atomworks-studio 0.0.1__tar.gz

atomworks_studio-0.0.1/.gitignore

@@ -0,0 +1,25 @@
+**/__pycache__/
+**/.pytest_cache/
+**/.ruff_cache/
+**/target/
+**/node_modules
+**/dist/
+**/build/
+**/*.egg-info/
+*.vsix
+*.whl
+*.tgz
+!packages/web/vendor/patinae-viewer-0.5.1-studio.1.tgz
+artifacts/
+.cache/
+.coverage
+.env
+packages/web/src/wasm/
+!packages/web/public/annotation-studio.svg
+
+.venv/
+
+docs/_build/
+
+external/
+examples/space/wheels/

atomworks_studio-0.0.1/LICENSE.md

@@ -0,0 +1,31 @@
+BSD 3-Clause License
+
+Copyright (c) 2026, Institute for Protein Design, University of Washington
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
+
+Third-party dependencies and the Patinae patch series retain their respective
+licenses. See `docs/PROVENANCE.md` and `vendor/patinae/UPSTREAM.toml`.

atomworks_studio-0.0.1/PKG-INFO

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+Metadata-Version: 2.5
+Name: atomworks-studio
+Version: 0.0.1
+Summary: Inspect and edit annotated molecular structures
+Project-URL: Documentation, https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/index.md
+Project-URL: Source, https://github.com/RosettaCommons/atomworks-studio
+License-Expression: BSD-3-Clause
+License-File: LICENSE.md
+Requires-Python: <3.13,>=3.12
+Requires-Dist: atomworks[ml]==3.0.1
+Requires-Dist: fastapi<2,>=0.115
+Requires-Dist: numpy<3,>=1.26
+Requires-Dist: pydantic<3,>=2.10
+Requires-Dist: python-multipart<1,>=0.0.20
+Requires-Dist: uvicorn<1,>=0.34
+Provides-Extra: gradio
+Requires-Dist: gradio<7,>=6.29; extra == 'gradio'
+Requires-Dist: httpx<1,>=0.28; extra == 'gradio'
+Provides-Extra: pymol-pip
+Requires-Dist: pymol-open-source>=3.2.0a0; extra == 'pymol-pip'
+Requires-Dist: pyqt5>=5.15.11; extra == 'pymol-pip'
+Provides-Extra: test
+Requires-Dist: httpx2<3,>=2.8; extra == 'test'
+Requires-Dist: pytest<10,>=8.2; extra == 'test'
+Description-Content-Type: text/markdown
+
+<h1 align="center">AtomWorks Studio</h1>
+
+<p align="center"><b>Inspect, annotate and edit molecular structures in a browser, VS Code or PyMOL.</b></p>
+
+<p align="center">
+<a href="https://github.com/RosettaCommons/atomworks-studio/actions/workflows/ci.yaml"><img src="https://github.com/RosettaCommons/atomworks-studio/actions/workflows/ci.yaml/badge.svg" alt="CI"></a>
+<a href="https://pypi.org/project/atomworks-studio/"><img src="https://img.shields.io/pypi/v/atomworks-studio.svg" alt="PyPI"></a>
+<a href="https://pypi.org/project/atomworks-studio/"><img src="https://img.shields.io/pypi/pyversions/atomworks-studio.svg" alt="Python"></a>
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/LICENSE.md"><img src="https://img.shields.io/badge/license-BSD--3--Clause-blue.svg" alt="License: BSD-3-Clause"></a>
+<a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff"></a>
+</p>
+
+<p align="center">
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/index.md">Documentation</a> ·
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/INSTALLATION.md">Installation</a> ·
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/TUTORIAL.md">Tutorial</a>
+</p>
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/docs/images/web-molstar-editor.png" alt="AtomWorks Studio in the browser: sequence view, Mol* viewer and annotation panel" width="860"></p>
+
+Studio is a structure and annotation editor for [AtomWorks](https://github.com/RosettaCommons/atomworks)
+annotated CIF files. Select atoms, attach conditioning annotations (sequence, coordinates, hotspots,
