Struct TopologyColumns 

pub struct TopologyColumns { /* private fields */ }

Boundary-ready, frame-independent topology columns.

Built once per Arc<AtomicHierarchy> and reused for every frame that shares it (see Self::frame). Columns whose in-memory representation is already a plain numeric array (sequence ids, segment offsets, bonds) are borrowed from the hierarchy; everything else is encoded into owned buffers:

Column	Type	Encoding
atom.element	u8	atomic number
atom.alt_loc	u32	Unicode scalar, NO_ALT_LOC if absent
atom.formal_charge	i8	charge, NO_FORMAL_CHARGE if absent
residue.ins_code	u32	Unicode scalar, NO_INS_CODE if absent
residue.group	u8	RESIDUE_GROUP_POLYMER / RESIDUE_GROUP_NON_POLYMER
residue.label_seq_id	i32	MISSING_SEQ_ID if absent
string fields	u32 codes	StringDictionary

Ownership and invalidation

The snapshot holds a clone of the Arc<AtomicHierarchy> it was built from. While it is alive, that hierarchy cannot be mutated in place: Arc::get_mut fails and Arc::make_mut clones. So the snapshot never silently goes out of date — a model whose hierarchy was replaced or copied-on-write simply stops matching, which Self::is_current_for and Self::frame detect by pointer identity.

Implementations

impl TopologyColumns

pub fn encode(hierarchy: &Arc<AtomicHierarchy>) -> Result<Self, BoundaryError>

Validate hierarchy and encode its columns.

pub fn from_model(model: &Model) -> Result<Self, BoundaryError>

Encode the topology of model.

pub fn hierarchy(&self) -> &Arc<AtomicHierarchy>

The hierarchy this snapshot was built from (and keeps alive).

pub fn is_current_for(&self, model: &Model) -> bool

Whether model still uses the exact hierarchy this snapshot describes.

pub fn frame<'m>( &self, model: &'m Model, ) -> Result<FrameColumns<'m>, BoundaryError>

Borrow the per-frame columns of model, checking it shares this topology.

Fails with StaleTopology if it does not.

pub fn n_atoms(&self) -> u32

Number of atoms.

pub fn n_residues(&self) -> u32

Number of residues.

pub fn n_chains(&self) -> u32

Number of chains.

pub fn n_bonds(&self) -> u32

Number of bonds.

pub fn atom_name(&self) -> &StringDictionary

atom.name (label_atom_id).

pub fn auth_atom_name(&self) -> &StringDictionary

atom.auth_name (auth_atom_id).

pub fn element(&self) -> &[u8]

atom.element as atomic numbers.

pub fn alt_loc(&self) -> &[u32]

atom.alt_loc as Unicode scalars (NO_ALT_LOC if absent).

pub fn formal_charge(&self) -> &[i8]

atom.formal_charge (NO_FORMAL_CHARGE if absent).

pub fn comp_id(&self) -> &StringDictionary

residue.comp_id (label_comp_id).

pub fn auth_comp_id(&self) -> &StringDictionary

residue.auth_comp_id.

pub fn label_seq_id(&self) -> &[i32]

residue.label_seq_id (borrowed from the hierarchy).

pub fn auth_seq_id(&self) -> &[i32]

residue.auth_seq_id (borrowed from the hierarchy).

pub fn ins_code(&self) -> &[u32]

residue.ins_code as Unicode scalars (NO_INS_CODE if absent).

pub fn residue_group(&self) -> &[u8]

residue.group codes.

pub fn label_asym_id(&self) -> &StringDictionary

chain.label_asym_id.

pub fn auth_asym_id(&self) -> &StringDictionary

chain.auth_asym_id.

pub fn entity_id(&self) -> &StringDictionary

chain.entity_id.

pub fn residue_atom_offsets(&self) -> &[u32]

CSR offsets grouping atoms into residues (n_residues + 1 entries).

pub fn chain_residue_offsets(&self) -> &[u32]

CSR offsets grouping residues into chains (n_chains + 1 entries).

pub fn bond_atom_a(&self) -> &[u32]

First atom of each bond, sorted ascending.

pub fn bond_atom_b(&self) -> &[u32]

Second atom of each bond.

pub fn bond_order(&self) -> &[u8]

Bond order of each bond.

pub fn atom_bond_offsets(&self) -> &[u32]

CSR offsets grouping bonds by atom_a (n_atoms + 1 entries).

pub fn columns(&self) -> Vec<Column<'_>>

Every numeric topology column, including dictionary codes, by stable name.

Dictionary value tables are not listed; fetch them from the matching StringDictionary accessor.

pub fn bond_line_indices(&self) -> GpuBuffer<'static>

Bonds as an interleaved [atom_a, atom_b] u32 index buffer, ready to use as a GPU line-list index buffer. Always an owned copy.

pub fn residue_of( &self, atom: AtomHandle, ) -> Result<ResidueHandle, BoundaryError>

Residue containing atom.

pub fn chain_of( &self, residue: ResidueHandle, ) -> Result<ChainHandle, BoundaryError>

Chain containing residue.

pub fn atoms_of( &self, residue: ResidueHandle, ) -> Result<Range<u32>, BoundaryError>

Atom rows belonging to residue.

pub fn residues_of( &self, chain: ChainHandle, ) -> Result<Range<u32>, BoundaryError>

Residue rows belonging to chain.

Trait Implementations

impl Clone for TopologyColumns

fn clone(&self) -> TopologyColumns

Returns a duplicate of the value.

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

Performs copy-assignment from source.

impl Debug for TopologyColumns

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

Formats the value using the given formatter.