Struct AtomGeneric 

pub struct AtomGeneric {
    pub serial_number: u32,
    pub posit: Vec3,
    pub element: Element,
    pub type_in_res: Option<AtomTypeInRes>,
    pub type_in_res_general: Option<String>,
    pub force_field_type: Option<String>,
    pub partial_charge: Option<f32>,
    pub hetero: bool,
    pub occupancy: Option<f32>,
    pub alt_conformation_id: Option<String>,
}

This represents an atom, and can be used for various purposes. It is used in various format-specific molecules in this library. You may wish to augment the data here with a custom application-specific format.

Fields

serial_number: u32

A unique identifier for this atom, within its molecule. This may originate from data in mmCIF files, Mol2, SDF files, etc.

posit: Vec3

element: Element

type_in_res: Option<AtomTypeInRes>

This identifier will be unique within a given residue. For example, within an amino acid on a protein. Different residues will have different sets of these. e.g. “CG1”, “CA”, “O”, “C”, “HA”, “CD”, “C9” etc. todo: This setup might be protein/aa specific.

type_in_res_general: Option<String>

There are too many variants of this (with different numbers) for lipids, nucleic acids etc to use an enum effectively.

force_field_type: Option<String>

Used by Amber and other force fields to apply the correct molecular dynamics parameters for this atom. E.g. “c6”, “ca”, “n3”, “ha”, “h0” etc, as seen in Mol2 files from AMBER. e.g.: “ha”: hydrogen attached to an aromatic carbon. “ho”: hydrogen on a hydroxyl oxygen “n3”: sp³ nitrogen with three substitutes “c6”: sp² carbon in a pure six-membered aromatic ring (new in GAFF2; lets GAFF distinguish a benzene carbon from other aromatic caca carbons) For proteins, this appears to be the same as for name.

partial_charge: Option<f32>

An atom-centered electric charge, used in molecular dynamics simulations. In elementary charge units. These are sometimes loaded from Amber-provided Mol2 or SDF files, and sometimes added after. We get partial charge for ligands from (e.g. Amber-provided) Mol files, so we load it from the atom, vice the loaded FF params. Convert to appropriate units prior to running dynamics.

hetero: bool

Indicates, in proteins, that the atom isn’t part of an amino acid. E.g., water or ligands.

occupancy: Option<f32>

alt_conformation_id: Option<String>

Used by mmCIF files to store alternate conformations. If this isn’t None, there may be, for example, an “A” and “B” variant of this atom at slightly different positions.

Trait Implementations

impl Clone for AtomGeneric

fn clone(&self) -> AtomGeneric

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AtomGeneric

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

Formats the value using the given formatter.

impl Default for AtomGeneric

fn default() -> AtomGeneric

Returns the “default value” for a type.

impl Display for AtomGeneric

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

Formats the value using the given formatter.