+index groups and more), fix bonds and charges, protonate, edit chains and expandable segments, and save a
+CIF that any Studio interface reopens. It is built for preparing inputs to structure-design models such as
+[RFD4-Proteina](https://github.com/RosettaCommons/RFD4-Proteina). No model runtime or weights are needed.
+
+## Features
+
+- **One editor, three interfaces.** The browser, VS Code and native PyMOL share annotation definitions,
+  editing operations, CIF storage and Undo.
+- **Annotations you can see.** Pick a condition, apply it to a selection, and color or inspect the stored values.
+- **Selections with AtomWorks queries.** Expressions such as `chain_id == 'A' & res_id > 50` work everywhere.
+- **Structure edits with Undo.** Bonds, charges, pH-based protonation, chains, segments and validation.
+- **Two renderers in the browser.** Mol* (WebGL) by default and Patinae (WebGPU), both bundled.
+- **Design-ready examples.** Protein and small-molecule binders, antibody and nanobody CDRs, enzyme motifs,
+  motif scaffolding, inverse folding and partial diffusion.
+- **Optional Gradio host.** Adds generation controls around the same editor for hosted demos and Spaces.
+
+## Install
+
+Studio needs Python 3.12.
+
+```bash
+python -m pip install atomworks-studio
+atomworks-studio
+```
+
+Open <http://127.0.0.1:8000/>. The guide is at <http://127.0.0.1:8000/guide/>. Mol* and Patinae are
+included in the package; Node and Rust are only needed to build from source.
+
+<table>
+<tr>
+<td width="50%"><b>Browser and VS Code</b><br>Run <code>atomworks-studio</code>, or install the VSIX from the
+<a href="https://github.com/RosettaCommons/atomworks-studio/releases">releases</a> and run
+<b>AtomWorks: Open Studio</b>. The extension starts its Python backend for you.</td>
+<td width="50%"><b>PyMOL</b><br>Install the package in PyMOL's Python environment, run
+<code>atomworks-studio-pymol install</code>, then open <b>Plugin → AtomWorks Studio</b>.
+PyMOL and Qt come from your PyMOL installation.</td>
+</tr>
+</table>
+
+## Use
+
+Open a CIF, select atoms, and choose an annotation in **Edit → Annotations**. Inspect the stored values,
+change bonds or charges, protonate, or edit chains and segments. **Save CIF** writes a file that opens in any
+interface.
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/docs/images/web-annotations.png" alt="Annotations tab showing sequence, coordinate and hotspot conditioning counts" width="860"></p>
+
+The PyMOL plugin offers the same controls natively, here on a nanobody design with a hotspot on the target:
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/packages/pymol-plugin/assets/antibody_design.png" alt="AtomWorks Studio panel inside PyMOL on a nanobody design" width="860"></p>
+
+See the [documentation](https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/index.md) for selection syntax, interface guides, Python and HTTP
+integration, and development notes.
+
+## Build from source
+
+```bash
+make bootstrap
+make test
+make build
+make run
+```
+
+The RFD4 annotation definitions and license are bundled in source and release builds and verified against the
+SHA-256 hashes in `providers/rfd4/UPSTREAM.toml`. See [provenance](https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/PROVENANCE.md).
+
+## License
+
+BSD-3-Clause. See [LICENSE.md](https://github.com/RosettaCommons/atomworks-studio/blob/main/LICENSE.md).

