Struct AtomDynamics 

pub struct AtomDynamics {

    pub serial_number: u32,
    pub static_: bool,
    pub bonded_only: bool,
    pub force_field_type: String,
    pub element: Element,
    pub posit: Vec3,
    pub vel: Vec3,
    pub accel: Vec3,
    pub force: Vec3,
    pub mass: f32,
    pub partial_charge: f32,
    pub lj_sigma: f32,
    pub lj_eps: f32,
}

A trimmed-down atom for use with molecular dynamics. Contains parameters for single-atom, but we use ParametersIndex for multi-atom parameters.

Fields

serial_number: u32

static_: bool

Sources that affect atoms in the system, but are not themselves affected by it. E.g. in docking, this might be a rigid receptor. They serve as sources for Coulomb and LJ (non-bonded) interactions, and as anchors for bonded ones.

bonded_only: bool

If true, this atom exerts and experiences non-bonded forces only. This may be useful for protein atoms that aren’t near a docking site.

force_field_type: String

element: Element

posit: Vec3

vel: Vec3

Å / ps

accel: Vec3

Å / ps²

force: Vec3

Å • amu / ps²

mass: f32

Daltons or amu

partial_charge: f32

Amber charge units. This is not the elementary charge units found in amino19.lib and gaff2.dat; it’s scaled by the electrostatic constant.

lj_sigma: f32

Å

lj_eps: f32

kcal/mol

Implementations

impl AtomDynamics

pub fn new( atom: &AtomGeneric, atom_posits: &[Vec3], i: usize, static_: bool, bonded_only: bool, ) -> Result<Self, ParamError>

Trait Implementations

impl Clone for AtomDynamics

fn clone(&self) -> AtomDynamics

Returns a duplicate of the value.

fn clone_from(&mut self, source: &Self)

Performs copy-assignment from source.

impl Debug for AtomDynamics

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

Formats the value using the given formatter.

impl Default for AtomDynamics

fn default() -> AtomDynamics

Returns the “default value” for a type.

impl Display for AtomDynamics

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

Formats the value using the given formatter.