doc update for #172: updating the docs to correctly reflect that msa … - #337
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Pana-TsK wants to merge 5 commits into
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doc update for #172: updating the docs to correctly reflect that msa …#337Pana-TsK wants to merge 5 commits into
Pana-TsK wants to merge 5 commits into
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…ct that msa related features are defined at the query level, and not at the per-chain level.
jandom
self-requested a review
July 27, 2026 13:00
jandom
approved these changes
Jul 27, 2026
Per @jnwei's review on aqlaboratory#337: the pipeline already falls back to a single-sequence MSA automatically whenever use_msas is false (data_module.py's prepare_data() calls augment_main_msa_with_query_sequence() unconditionally when use_msa_server=False), so the old wording implying users need to construct a dummy MSA themselves was inaccurate.
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Should be alright now, let me know |
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Fixes #172
use_msas,use_main_msas, anduse_paired_msasare defined onQuery(openfold3/projects/of3_all_atom/config/inference_query_format.py), not on
Chain. SinceChainhasextra: "forbid", setting any of these at thechain level raises a pydantic validation error.
This moves the field docs and examples from the per-chain sections
(3.1 Protein chains, 3.2 RNA chains) to the query-level section (Section 2),
adds a note in Section 3 pointing readers to the query-level fields, and
updates the full example JSON in Section 4 accordingly. No code changes.
Note: this branch's CI may show the "Linting code" / ruff check as failing
on docs/source/debugging_how_to.md — that's pre-existing, caused by
astral-sh/ruff-action@v3 picking up ruff 0.16.0 (which made Markdown
Python-code-block formatting default-on), unrelated to this change.