boltz2-python-client 0.5.2.post1__tar.gz → 0.6.0__tar.gz

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/CHANGELOG.md

@@ -1,3 +1,21 @@
+# 0.6.0 — 2026-09-11
+
+- Target NIM 1.9.0: diffusion concurrency and affinity embeddings.
+- Correct PAE/PDE documentation to server-side NPZ artifacts.
+- Reject unknown/malformed request fields; accept protein X residues.
+- Fix YAML affinity conversion and missing-MSA handling.
+- Bound hosted polling, preserve HTTP errors, choose hosted URL automatically.
+- Save complete responses, all scores, and affinity embeddings.
+- Refresh notebooks, deployment instructions, examples and release validation.
+- Consolidate seven notebooks into five numbered workflows, fold A3M pairing
+  into protein complexes, and move the SageMaker connection example into docs.
+  Show actual NIM/client versions, restore the mature barstar sequence, correct
+  DNA strand complementarity, and validate supplied MSA query sequences.
+- Require Python 3.10+; make visualization an optional notebook extra.
+- Forward NIM parameters through async/sync multi-endpoint methods.
+- Return a nonzero CLI status when compound screening fails; report unsupported hosted readiness/metadata calls explicitly.
+- Consolidate duplicate examples and guides; validate actual notebook kernels, viewers, Python methods and Bash CLI workflows.
+
 # Changelog
 
 All notable changes to this project will be documented in this file.
@@ -18,9 +36,9 @@ environment should upgrade to `0.5.2.post1`; users who already have
   followed by `import boltz2_client` raised
   `ModuleNotFoundError: No module named 'pandas'`. The pandas import is
   now deferred into the four methods that actually need it
-  (`CompoundLibrary.from_csv`, `ScreeningResults.to_dataframe`,
-  `ScreeningResults.get_top_hits`,
-  `ScreeningResults.get_statistics_by_group`); calling any of those
+  (`CompoundLibrary.from_csv`, `VirtualScreeningResult.to_dataframe`,
+  `VirtualScreeningResult.get_top_hits`,
+  `VirtualScreeningResult.get_statistics_by_group`); calling any of those
   methods still requires pandas, but importing the package, the CLI,
   and every other code path no longer does. Callers who use the virtual
   screening DataFrame helpers should install with

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/MANIFEST.in

@@ -5,7 +5,9 @@ recursive-include docs *.md
 recursive-include licenses *.md *.txt LICENSE* *-LICENSE
 recursive-include boltz2_client *.py
 recursive-include examples *.py *.yaml *.a3m *.ipynb *.md *.json *.txt *.sh
-recursive-include tests *.py
+recursive-include tests *.py *.json *.a3m *.fasta
+recursive-include scripts *.py *.sh
+include pytest.ini
 recursive-exclude * __pycache__
 recursive-exclude * *.py[co]
 recursive-exclude * .DS_Store