atomworks_studio-0.0.1/README.md

@@ -0,0 +1,91 @@
+<h1 align="center">AtomWorks Studio</h1>
+
+<p align="center"><b>Inspect, annotate and edit molecular structures in a browser, VS Code or PyMOL.</b></p>
+
+<p align="center">
+<a href="https://github.com/RosettaCommons/atomworks-studio/actions/workflows/ci.yaml"><img src="https://github.com/RosettaCommons/atomworks-studio/actions/workflows/ci.yaml/badge.svg" alt="CI"></a>
+<a href="https://pypi.org/project/atomworks-studio/"><img src="https://img.shields.io/pypi/v/atomworks-studio.svg" alt="PyPI"></a>
+<a href="https://pypi.org/project/atomworks-studio/"><img src="https://img.shields.io/pypi/pyversions/atomworks-studio.svg" alt="Python"></a>
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/LICENSE.md"><img src="https://img.shields.io/badge/license-BSD--3--Clause-blue.svg" alt="License: BSD-3-Clause"></a>
+<a href="https://github.com/astral-sh/ruff"><img src="https://img.shields.io/endpoint?url=https://raw.githubusercontent.com/astral-sh/ruff/main/assets/badge/v2.json" alt="Ruff"></a>
+</p>
+
+<p align="center">
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/index.md">Documentation</a> ·
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/INSTALLATION.md">Installation</a> ·
+<a href="https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/TUTORIAL.md">Tutorial</a>
+</p>
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/docs/images/web-molstar-editor.png" alt="AtomWorks Studio in the browser: sequence view, Mol* viewer and annotation panel" width="860"></p>
+
+Studio is a structure and annotation editor for [AtomWorks](https://github.com/RosettaCommons/atomworks)
+annotated CIF files. Select atoms, attach conditioning annotations (sequence, coordinates, hotspots,
+index groups and more), fix bonds and charges, protonate, edit chains and expandable segments, and save a
+CIF that any Studio interface reopens. It is built for preparing inputs to structure-design models such as
+[RFD4-Proteina](https://github.com/RosettaCommons/RFD4-Proteina). No model runtime or weights are needed.
+
+## Features
+
+- **One editor, three interfaces.** The browser, VS Code and native PyMOL share annotation definitions,
+  editing operations, CIF storage and Undo.
+- **Annotations you can see.** Pick a condition, apply it to a selection, and color or inspect the stored values.
+- **Selections with AtomWorks queries.** Expressions such as `chain_id == 'A' & res_id > 50` work everywhere.
+- **Structure edits with Undo.** Bonds, charges, pH-based protonation, chains, segments and validation.
+- **Two renderers in the browser.** Mol* (WebGL) by default and Patinae (WebGPU), both bundled.
+- **Design-ready examples.** Protein and small-molecule binders, antibody and nanobody CDRs, enzyme motifs,
+  motif scaffolding, inverse folding and partial diffusion.
+- **Optional Gradio host.** Adds generation controls around the same editor for hosted demos and Spaces.
+
+## Install
+
+Studio needs Python 3.12.
+
+```bash
+python -m pip install atomworks-studio
+atomworks-studio
+```
+
+Open <http://127.0.0.1:8000/>. The guide is at <http://127.0.0.1:8000/guide/>. Mol* and Patinae are
+included in the package; Node and Rust are only needed to build from source.
+
+<table>
+<tr>
+<td width="50%"><b>Browser and VS Code</b><br>Run <code>atomworks-studio</code>, or install the VSIX from the
+<a href="https://github.com/RosettaCommons/atomworks-studio/releases">releases</a> and run
+<b>AtomWorks: Open Studio</b>. The extension starts its Python backend for you.</td>
+<td width="50%"><b>PyMOL</b><br>Install the package in PyMOL's Python environment, run
+<code>atomworks-studio-pymol install</code>, then open <b>Plugin → AtomWorks Studio</b>.
+PyMOL and Qt come from your PyMOL installation.</td>
+</tr>
+</table>
+
+## Use
+
+Open a CIF, select atoms, and choose an annotation in **Edit → Annotations**. Inspect the stored values,
+change bonds or charges, protonate, or edit chains and segments. **Save CIF** writes a file that opens in any
+interface.
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/docs/images/web-annotations.png" alt="Annotations tab showing sequence, coordinate and hotspot conditioning counts" width="860"></p>
+
+The PyMOL plugin offers the same controls natively, here on a nanobody design with a hotspot on the target:
+
+<p align="center"><img src="https://raw.githubusercontent.com/RosettaCommons/atomworks-studio/main/packages/pymol-plugin/assets/antibody_design.png" alt="AtomWorks Studio panel inside PyMOL on a nanobody design" width="860"></p>
+
+See the [documentation](https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/index.md) for selection syntax, interface guides, Python and HTTP
+integration, and development notes.
+
+## Build from source
+
+```bash
+make bootstrap
+make test
+make build
+make run
+```
+
+The RFD4 annotation definitions and license are bundled in source and release builds and verified against the
+SHA-256 hashes in `providers/rfd4/UPSTREAM.toml`. See [provenance](https://github.com/RosettaCommons/atomworks-studio/blob/main/docs/PROVENANCE.md).
+
+## License
+
+BSD-3-Clause. See [LICENSE.md](https://github.com/RosettaCommons/atomworks-studio/blob/main/LICENSE.md).

atomworks_studio-0.0.1/examples/README.md

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+# Example structures
+
+The **Edit → Examples** menu uses the packaged catalog in
+`packages/api/annotation_studio/examples/`. The PD-L1 protein binder and eight
+NIM inputs also power the Gradio demo; model execution is optional.
+
+The files below remain regression fixtures and can be opened with **Open CIF**:
+
+- `mcsa_ph2.cif`: catalytic residues and PH2 ligand with a 180 residue expandable
+  segment. Source: RFD4 `mcsa_40_fixed_ligand.json:M0664_2dhn`.
+- `disco_iai.cif`: IAI ligand with a 150 residue expandable segment.
+  Source: RFD4 `sm_binder.json:IAI`.
+
+The files illustrate stored annotations, ligand editing, and expandable segments.
+They open in browser, VS Code, and PyMOL without a model runtime.

