atomworks-studio 0.0.1__py3-none-any.whl

annotation_studio/__init__.py

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+"""AtomWorks Studio service and provider contracts.
+
+Keep package imports lightweight so the launch command can show help/version
+without initializing AtomWorks, model providers, or a GPU runtime.
+"""
+
+from importlib import import_module
+from typing import TYPE_CHECKING
+
+from .version import __version__
+
+if TYPE_CHECKING:
+    from .contracts import ConditionProvider, ValidationProvider
+    from .core import StudioDocument
+
+__all__ = [
+    "ConditionProvider",
+    "StudioDocument",
+    "ValidationProvider",
+    "__version__",
+]
+
+
+def __getattr__(name: str):
+    if name not in __all__:
+        raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
+    module = ".core" if name == "StudioDocument" else ".contracts"
+    value = getattr(import_module(module, __name__), name)
+    globals()[name] = value
+    return value

annotation_studio/cli.py

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+"""Launch the packaged Studio web application."""
+
+from __future__ import annotations
+
+import argparse
+import os
+from pathlib import Path
+
+from annotation_studio.version import __version__
+
+
+def main(argv: list[str] | None = None) -> None:
+    parser = argparse.ArgumentParser(description="Open AtomWorks Studio in a browser.")
+    parser.add_argument("--version", action="version", version=f"AtomWorks Studio {__version__}")
+    parser.add_argument("--host", default="127.0.0.1", help="Listen address (default: 127.0.0.1)")
+    parser.add_argument("--port", type=int, default=8000, help="Listen port (default: 8000)")
+    parser.add_argument("--vscode", action="store_true", help="Allow embedding in VS Code and Cursor")
+    args = parser.parse_args(argv)
+    if not 1 <= args.port <= 65535:
+        parser.error("--port must be between 1 and 65535")
+    package = Path(__file__).resolve().parent
+    if not any((path / "index.html").is_file() for path in (package / "web", package.parents[1] / "web" / "dist")):
+        parser.error("Browser assets are missing. Install a built wheel, or run `pnpm --dir packages/web build` first.")
+    import uvicorn
+
+    if args.vscode:
+        os.environ["ANNOTATION_STUDIO_FRAME_ANCESTORS"] = (
+            "'self' vscode-webview: vscode-file://vscode-app https://*.vscode-cdn.net"
+        )
+    print(f"AtomWorks Studio: http://{args.host}:{args.port}/", flush=True)
+    uvicorn.run("annotation_studio.main:app", host=args.host, port=args.port)

annotation_studio/contracts.py

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+"""Session errors and shared document contracts."""
+
+from __future__ import annotations
+
+from atomworks_studio_editing.contracts import (
+    NEUTRAL_CONDITION_PROVIDER as NEUTRAL_CONDITION_PROVIDER,
+)
+from atomworks_studio_editing.contracts import (
+    NEUTRAL_VALIDATION_PROVIDER as NEUTRAL_VALIDATION_PROVIDER,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionDefault as ConditionDefault,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionDefinition as ConditionDefinition,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionKind as ConditionKind,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionOperation as ConditionOperation,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionProvider as ConditionProvider,
+)
+from atomworks_studio_editing.contracts import (
+    ConditionValue as ConditionValue,
+)
+from atomworks_studio_editing.contracts import (
+    CountUnit as CountUnit,
+)
+from atomworks_studio_editing.contracts import (
+    NeutralConditionProvider as NeutralConditionProvider,
+)
+from atomworks_studio_editing.contracts import (
+    NeutralValidationProvider as NeutralValidationProvider,
+)
+from atomworks_studio_editing.contracts import (
+    ValidationProvider as ValidationProvider,
+)
+
+
+class SessionNotFoundError(KeyError):
+    """A session store could not resolve a session for the current owner."""
+
+
+class CapacityExceededError(RuntimeError):
+    """A bounded local or shared resource has reached its configured limit."""

annotation_studio/core.py

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+"""Compatibility exports for the shared Studio editing package."""
+
+from atomworks_studio_editing.document import (
+    BOND_TYPES,
+    INTERACTION_TYPES,
+    StudioDocument,
+    parse_annotated_cif,
+)
+
+__all__ = ["BOND_TYPES", "INTERACTION_TYPES", "StudioDocument", "parse_annotated_cif"]

annotation_studio/examples/README.md

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+# Design examples
+
+Eight inputs from the private RFD4 NIM, revision
+`3a8a1f6f2ed6bab37757d2471b5007971175225d`, under `nim/examples/*/request.json`.
+Motif, partial-diffusion and inverse-folding CIF contents are unchanged.
+Enzyme and VHH inputs include missing heavy atoms with free coordinates.
+Antibody and unconditional condition specs use the standard-annotation serializer;
+the antibody uses separate internal heavy/light framework groups and a fixed target.
+SAM uses the positioned conformer from RFD4’s interaction examples while leaving
+coordinate conditioning off. See `docs/PROVENANCE.md` for sources and preparation.
+
+`examples.json` pairs each CIF with its sampling task. Partial diffusion uses
+40% of the trajectory; inverse folding uses the native inverse-folding sampler.
+The model deployment chooses the native recycling preset and design count.
+Example selection does not enable refolding or establish biological design quality.
+
+`protein_binder.cif` comes from RFD4 `all_ppi.yaml:rfd3_pdl1`: a fixed PD-L1
+target, six hotspot atoms on residues 56, 115 and 123, and a separate 50–120
+residue binder segment. It uses the standard protein sampler with these conditions.
+
+Keep this directory nonpublic until release review.