Struct AtomicHierarchy 

pub struct AtomicHierarchy {
    pub atoms: AtomsTable,
    pub residues: ResiduesTable,
    pub chains: ChainsTable,
    pub atom_to_residue: Segmentation,
    pub residue_to_chain: Segmentation,
    pub bonds: Bonds,
}

Topology layer: all structural data that is constant across trajectory frames.

Wrap in Arc<AtomicHierarchy> so multiple Models (frames) share one topology without duplication.

Hierarchy

Chain  ──┐
          ├── Residue ──┐
                         └── Atom

The atom_to_residue and residue_to_chain segmentations provide O(1) range queries and O(log n) reverse lookups.

Fields

atoms: AtomsTable

Per-atom topology data.

residues: ResiduesTable

Per-residue topology data.

chains: ChainsTable

Per-chain topology data.

atom_to_residue: Segmentation

Segmentation mapping atom index → residue index.

atom_to_residue.segment(res_idx) gives the range of atom indices belonging to residue res_idx.

residue_to_chain: Segmentation

Segmentation mapping residue index → chain index.

residue_to_chain.segment(chain_idx) gives the range of residue indices belonging to chain chain_idx.

bonds: Bonds

Bond connectivity.

Implementations

impl AtomicHierarchy

pub fn n_atoms(&self) -> usize

Total number of atoms.

pub fn n_residues(&self) -> usize

Total number of residues.

pub fn n_chains(&self) -> usize

Total number of chains.

pub fn atoms_in_residue(&self, res_idx: usize) -> Range<usize>

Returns the range of atom indices belonging to residue res_idx.

Panics

Panics if res_idx >= n_residues().

pub fn residues_in_chain(&self, chain_idx: usize) -> Range<usize>

Returns the range of residue indices belonging to chain chain_idx.

Panics

Panics if chain_idx >= n_chains().

pub fn residue_of_atom(&self, atom_idx: usize) -> usize

Returns the residue index that contains atom atom_idx.

O(log n) binary search over residue boundaries.

Panics

Panics if atom_idx >= n_atoms().

pub fn chain_of_residue(&self, res_idx: usize) -> usize

Returns the chain index that contains residue res_idx.

O(log n) binary search over chain boundaries.

Panics

Panics if res_idx >= n_residues().

Trait Implementations

impl Clone for AtomicHierarchy

fn clone(&self) -> AtomicHierarchy

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for AtomicHierarchy

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

Formats the value using the given formatter.