Annotations

Variants

pefftacular.VariantSimple dataclass

VariantSimple(
    position: int | str,
    new_amino_acid: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Single amino-acid substitution.

pefftacular.VariantComplex dataclass

VariantComplex(
    start_pos: int | str,
    end_pos: int | str,
    new_sequence: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Multi-residue variant (insertion, deletion, or substitution).

Modifications

pefftacular.ModResUnimod dataclass

ModResUnimod(
    positions: tuple[int | str, ...],
    accession: str,
    name: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Modification annotated with a UNIMOD accession.

pefftacular.ModResPsi dataclass

ModResPsi(
    positions: tuple[int | str, ...],
    accession: str,
    name: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Modification annotated with a PSI-MOD accession.

pefftacular.ModRes dataclass

ModRes(
    positions: tuple[int | str, ...],
    accession: str,
    name: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Modification with a generic accession.

Processing, bonds and proteoforms

pefftacular.Processed dataclass

Processed(
    start_pos: int | str,
    end_pos: int | str,
    accession: str,
    name: str,
    tag: str | None = None,
    annot_id: int | None = None,
)

Processed molecule annotation (signal peptide, mature protein, etc.).

pefftacular.DisulfideBond dataclass

DisulfideBond(
    annot_id_refs: tuple[int | str, ...],
    description: str | None = None,
    annot_id: int | None = None,
)

Disulfide bond linking two previously-declared modification annotations.

Per spec section 3.4.2, a \DisulfideBond references two prior ModResPsi (half-cystine) entries by their annotation IDs — not by sequence position. annot_id_refs therefore holds those referenced IDs.

pefftacular.Proteoform dataclass

Proteoform(
    proteoform_id: str,
    ranges: tuple[SequenceRange, ...],
    annot_id_refs: tuple[int, ...],
    name: str | None = None,
    annot_id: int | None = None,
)

A specific proteoform — a combination of processing events and modifications.

pefftacular.SequenceRange dataclass

SequenceRange(start: int | str, end: int | str)

A contiguous start–end range within a sequence (1-based, inclusive).