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chore: add cache_so3_dir to sample.main #98

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Merged
sarahnlewis merged 4 commits into from
Apr 22, 2025
Merged

chore: add cache_so3_dir to sample.main #98

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7506581
conda prefix
josejimenezluna Apr 7, 2025
d1a5f9c
fix conflicts
josejimenezluna Apr 10, 2025
2de9c6e
add cache_so3_dir
josejimenezluna Apr 10, 2025
8816f65
Merge branch 'main' of https://github.com/microsoft/bioemu into jjime…
josejimenezluna Apr 10, 2025
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5 changes: 5 additions & 0 deletions src/bioemu/sample.py
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Original file line number Diff line number Diff line change
Expand Up @@ -74,6 +74,7 @@ def main(
denoiser_type: SupportedDenoisersLiteral | None = "dpm",
denoiser_config_path: str | Path | None = None,
cache_embeds_dir: str | Path | None = None,
cache_so3_dir: str | Path | None = None,
msa_host_url: str | None = None,
filter_samples: bool = True,
) -> None:
Expand All @@ -95,6 +96,7 @@ def main(
denoiser_type: Denoiser to use for sampling, if `denoiser_config_path` not specified. Comes in with default parameter configuration. Must be one of ['dpm', 'heun']
denoiser_config_path: Path to the denoiser config, defining the denoising process.
cache_embeds_dir: Directory to store MSA embeddings. If not set, this defaults to `COLABFOLD_DIR/embeds_cache`.
cache_so3_dir: Directory to store SO3 precomputations. If not set, this defaults to `~/sampling_so3_cache`.
msa_host_url: MSA server URL. If not set, this defaults to colabfold's remote server. If sequence is an a3m file, this is ignored.
filter_samples: Filter out unphysical samples with e.g. long bond distances or steric clashes.
"""
Expand All @@ -111,6 +113,9 @@ def main(
with open(model_config_path) as f:
model_config = yaml.safe_load(f)

if cache_so3_dir is not None:
model_config["sdes"]["node_orientations"]["cache_dir"] = cache_so3_dir

# User may have provided an MSA file instead of a sequence. This will be used for embeddings.
msa_file = sequence if str(sequence).endswith(".a3m") else None

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