Fix unhandled exceptions in MSA parsing and PDB serialization

[mauritaniacoder99]

Description

This PR addresses two edge-case logic flaws that can cause the pipeline to crash completely due to unhandled exceptions during data processing.

1. MSA Parsing OOB Access: In alphafold/data/parsers.py, if a provided MSA contains a truncated sequence hit that is shorter than the query's active columns, the list comprehension throws an unhandled IndexError. Added a length boundary check to raise a descriptive ValueError.
2. PDB Serialization Column Shift: In alphafold/common/protein.py, if an excessively large sequence is processed, the Python formatter {:>5} dynamically expands to 6 characters. This breaks the strict fixed-width PDB format, causing OpenMM to fail with ValueError. Added a modulo truncation (% 100000) to strictly enforce PDB column boundaries.

These fixes improve the robustness of the pipeline when processing large or manually crafted datasets.

[google-cla]

Thanks for your pull request! It looks like this may be your first contribution to a Google open source project. Before we can look at your pull request, you'll need to sign a Contributor License Agreement (CLA).

View this failed invocation of the CLA check for more information.

For the most up to date status, view the checks section at the bottom of the pull request.

[mauritaniacoder99]

Hi team, just a gentle ping on this PR. The CLA is signed, all checks have passed, and there are no merge conflicts. Please let me know if you need any adjustments to the patch or if there's anything else I can provide. Thanks!