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 calculate_displacement(&self)

pub fn calculate_distance(&self, _atoms: AtomCollection)

pub fn connect_via_residue_names(&mut self)

pub fn connect_via_distance(&self) -> Vec<Bond>

pub fn get_size(&self) -> usize

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

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

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

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) -> &Vec<String>

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

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

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

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

pub fn iter_residues_all(&self) -> ResidueIter<'_>

Iter_Residues Will Iterate Through the AtomCollection one Residue at a time.

This is the base for any other residue filtration code.

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

pub fn select(&self) -> AtomSelector<'_>

pub fn select_by_chain(&self, chain_id: &str) -> Selection

pub fn select_by_residue(&self, res_name: &str) -> Selection

pub fn view(&self, selection: Selection) -> AtomView<'_>

Trait Implementations

impl From<&PDB> for AtomCollection

fn from(pdb_data: &PDB) -> Self

Converts to this type from the input type.

impl<'a> FromIterator<ResidueAtoms<'a>> for AtomCollection

fn from_iter<T: IntoIterator<Item = ResidueAtoms<'a>>>(iter: T) -> Self

Creates a value from an iterator.

impl StructureFeatures for AtomCollection

fn decode_amino_acids(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn encode_amino_acids(&self, device: &Device) -> Result<Tensor>

Convert amino acid sequence to numeric representation

fn create_CB(&self, device: &Device) -> Result<Tensor>

Calcualte CB for each residue

fn get_res_index(&self) -> Vec<u32>

Get residue indices

fn to_numeric_backbone_atoms(&self, device: &Device) -> Result<Tensor>

create numeric Tensor of shape [1, , 4, 3] where the 4 is N/CA/C/O

fn to_numeric_atom37(&self, device: &Device) -> Result<Tensor>

create numeric Tensor of shape [1, , 37, 3]

fn to_numeric_ligand_atoms( &self, device: &Device, ) -> Result<(Tensor, Tensor, Tensor)>

Extract ligand atom coordinates and properties