boltz-vsynthes 1.0.3__py3-none-any.whl → 1.0.4__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
boltz/main.py CHANGED
@@ -678,19 +678,6 @@ def process_inputs(
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  # Create a subdirectory for this input file
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  file_out_dir = out_dir / input_file.stem
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  file_out_dir.mkdir(parents=True, exist_ok=True)
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-
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- # Check if records exist at output path
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- records_dir = file_out_dir / "processed" / "records"
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- if records_dir.exists():
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- # Load existing records
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- existing = [Record.load(p) for p in records_dir.glob("*.json")]
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- processed_ids = {record.id for record in existing}
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-
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- # Skip if already processed
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- if input_file.stem in processed_ids:
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- click.echo(f"Found existing processed input for {input_file.stem}, skipping.")
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- all_records.extend(existing)
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- continue
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  # Create output directories for this file
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  msa_dir = file_out_dir / "msa"
@@ -952,11 +939,6 @@ def cli() -> None:
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  is_flag=True,
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  help="Whether to disable the kernels. Default False",
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  )
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- @click.option(
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- "--skip_structure",
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- is_flag=True,
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- help="Skip structure prediction and go straight to affinity prediction. Default is False.",
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- )
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  def predict( # noqa: C901, PLR0915, PLR0912
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  data: str,
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  out_dir: str,
@@ -990,7 +972,6 @@ def predict( # noqa: C901, PLR0915, PLR0912
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  subsample_msa: bool = True,
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  num_subsampled_msa: int = 1024,
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  no_kernels: bool = False,
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- skip_structure: bool = False,
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  ) -> None:
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  """Run predictions with Boltz."""
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  # If cpu, write a friendly warning
@@ -1151,7 +1132,7 @@ def predict( # noqa: C901, PLR0915, PLR0912
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  precision=32 if model == "boltz1" else "bf16-mixed",
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  )
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- if filtered_manifest.records and not skip_structure:
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+ if filtered_manifest.records:
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  msg = f"Running structure prediction for {len(filtered_manifest.records)} input"
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  msg += "s." if len(filtered_manifest.records) > 1 else "."
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  click.echo(msg)
@@ -1240,14 +1221,6 @@ def predict( # noqa: C901, PLR0915, PLR0912
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  msg += "s." if len(manifest_filtered.records) > 1 else "."
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  click.echo(msg)
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- # When skipping structure prediction, we need to ensure structure files exist
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- if skip_structure:
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- for record in manifest_filtered.records:
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- structure_path = out_dir / "predictions" / record.id / f"pre_affinity_{record.id}.npz"
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- if not structure_path.exists():
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- msg = f"Structure file not found for {record.id}. Cannot run affinity prediction without structure."
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- raise FileNotFoundError(msg)
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-
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  pred_writer = BoltzAffinityWriter(
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  data_dir=processed.targets_dir,
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  output_dir=out_dir / "predictions",
@@ -1,6 +1,6 @@
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  Metadata-Version: 2.4
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  Name: boltz-vsynthes
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- Version: 1.0.3
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+ Version: 1.0.4
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  Summary: Boltz for V-Synthes
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  Requires-Python: <3.13,>=3.10
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  Description-Content-Type: text/markdown
@@ -1,5 +1,5 @@
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  boltz/__init__.py,sha256=F_-so3S40iZrSZ89Ge4TS6aZqwWyZXq_H4AXGDlbA_g,187
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- boltz/main.py,sha256=p-iXEzVh_CAkKZs2MJ7EojQQdIZnC9cYXr9Bax_PrU4,41377
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+ boltz/main.py,sha256=ZNaNplHLMr9OmLMhbivgducwbGCrn8g67WRPpuhh9GA,40084
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  boltz/data/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  boltz/data/const.py,sha256=1M-88Z6HkfKY6MkNtqcj3b9P-oX9xEXluh3qM_u8dNU,26779
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  boltz/data/mol.py,sha256=maOpPHEGX1VVXCIFY6pQNGF7gUBZPAfgSvuPf2QO1yc,34268
@@ -104,9 +104,9 @@ boltz/model/optim/scheduler.py,sha256=nB4jz0CZ4pR4n08LQngExL_pNycIdYI8AXVoHPnZWQ
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  boltz/model/potentials/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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  boltz/model/potentials/potentials.py,sha256=vev8Vjfs-ML1hyrdv_R8DynG4wSFahJ6nzPWp7CYQqw,17507
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  boltz/model/potentials/schedules.py,sha256=m7XJjfuF9uTX3bR9VisXv1rvzJjxiD8PobXRpcBBu1c,968
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- boltz_vsynthes-1.0.3.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
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- boltz_vsynthes-1.0.3.dist-info/METADATA,sha256=KQnSi_PP-_Gkz8yG3ED3-a_R4-IUlX92QZxwG8eQe8w,7171
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- boltz_vsynthes-1.0.3.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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- boltz_vsynthes-1.0.3.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
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- boltz_vsynthes-1.0.3.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
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- boltz_vsynthes-1.0.3.dist-info/RECORD,,
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+ boltz_vsynthes-1.0.4.dist-info/licenses/LICENSE,sha256=8GZ_1eZsUeG6jdqgJJxtciWzADfgLEV4LY8sKUOsJhc,1102
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+ boltz_vsynthes-1.0.4.dist-info/METADATA,sha256=5oK6_h_oPquPVFGAwT9rRFOd7F9RJ8jrC7UGKR8tRVQ,7171
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+ boltz_vsynthes-1.0.4.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
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+ boltz_vsynthes-1.0.4.dist-info/entry_points.txt,sha256=n5a5I35ntu9lmyr16oZgHPFY0b0YxjiixY7m7nbMTLc,41
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+ boltz_vsynthes-1.0.4.dist-info/top_level.txt,sha256=MgU3Jfb-ctWm07YGMts68PMjSh9v26D0gfG3dFRmVFA,6
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+ boltz_vsynthes-1.0.4.dist-info/RECORD,,