fix ion feature metadata

[MoritzErtelt]

Summary

• Fix ion-containing inference inputs, such as protein + Zn, when MSA or template features are enabled.
• Preserve ion entities in the asymmetric-chain metadata used for feature-coordinate mapping.
• Prevent map_to_standard() failures caused by missing or shifted ion chain metadata.

Root cause

• The general input parser supported ion entities, but the inference MSA and template featurizers only constructed metadata for proteins, nucleic acids, and ligands.
• Ion entities therefore did not advance the asymmetric-chain index or receive placeholder sequence metadata.
• This caused missing or shifted asymmetric-chain IDs when mapping complete atom/token representations into MSA and template coordinates.

Changes

• Add explicit ion handling to InferenceMSAFeaturizer.
• Add equivalent ion handling to InferenceTemplateFeaturizer.
• Treat ions as non-polymer entities while preserving the existing ligand path.
• Generate the placeholder sequence independently for each ion copy from its centre-atom count.
• Correctly advance asymmetric-chain indexing for single ions, multiple ion copies, and separate ion entities.
• Keep the implementation generic for supported ions rather than special-casing Zn.

Test coverage

• Add CPU regression tests for both MSA and template feature construction.
• Cover protein followed by an ion.
• Cover an ion followed by protein.
• Cover an ion entity with count: 2.
• Cover protein + ligand + ion inputs.
• Cover multiple independent ion entities.
• Cover an ion positioned between two protein entities.
• Verify that MSA, profile, and template feature dimensions match the complete atom/token representation.

Validation

• Confirmed that the regression tests reproduce the original asymmetric-chain mapping failure before the fix.
• Confirmed that the focused ion metadata tests pass after the fix.
• Confirmed that the full CPU test suite passes.
• Confirmed successful GPU inference for a protein + Zn input with MSA enabled.
• Confirmed that the resulting structure and confidence outputs are generated with valid indexing.

[mrzzmrzz]

LGTM. Thanks for fixing the ion feature metadata and adding regression coverage!