boltz2_python_client-0.6.0/PKG-INFO

@@ -0,0 +1,221 @@
+Metadata-Version: 2.2
+Name: boltz2-python-client
+Version: 0.6.0
+Summary: Python client for Boltz-2 protein structure prediction API with covalent complex and multi-endpoint support
+Author-email: NVIDIA Corporation <bionemo-support@nvidia.com>
+Maintainer-email: NVIDIA Corporation <bionemo-support@nvidia.com>
+License: MIT
+Project-URL: Homepage, https://github.com/NVIDIA/digital-biology-examples/tree/main/examples/nims/boltz-2
+Project-URL: Repository, https://github.com/NVIDIA/digital-biology-examples
+Project-URL: Documentation, https://github.com/NVIDIA/digital-biology-examples/tree/main/examples/nims/boltz-2/docs
+Project-URL: Changelog, https://github.com/NVIDIA/digital-biology-examples/blob/main/examples/nims/boltz-2/CHANGELOG.md
+Project-URL: Bug Reports, https://github.com/NVIDIA/digital-biology-examples/issues
+Keywords: protein,structure,prediction,AI,machine learning,bioinformatics,covalent,complex,boltz2
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Science/Research
+Classifier: Intended Audience :: Developers
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Programming Language :: Python :: 3.12
+Classifier: Programming Language :: Python :: 3.13
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Topic :: Scientific/Engineering :: Artificial Intelligence
+Classifier: Topic :: Software Development :: Libraries :: Python Modules
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: httpx>=0.24.0
+Requires-Dist: pydantic>=2.0.0
+Requires-Dist: typing-extensions>=4.0.0
+Requires-Dist: aiofiles>=23.0.0
+Requires-Dist: rich>=13.0.0
+Requires-Dist: click>=8.0.0
+Requires-Dist: PyYAML>=6.0.0
+Requires-Dist: aiohttp>=3.8.0
+Provides-Extra: screening
+Requires-Dist: pandas>=1.5; extra == "screening"
+Provides-Extra: notebooks
+Requires-Dist: jupyterlab>=4; extra == "notebooks"
+Requires-Dist: ipykernel>=6; extra == "notebooks"
+Requires-Dist: py3Dmol>=2.0; extra == "notebooks"
+Requires-Dist: matplotlib>=3.6; extra == "notebooks"
+Requires-Dist: numpy>=1.23; extra == "notebooks"
+Provides-Extra: analysis
+Requires-Dist: numpy>=1.23; extra == "analysis"
+Requires-Dist: biopython>=1.80; extra == "analysis"
+Provides-Extra: sagemaker
+Requires-Dist: boto3>=1.26.0; extra == "sagemaker"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.0.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
+Requires-Dist: pandas>=1.5.0; extra == "dev"
+Requires-Dist: biopython>=1.80; extra == "dev"
+Requires-Dist: nbformat>=5.7; extra == "dev"
+Requires-Dist: jsonschema>=4.17; extra == "dev"
+Requires-Dist: py3Dmol>=2.0; extra == "dev"
+Requires-Dist: nbclient>=0.7; extra == "dev"
+Requires-Dist: ipykernel>=6; extra == "dev"
+Requires-Dist: build>=1; extra == "dev"
+Requires-Dist: twine>=6; extra == "dev"
+
+# Boltz-2 Python Client
+
+Copyright (c) 2025-2026, NVIDIA CORPORATION. All rights reserved.
+
+[![PyPI](https://img.shields.io/pypi/v/boltz2-python-client)](https://pypi.org/project/boltz2-python-client/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+Python and command-line interfaces for NVIDIA Boltz-2 NIM: protein, DNA/RNA,
+ligand and covalent complexes, binding affinity, MSA integration, templates,
+and multi-endpoint screening.
+
+Version **0.6.0** targets **NIM 1.9.0**. Releases are validated on
+[TestPyPI](https://test.pypi.org/project/boltz2-python-client/0.6.0/)
+before production publication. Select the matching index when installing.
+See [migration and compatibility](docs/migration-0.6.md).
+
+The source archive (`.tar.gz`) under the release page's **Download files** includes
+the current guides, scripts and notebooks. Relative links in this README refer
+to files in that extracted archive or a matching repository checkout.
+
+## Install
+
+Python 3.10 or newer:
+
+```bash
+# PyPI, after production publication
+python -m pip install boltz2-python-client==0.6.0
+
+# TestPyPI release and dependencies from PyPI
+python -m pip install --index-url https://test.pypi.org/simple/ \
+  --extra-index-url https://pypi.org/simple/ boltz2-python-client==0.6.0
+
+# From this checkout or the extracted source archive
+python -m pip install -e '.[dev,notebooks]'
+```
+
+Optional extras: `notebooks` (Jupyter and visualization), `sagemaker` (boto3),
+`analysis` (NumPy and structure conversion), and `screening` (pandas for CSV and
+DataFrame helpers). The Python client itself needs no GPU;
+a running NIM server performs inference.
+
+## Quick start
+
+Run against a ready local server. This sequence is an input-format example;
+confidence scores do not establish a biological interaction.
+
+```python
+from pathlib import Path
+from boltz2_client import Boltz2SyncClient
+
+client = Boltz2SyncClient(base_url="http://localhost:8000", timeout=600)
+result = client.predict_protein_structure(
+    sequence="MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG",
+    output_dir=Path("results/protein"),
+)
+print(result.confidence_scores)
+```
+
+For notebooks and asynchronous programs, use `Boltz2Client` and `await`:
+
+```python
+from boltz2_client import Boltz2Client, Ligand, Polymer, PredictionRequest
+
+client = Boltz2Client(timeout=600)
+request = PredictionRequest(
