Set nonzero vina seed for determinism

[jberg5]

Should fix this failing test:

=========================== short test summary info ============================
FAILED tests/application/test_autodock.py::test_docking[True] - assert np.float32(2.6669219) < 2.0
 +  where np.float32(2.6669219) = <function max at 0x7feb411b0f70>(array([0., 0., 0., ..., 0., 0., 0.], shape=(1776,), dtype=float32))
 +    where <function max at 0x7feb411b0f70> = np.max
 +    and   array([0., 0., 0., ..., 0., 0., 0.], shape=(1776,), dtype=float32) = <function distance at 0x7feb189d28e0>(array([[38.607, 14.202, 18.949],\n       [39.073, 14.187, 17.510],\n       [38.898, 15.623, 16.986],\n       ...,\n       ...49, 23.656,  8.504],\n       [49.002, 21.454,  6.825],\n       [50.497, 22.367,  7.110]], shape=(1776, 3), dtype=float32), array([\n	Atom(np.array([ 31.137,  21.711, -13.344], dtype=float32), chain_id="B", res_id=84, ins_code="", res_name="ARG", hetero=False, atom_name="CD", element="C", charge=0),\n	...,\n]))
 +      where <function distance at 0x7feb189d28e0> = struc.distance
= 1 failed, 943 passed, 7 skipped, 4 xpassed, 14 warnings in 157.23s (0:02:37) =

Reason for this is pretty wild, apparently Vina interprets 0 as "please give me a random seed"

https://github.com/ccsb-scripps/AutoDock-Vina/blob/3c65c0b3e6c2c1d183f6a175ecb65e3c5ba91645/src/lib/vina.cpp#L56

[padix-key]

Nice find! I already wondered why the docking results in the tests were still not deterministic.

[codspeed-hq]

Merging this PR will improve performance by 15.07%

⚡ 2 improved benchmarks
✅ 101 untouched benchmarks
⏩ 14 skipped benchmarks¹

Performance Changes

	Benchmark	BASE	HEAD	Efficiency
⚡	benchmark_match_kmer_selection[BucketKmerTable(10000)-None]	353.3 µs	303.7 µs	+16.32%
⚡	benchmark_match[BucketKmerTable(10000)-None]	401.2 µs	352.5 µs	+13.82%

Tip

Curious why this is faster? Comment @codspeedbot explain why this is faster on this PR, or directly use the CodSpeed MCP with your agent.

---

_{Comparing jberg5:set-vina-seed (e46d9e8) with main (1fa1b70)}

Footnotes

1. 14 benchmarks were skipped, so the baseline results were used instead. If they were deleted from the codebase, click here and archive them to remove them from the performance reports. ↩

[jberg5]

Thank you!! It is totally reasonable to assume that seed(0) means "use 0 as the random seed", I was extremely surprised to find out that autodock-vina has other ideas :)