fix: improve error handling when no designed residues found

[buerbaumer]

Summary

Add validation in analyze.py to gracefully handle empty design masks.

Problem

When users run BoltzGen with a YAML configuration that has zero designed residues, the analysis step crashes with:

• IndexError: index 0 is out of bounds for dimension 0 with size 0

This provides no guidance on what went wrong or how to fix it.

Solution

Add early validation in compute_metrics() that detects empty design masks and returns a helpful error message:

Skipping {file}: No designed residues found. The design_mask has 0 marked residues...
Please check your design specification YAML file:

Ensure you have a 'design:' block specifying residues to redesign
Verify chain IDs and residue indices are correct
Run 'boltzgen check your_file.yaml' to validate your configuration

Test plan

• Verified patched code imports correctly
• Verified normal 6-step pipeline completes with valid YAML (1brs.yaml)
• Verified helpful error message appears with 0 designed residues
• Tested on EC2 with NVIDIA A10G GPU