create_A3: Create an A3 object from sequence, annotations, and metadata

In rtemis.a3: Amino Acid Annotation (A3) Format

Create an A3 object from sequence, annotations, and metadata

Description

Create an A3 object from sequence, annotations, and metadata

Usage

create_A3(
  sequence,
  site = list(),
  region = list(),
  ptm = list(),
  processing = list(),
  variant = list(),
  uniprot_id = NULL,
  description = NULL,
  reference = NULL,
  organism = NULL
)

Arguments

sequence	Character scalar: Amino acid sequence string.
site	Named list of site annotations
region	Named list of region annotations
ptm	Named list of PTM annotations
processing	Named list of processing annotations
variant	Named list of variant annotations
uniprot_id	Optional character scalar: UniProt accession.
description	Optional character scalar: Protein description.
reference	Optional character scalar: Citation or URL.
organism	Optional character scalar: Species name.

Value

A3 object

Author(s)

EDG

Examples

# Minimal: sequence only
a <- create_A3("MAEPRQEFEVMEDHAGTYGLGDRK")

# With site, region, and PTM annotations
a <- create_A3(
  "MAEPRQEFEVMEDHAGTYGLGDRK",
  site = list(
    Active_site = annotation_position(c(5L, 17L), type = "active site")
  ),
  region = list(
    Domain = annotation_range(rbind(c(3L, 10L), c(15L, 22L)),
      type = "repeat"
    )
  ),
  ptm = list(
    Phosphorylation = annotation_position(c(2L, 18L), type = "phosphoserine")
  ),
  uniprot_id = "P10636",
  organism = "Homo sapiens"
)

rtemis.a3 documentation built on April 29, 2026, 1:06 a.m.