rfd4-proteina-annotated-cif

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.

Use the user-selected model checkout at RFPROTEINA_ROOT for model commands, configs, and upstream manuals. This catalog contains the skills, not that checkout. In helper examples, resolve open-models-skills/rfd4-proteina/<name>/... to its absolute installed path when the catalog and model checkout are separate.

Inputs

Required: the user-requested operation, source structure paths/provenance, and destination for authored CIFs. Optional: assembly, chains, and conditioning selections when already unambiguous. Reuse established intent; resolve any ambiguity that changes the design problem.

Instructions

1. Inspect the source, existing conditions, requested assembly, and design intent.

Ask only about ambiguities that change the design problem.

1. Read python-authoring.md for registry import,

parser selection, condition edits, expandable segments, and combining arrays.

1. Read annotators-and-selections.md

when translating structural intent into atom masks or checking installed annotation support.

1. Use the canonical condition reference

and interaction rules for condition levels, values, and model support. Do not infer support from an annotation's ability to round-trip.

1. Complete validation.md, including chemistry and

indexing review, pre-save checks, and save/reload comparison.

For a saved CIF, use bash open-models-skills/rfd4-proteina/rfd4-proteina-annotated-cif/scripts/inspect_cif.sh <file.cif> to inventory its structure, chemistry, expandable segments, and conditions. Use bash open-models-skills/rfd4-proteina/rfd4-proteina-annotated-cif/scripts/check_annotated_cif.sh <file.cif> for pipeline validation and chemistry checks. Both helpers are read-only; see the validation reference for options and limits.

Output standard

Return the annotated CIF artifacts required by the task, identifying source templates and any sampled children. Report input provenance and parse preset, selections and conditioning counts, segment and chemistry edits, validation results, and any unresolved scientific ambiguity.

Limitations

Successful parsing and round-trip checks do not establish biological correctness. Pipeline validation samples one expandable-segment realization, not every possible length.

Troubleshooting

If an import or annotation is unavailable, check the selected environment and installed registries. If validation or round-trip comparison fails, retain the source and report the specific condition or chemistry mismatch.

Examples

Inspect and validate a saved input without modifying it:

bash open-models-skills/rfd4-proteina/rfd4-proteina-annotated-cif/scripts/inspect_cif.sh input.cif
bash open-models-skills/rfd4-proteina/rfd4-proteina-annotated-cif/scripts/check_annotated_cif.sh input.cif --strict

For authoring, follow the Python recipes and save/round-trip checks.

Available Scripts