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ev-a71-2a-syndirella-run's Issues

Comparing placements on IRIS vs local

I've noticed repeatedly that some placements using Wictor fail on IRIS but are able to minimise fine locally. I'm trying to figure out why that is the case.

I've made a test_placements folder where the script wictor_place.py runs Wictor placement for two compounds in the test.csv.

Run locally I get successful minimisation. But run on IRIS I don't see successful minimisation and see this .log output:

[2024-04-04 13:41:42,252] INFO - x0528-x0450-merge-1-2 - Time taken: 0.007084369659423828
[2024-04-04 13:41:42,252] INFO - x0528-x0450-merge-1-2 - Starting work
[2024-04-04 13:41:42,253] INFO - x0528-x0450-merge-1-1 - Time taken: 0.0060999393463134766
[2024-04-04 13:41:42,254] INFO - x0528-x0450-merge-1-1 - Starting work
[2024-04-04 13:41:42,960] ERROR - x0528-x0450-merge-1-1 ?~@~T PoisonError: None has poison atoms [3, 1, 2, 0, 2, 1, 3, 0, 3, 1, 0, 2, 0, 1, 3, 2, 2, 1, 0, 3, 4, 0, 1, 2, 3, 4, 11, 7, 8, 10, 11, 7, 8, 10, 11, 7, 8, 10, 11, 7, 8, 10, 11, 5, 7, 8, 10, 11, 5, 7, 8, 10]
[2024-04-04 13:41:42,960] INFO - x0528-x0450-merge-1-1 - Time taken: 0.7128973007202148
[2024-04-04 13:41:42,965] ERROR - x0528-x0450-merge-1-2 ?~@~T PoisonError: None has poison atoms [3, 1, 2, 0, 2, 1, 3, 0, 3, 1, 0, 2, 0, 1, 3, 2, 2, 1, 0, 3, 4, 0, 1, 2, 3, 4, 10, 5, 6, 7, 10, 5, 6, 7, 10, 5, 6, 7, 10, 5, 6, 7, 10, 5, 6, 7, 9, 10, 5, 6, 7, 9]
[2024-04-04 13:41:42,966] INFO - x0528-x0450-merge-1-2 - Time taken: 0.7215840816497803

The conda environments are slightly different:
iris_environment.yml
local_environment.yml

Specifically on IRIS important packages versions:

      - rdkit==2023.3.3
      - rdkit-to-params==1.2.5
      - openbabel=3.1.1=py39hee2736e_2
      - pyrosetta=2023.40+release.96fa3c5=py39_0
      - fragmenstein==1.0.2
      - numpy==1.26.1
      - python=3.9.18=h955ad1f_0

Whereas locally:

      - rdkit==2023.3.2
      - rdkit-to-params==1.2.5
      - openbabel=3.1.1=py39h0e0ec99_2
      - pyrosetta=2023.21+release.9b3660a8932=py39_0
      - fragmenstein==1.0.2
      - numpy=1.26.4=py39h3b2db8e_0
      - python=3.9.7=hc0da0df_3_cpython

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