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Set nonzero vina seed for determinism #929

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Merged
padix-key merged 1 commit into from
Jul 18, 2026
Merged

Set nonzero vina seed for determinism #929

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3 changes: 2 additions & 1 deletion doc/examples/scripts/structure/modeling/docking.py
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Original file line number Diff line number Diff line change
Expand Up @@ -65,7 +65,8 @@
# of the original ligand position
app = autodock.VinaApp(ligand, receptor, ref_ligand_center, [20, 20, 20])
# For reproducibility
app.set_seed(0)
# (Vina interprets seed 0 as a request for a random seed, so use a non-zero one)
app.set_seed(42)
app.set_cpu(1)
# This is the maximum number:
# Vina may find less interesting binding modes
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4 changes: 3 additions & 1 deletion tests/application/test_autodock.py
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Expand Up @@ -49,7 +49,9 @@ def test_docking(flexible):
[20, 20, 20],
flexible=flexible_mask,
)
app.set_seed(0)
# A non-zero seed is required: Vina interprets seed 0 as a request for
# a random seed, which would make this test non-deterministic
app.set_seed(42)
# Single-threaded execution is required for fully reproducible
# results — even with a fixed seed, parallel Vina is not deterministic
app.set_cpu(1)
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