RFProteína annotated CIF authoring

Purpose

An annotated CIF is a structure plus AtomWorks StandardAnnotation columns that encode the RFProteína design problem. Prefer direct Python manipulation of an AtomArrayPlus: parse, derive selection annotations, set conditions, validate, write, and round-trip. Visually inspect chemistry and intent, especially for ligands, metals, PTMs, or PDB sources.

This skill defines CIF authoring semantics. Workspace instructions and the active campaign govern shared-input ownership, output locations, length materialization, generation, and database accounting. Authoring a CIF does not by itself authorize a generation run or establish a campaign ledger policy.

Prerequisites

An RFD4-Proteina environment with AtomWorks, NumPy, Biotite, and Python Fire; access to the matching input manual and source structures.