.