[mjslee0921]

RDKit EmbedMolecule can return -1 when embedding fails without raising an exception. The CCD cache generator currently treats that return as success: it changes the selected conformer ID to -1, labels it rdkit, and sets every reference-coordinate mask entry to true. This can mark missing Ideal coordinates as valid.

Preserve the initialized Ideal conformer ID, type, and per-atom mask when the returned ID is negative. Successful embeddings still select the newly generated conformer and its all-valid mask; the existing exception fallback is unchanged.

Regression tests exercise the actual RDKit failure sentinel using inconsistent distance bounds, both partial and entirely missing Ideal coordinates, actual successful conformer generation, and the exception path. They check selected metadata, unchanged existing conformers, and atom-name mapping.

Validation: all four focused tests pass. Scoped repository hooks pass after adding the required license header.

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