Struct AtomCollection 

pub struct AtomCollection { /* private fields */ }

Atom Collection

The core data structure of ferritin-core.

it strives to be simple, high performance, and extensible using traits.

Implementations

impl AtomCollection

pub fn new( size: usize, coords: Vec<[f32; 3]>, res_ids: Vec<i32>, res_names: Vec<String>, is_hetero: Vec<bool>, elements: Vec<Element>, atom_names: Vec<String>, chain_ids: Vec<String>, bonds: Option<Vec<Bond>>, ) -> Self

pub fn with_b_factor(self, values: Vec<f32>) -> Self

Attach per-atom B-factor (crystallographic) or pLDDT confidence values.

Used by the Uncertainty and PlddtConfidence color themes.

Panics

Panics if values.len() != self.get_size().

pub fn with_occupancy(self, values: Vec<f32>) -> Self

Attach per-atom occupancy values (0.0-1.0). Used by the Occupancy color theme.

Panics

Panics if values.len() != self.get_size().

pub fn get_b_factor(&self, idx: usize) -> Option<f32>

pub fn get_b_factors(&self) -> Option<&[f32]>

pub fn get_occupancy(&self, idx: usize) -> Option<f32>

pub fn get_occupancies(&self) -> Option<&[f32]>

pub fn calculate_chain_indices(&mut self)

pub fn connect_via_residue_names(&mut self)

pub fn get_size(&self) -> usize

pub fn get_atom_name(&self, idx: usize) -> &str

pub fn get_bonds(&self) -> Option<&Vec<Bond>>

pub fn get_chain_id(&self, idx: usize) -> &str

pub fn get_coord(&self, idx: usize) -> &[f32; 3]

pub fn get_coords(&self) -> &Vec<[f32; 3]>

pub fn get_element(&self, idx: usize) -> &Element

pub fn get_elements(&self) -> &Vec<Element>

pub fn get_is_hetero(&self, idx: usize) -> bool

pub fn get_resnames(&self) -> &[CompactString]

pub fn get_res_id(&self, idx: usize) -> &i32

pub fn get_resids(&self) -> &Vec<i32>

pub fn get_res_name(&self, idx: usize) -> &str

pub fn get_residue_start_indices(&self) -> Option<&Vec<usize>>

pub fn filter(&self, mask: &[bool]) -> AtomCollection

Filter atoms using a boolean mask, returning a new AtomCollection.

Bonds are remapped — only bonds where both endpoints survive the mask are kept, with indices adjusted to the new compact numbering.

Panics

Panics if mask.len() != self.size.

pub fn select_chain(&self, chain_id: &str) -> Vec<bool>

Build a boolean mask selecting atoms belonging to chain_id.

pub fn select_hetero(&self) -> Vec<bool>

Build a boolean mask selecting hetero atoms (ligands, solvent, etc.).

pub fn select_water(&self) -> Vec<bool>

Build a boolean mask selecting solvent atoms (HOH, WAT, H2O).

pub fn select_ion(&self) -> Vec<bool>

Build a boolean mask selecting single-atom hetero residues that are not water (ions).

pub fn select_backbone(&self) -> Vec<bool>

Build a boolean mask selecting backbone atoms (N, CA, C, O).

pub fn select_atom_name(&self, atom_name: &str) -> Vec<bool>

Build a boolean mask selecting atoms with atom_name.

pub fn select_residue_name(&self, res_name: &str) -> Vec<bool>

Build a boolean mask selecting residues with res_name (e.g. "ALA").

pub fn iter_coords_and_elements( &self, ) -> impl Iterator<Item = (&[f32; 3], &Element)>

pub fn iter_chains(&self) -> impl Iterator<Item = ChainView<'_>>

pub fn iter_residues(&self) -> impl Iterator<Item = ResidueView<'_>>

pub fn iter_residues_aminoacid(&self) -> impl Iterator<Item = ResidueView<'_>>

Iterates over amino acid residues in the collection

Returns a filtered iterator that only includes standard amino acid residues

pub fn to_model(&self) -> Model

Convert this AtomCollection to a Model representation.

Lifts the flat per-atom vectors into the hierarchical Model structure (AtomicHierarchy + AtomicConformation).

Trait Implementations

impl Clone for AtomCollection

fn clone(&self) -> AtomCollection

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl From<&Model> for AtomCollection

fn from(model: &Model) -> Self

Convert a Model to an AtomCollection.

Regenerates per-atom vectors from the hierarchy and conformation.