Edits
molex::ops::edit (source: src/ops/edit/) is the typed cross-crate
mutation route for an Assembly. The direct content mutators on Assembly
are crate-internal; an external caller mutates by building AssemblyEdit
values and applying them, so the host’s broadcast routing has a single typed
funnel. AssemblyEdit, EditError, and BulkEditError are re-exported from
molex::ops.
AssemblyEdit
AssemblyEdit covers the steady-state mutation vocabulary. Residues are
addressed by index within their parent entity’s residue list; EntityId is
the stable identifier across edits.
| Variant | Fields | Effect |
|---|---|---|
SetEntityCoords | entity, coords | Replace every atom position in the entity (coords.len() must equal atom_count) |
SetResidueCoords | entity, residue_idx, coords | Replace one residue’s atom positions (count must match; shape unchanged) |
MutateResidue | entity, residue_idx, new_name, new_atoms, new_variants | Replace a residue’s identity and atoms (count may change; later residues’ atom ranges shift) |
SetVariants | entity, residue_idx, variants | Replace a residue’s variant tag list |
AddEntity | entity (boxed) | Append an entity (id must not collide) |
RemoveEntity | entity | Remove an entity by id |
Per-residue topology (inserting or deleting a residue inside an entity) is not
enumerated; bridge consumers fall back to a full pose rebuild for that class
of change. The two topology variants (AddEntity / RemoveEntity) are
representable in memory but not on the delta wire.
Apply path
use molex::ops::AssemblyEdit;
assembly.apply_edit(&edit)?; // single edit
assembly.apply_edits(&edits)?; // batch, in orderEach successful apply bumps the assembly’s generation counter. Secondary
structure is not recomputed; call recompute_ss() afterward if a consumer
needs it. apply_edits stops at the first failing edit and returns a
BulkEditError carrying that edit’s index plus the underlying EditError;
edits applied before it stay applied.
EditError distinguishes the failure modes: UnknownEntity,
UnknownResidue, CountMismatch, NotPolymer (a per-residue edit aimed at a
non-polymer entity), and DuplicateEntity (an AddEntity whose id already
exists).
The delta wire format (Wire Format) serializes a
Vec<AssemblyEdit> for transport; topology edits are excluded there.