Prevent Atlas crash when PDBe returns no exact SIFTS mapping

[CedricHermansBIT]

Bug

The Atlas verifier assumed every successful PDBe updated-mmCIF request contains exact matching SIFTS residue rows. When rows=[], ram_atlas_exact_sifts_map() returned ram_canonical_empty_map(), which lacks the Atlas-specific observed column. The subsequent ram_atlas_sifts_summary() threw Invalid exact SIFTS mapping outside the observer's tryCatch.

Fix

• Return a correctly typed, empty Atlas mapping (including observed, mon_id, label_seq_id) instead of the incomplete generic mapping.
• Add ram_atlas_verified_sifts() to validate and summarize per entity and reject an empty exact mapping with a specific, actionable message, while retaining successful mappings unchanged.
• Guard the combined mapping+summary in the Shiny observer. A failed entity displays a visible SIFTS unavailable message; sequential batch verification can continue to subsequent structures.
• A structure without exact mapping is not labelled verified and cannot silently be used in geometric clustering.

Regression

• R scientific tests check empty mappings, safe summary, explicit rejection, malformed records and successful follow-up verification.
• Real Chromium Atlas workflow verifies synthetic 4AKE_1 with zero matching SIFTS rows, checks the card error/no Shiny output error, and verifies a valid 1CRN_1 in the same session.
• Eight PR-ready CI workflows; merge only once green.

No change to the live Shinylive deployment.

[Copilot]

Copilot was unable to review this pull request because the user who requested the review has reached their quota limit.