Crate dnagent_domain

Expand description

Biological domain types shared by every DNAgent adapter.

Modules§

amplification: Bounded offline amplification design. Reference coordinates are zero-based; input identities are one-based. No filesystem, external tools or inferred assays.
compatibility: Sequence-only restriction-end compatibility; no ligation product prediction.
digest: Conservative complete restriction digests with explicit strand and end geometry.
existing_overlaps: Assembly of declared linear fragment views with explicit exact overlaps.
feature_match: Sequence identity for the feature library: a feature’s bases in its own direction, a strand-independent key, and exact occurrences on both strands (wrapping on circles).
fragment_annotations: Source-linked annotation projections onto each digest strand’s 5′→3′ frame.
gibson: Explicit PCR-tail Gibson candidates, not thermodynamically optimised primers.
ligation: Explicit complete restriction/ligation products; no implicit copies or end reuse.
primer_optimisation: Deterministic bounded optimisation: NN annealing Tm and sequence-only structure screens. Numerical parameter provenance and scope: docs/primer-optimisation.md.
restriction: Small, explicit restriction-enzyme catalogue and sequence-only cleavage geometry. Constants verified against Biopython 1.85 Bio.Restriction; see docs/restriction.md.
translation: Translation of DNA to protein and open-reading-frame discovery.

DisplayHints: Non-biological presentation hints imported from a format.
DnaSeq: Validated, canonical uppercase IUPAC DNA.
Feature: An annotated biological feature.
FeatureId: Stable feature identifier within an artifact.
ImportedPrimer: Primer content retained during migration import.
Length: Number of bases.
Location: A feature location preserving biological identity across one or more regions.
Position: Zero-based base-boundary position.
Qualifier: Ordered, repeatable feature qualifier. A None value represents a valueless qualifier.
Region: A checked zero-based, half-open region. Construction is only through checked methods. JSON retains the tagged linear / circular_arc representation.
SequenceRecord: Imported annotated DNA artifact.