SASA computation fails in analysis step for example inputs (Coordinates are empty) #166

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1. buerbaumer commented on Feb 1, 2026

   

   buerbaumer

   on Feb 1, 2026

   Contributor

   More actions

   I can confirm this issue.

   Environment:

   • AWS EC2 g5.2xlarge (NVIDIA A10G, 24GB VRAM)
   • BoltzGen via Docker (CUDA 12.2.2)
   • Ubuntu 22.04

   Reproduction:

   boltzgen run example/small_molecule_from_file_and_smiles/4g37.yaml \
     --output workbench \
     --protocol protein-anything \
     --num_designs 10
   Result:
   Pipeline fails at step 5 (analysis) with ValueError: Coordinates are empty.
   
   Steps 1-4 (design, inverse_folding, folding, design_folding) complete successfully before the crash.
   
   <details> <summary>Full traceback</summary>
   
   File "/app/src/boltzgen/task/analyze/analyze.py", line 237, in run
       self.distribute_tasks()
   File "/app/src/boltzgen/task/analyze/analyze.py", line 258, in distribute_tasks
       sample_ids = self.run_parallel(num, num_processes)
   File "/app/src/boltzgen/task/analyze/analyze.py", line 214, in run_parallel
       sid = f.result()
   File "/usr/lib/python3.11/concurrent/futures/_base.py", line 401, in __get_result
       raise self._exception
   ValueError: Coordinates are empty
   </details>
   Happy to test PR #167 if helpful.
2. buerbaumer commented on Feb 1, 2026

   

   buerbaumer

   on Feb 1, 2026

   Last edited by buerbaumer

   Contributor

   More actions

   Update: Tested PR #167 - Confirmed Fix

   I tested PR #167 and can confirm it resolves this issue.

   Installation:

   pip install git+https://github.com/HannesStark/boltzgen.git@refs/pull/167/head

   Test Command:
   boltzgen run /designs/4g37.yaml --output /output --protocol protein-anything --num_designs 2 --devices 1

   Result: All 6 pipeline steps completed successfully:

   ✓ Step design completed successfully in 149.6s
   ✓ Step inverse_folding completed successfully in 11.1s
   ✓ Step folding completed successfully in 209.0s
   ✓ Step design_folding completed successfully in 209.0s
   ✓ Step analysis completed successfully in 17.5s ← Previously crashed here
   ✓ Step filtering completed successfully in 10.4s

   Output verification:

   2/2 designs made it to final_ranked_designs/
   Metrics CSV generated with all expected columns
   SASA values are empty/NaN as expected (the fix returns NaN when atom selection fails rather than crashing)
   All other metrics computed normally (pLDDT, pTM, ipTM, liabilities, etc.)
   The fix gracefully handles the edge case where SASA atom selection is empty for small molecule conjugates.

   @juliocesar-io Nice fix! This PR is ready to merge.
3. fnachon

   added a commit that references this issue on Sep 27, 2026

   Guard get_delta_sasa against empty atom selections

   ...

   This issue will close once commit 181f4fd is merged into the 'main' branch.

   181f4fd