atomworks_studio-0.0.1/examples/space/README.md

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+---
+title: AtomWorks Studio
+sdk: docker
+app_port: 7860
+---
+
+# AtomWorks Studio
+
+This Docker Space runs the same editor and guide as the installed application.
+It edits structures; it does not run a model.
+
+Copy this directory to a Docker Space. Put the `atomworks_studio` wheel from a verified Studio build (or the
+matching release download) in `wheels/`.
+Once the version you deploy is on PyPI, you can instead replace the `COPY` and
+wheel `pip install` lines in the Dockerfile with `pip install atomworks-studio==<version>`.
+The Docker build installs public dependencies and runs as UID 1000 on port 7860.
+
+To test locally from this directory:
+
+```bash
+docker build -t atomworks-studio-space .
+docker run --rm -p 7860:7860 atomworks-studio-space
+```
+
+Open http://localhost:7860/ or http://localhost:7860/guide/.
+Download CIFs you want to retain: the Space filesystem is ephemeral and sessions
+expire. Space access controls protect the whole application; Studio does not
+turn Hugging Face visitor identities into per-user session authorization.
+
+For model inference, use the integration guide in Studio at `/guide/INTEGRATIONS.html`.
+This image installs CPU Torch. A GPU model deployment must supply its own tested
+CUDA environment, weights, and runner; selecting GPU hardware alone does not
+turn this editor-only image into an inference server.

atomworks_studio-0.0.1/hatch_build.py

@@ -0,0 +1,45 @@
+"""Bundle the already-built browser application into Python distributions."""
+
+from __future__ import annotations
+
+import hashlib
+import shutil
+import tomllib
+from pathlib import Path
+
+from hatchling.builders.hooks.plugin.interface import BuildHookInterface
+
+
+class CustomBuildHook(BuildHookInterface):
+    """Stage Vite output and verify the pinned RFD4 definitions before each build."""
+
+    PLUGIN_NAME = "custom"
+
+    def initialize(self, version: str, build_data: dict) -> None:
+        self._bundle_rfd4_definitions(build_data)
+        if version == "editable":
+            return
+        for source_dir, name in (("packages/web/dist", "web"), ("docs/_build/html", "guide")):
+            source = Path(self.root) / source_dir
+            destination = Path(self.root) / "packages/api/annotation_studio" / name
+            if (source / "index.html").is_file():
+                shutil.rmtree(destination, ignore_errors=True)
+                shutil.copytree(source, destination, ignore=shutil.ignore_patterns(".doctrees", "__pycache__", "*.bak"))
+            elif not (destination / "index.html").is_file():
+                raise RuntimeError(f"build {source_dir} before building Studio (make build)")
+            # Also include generated assets when rebuilding a wheel from its sdist.
+            prefix = "packages/api/" if self.target_name == "sdist" else ""
+            build_data.setdefault("force_include", {})[str(destination)] = f"{prefix}annotation_studio/{name}"
+
+    def _bundle_rfd4_definitions(self, build_data: dict) -> None:
+        """Verify every pinned definition file and ship its manifest beside them."""
+        provider = Path(self.root) / "providers/rfd4"
+        source = provider / "atomworks_studio_rfd4/_upstream"
+        manifest = provider / "UPSTREAM.toml"
+        metadata = tomllib.loads(manifest.read_text())
+        for name, expected in metadata["files"].items():
+            path = source / name
+            if not path.is_file() or hashlib.sha256(path.read_bytes()).hexdigest() != expected:
+                raise RuntimeError(f"RFD4 {name} does not match pinned RosettaCommons revision {metadata['revision']}")
+        if self.target_name == "wheel":
+            build_data.setdefault("force_include", {})[str(manifest)] = "atomworks_studio_rfd4/_upstream/UPSTREAM.toml"

atomworks_studio-0.0.1/packages/api/README.md

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+# Studio API
+
+The API is included in `atomworks-studio`. Start it with `atomworks-studio`;
+use `--vscode` to allow the VS Code webview to embed it. The default address is
+`http://127.0.0.1:8000`. Interactive API documentation is at `/docs`.
+
+The API owns bounded editor sessions and delegates every mutation to
+`atomworks_studio_editing`. It loads the same annotation adapter as PyMOL.
+Routes cover CIF loading and export, selections, annotations, groups, restraints,
+protonation, bonds, chains, segments, validation, and Undo. There are no design
+or job routes.
+
+See [architecture](../../docs/ARCHITECTURE.md) and [installation](../../docs/INSTALLATION.md).

atomworks_studio-0.0.1/packages/api/annotation_studio/__init__.py

@@ -0,0 +1,30 @@
+"""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

atomworks_studio-0.0.1/packages/api/annotation_studio/cli.py

@@ -0,0 +1,31 @@
+"""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)

atomworks_studio-0.0.1/packages/api/annotation_studio/contracts.py

@@ -0,0 +1,48 @@
+"""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."""

atomworks_studio-0.0.1/packages/api/annotation_studio/core.py

@@ -0,0 +1,10 @@
+"""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"]

atomworks_studio-0.0.1/packages/api/annotation_studio/examples/README.md

@@ -0,0 +1,21 @@
+# 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.