+    polymers=[Polymer(id="A", molecule_type="protein", sequence="MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPT")],
+    ligands=[Ligand(id="L1", smiles="CC(=O)Oc1ccccc1C(=O)O",
+                    predict_affinity=True, output_affinity_embedding=True)],
+    diffusion_samples=2,
+    max_parallel_samples=1,  # NIM 1.9+: lower peak GPU memory
+)
+result = await client.predict(request, output_dir="results/complex")
+print(result.affinities["L1"].affinity_pic50)
+print(result.affinities["L1"].affinity_embedding)
+```
+
+The second example demonstrates request syntax using a short protein fragment
+and aspirin; it is not a validated binding pair. Use full, appropriate target
+sequences and assess predictions against experimental evidence.
+
+## Endpoints
+
+| Deployment | Configuration | Prediction path |
+|---|---|---|
+| Local/self-hosted | `Boltz2Client(base_url="http://localhost:8000")` | `/biology/mit/boltz2/predict` |
+| NVIDIA hosted | `Boltz2Client(endpoint_type="nvidia_hosted")` | `/v1/biology/mit/boltz2/predict` |
+| SageMaker | `Boltz2Client(endpoint_type="sagemaker", sagemaker_endpoint_name="my-endpoint")` | boto3 `invoke_endpoint` |
+
+For hosted inference, supply the key through `NVIDIA_API_KEY` or `NGC_API_KEY`
+in the process environment (or `api_key` in Python). The default hosted base
+URL is `https://health.api.nvidia.com`. Local inference sends no authorization
+header. Hosted deployments may lag the container release; enable version-specific
+options only when that endpoint supports them.
+
+SageMaker requires the `sagemaker` extra and configured AWS credentials/region.
+See the [SageMaker connection example](docs/deployment.md#existing-sagemaker-endpoint).
+Use asynchronous clients in Jupyter; the synchronous wrapper uses `asyncio.run()`.
+
+## CLI
+
+```bash
+boltz2 health
+boltz2 protein ACDEFGHIKLMNPQRSTVWY --output-dir results/protein
+boltz2 protein ACDEFGHIKLMNPQRSTVWY --diffusion-samples 2 --max-parallel-samples 1
+boltz2 ligand ACDEFGHIKLMNPQRSTVWY --smiles CC --predict-affinity --output-affinity-embedding
+boltz2 advanced --config-file examples/data/nim_1_9_request.json --output-dir results/advanced
+boltz2 --endpoint-type nvidia_hosted protein ACDEFGHIKLMNPQRSTVWY
+boltz2 --multi-endpoint --base-url http://gpu1:8000,http://gpu2:8000 protein ACDEFGHIKLMNPQRSTVWY
+```
+
+These short sequences/ligands illustrate syntax. `boltz2 --help` lists all
+commands, including covalent constraints, YAML, MSA conversion and screening.
+
+## Results and matrices
+
+`predict()` saves every structure as `structure_0.cif`, `structure_1.cif`, etc.,
+plus `prediction_response.json` (complete response), `prediction_metadata.json`
+(scores, affinities, embeddings and runtime metrics), and `affinities.json` when
+present. Use `save_structures=False` or CLI `--no-save` to suppress client output.
+Use separate output directories for separate predictions to avoid overwriting files.
+
+**NIM 1.9 does not return full PAE/PDE matrices in JSON.** `write_full_pae=True`
+and `write_full_pde=True` create NPZ files on the server under
+`$NIM_OUTPUT_PATH/prediction_*/pae/` and `.../pde/`. `result.pae` and `result.pde`
+remain `None`. Mount the server output directory to retrieve these artifacts.
+Aggregate `complex_pde_scores` and `complex_ipde_scores` remain in the response.
+See [outputs](docs/outputs.md) for loading matrices and retaining results.
+
+## Deploy a local server
+
+Follow [local deployment](docs/deployment.md), including GPU/driver prerequisites,
+NGC login, cache and output mounts. The pinned image is
+`nvcr.io/nim/mit/boltz2:1.9.0`. The deployment script checks GPU access before
+starting a container:
+
+```bash
+# Set NGC_API_KEY (or NVIDIA_API_KEY) in the environment first.
+export LOCAL_NIM_CACHE="$HOME/.cache/nim"
+export LOCAL_NIM_OUTPUT="$HOME/boltz2-output"
+bash scripts/start_local_nim.sh
+```
+
+## Guides and examples
+
+Start with the [protein prediction notebook](examples/notebooks/01_protein_prediction.ipynb)
+and [example index](examples/README.md). Guides:
+
+- [Parameters](docs/parameters.md), [migration](docs/migration-0.6.md), [outputs](docs/outputs.md)
+- [Affinity](docs/affinity_prediction.md), [covalent complexes](docs/covalent_complex.md)
+- [MSA search](docs/msa_search.md), [A3M multimer pairing](docs/a3m_to_multimer_msa.md)
+- [YAML subset](docs/yaml.md), [async usage](docs/async.md)
+- [Multiple endpoints](docs/multi_endpoint.md), [virtual screening](docs/virtual_screening.md)
+- [Validation and release procedure](docs/development.md), [changelog](CHANGELOG.md)
+
+## License
+
+[MIT](LICENSE). Third-party assets retain their [licenses](licenses/README.md).
+NVIDIA NIM container and model terms are separate from the Python client license.

boltz2_python_client-0.6.0/README.md

@@ -0,0 +1,158 @@
+# Boltz-2 Python Client
+
+Copyright (c) 2025-2026, NVIDIA CORPORATION. All rights reserved.
+
+[![PyPI](https://img.shields.io/pypi/v/boltz2-python-client)](https://pypi.org/project/boltz2-python-client/)
+[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](LICENSE)
+
+Python and command-line interfaces for NVIDIA Boltz-2 NIM: protein, DNA/RNA,
+ligand and covalent complexes, binding affinity, MSA integration, templates,
+and multi-endpoint screening.
+
+Version **0.6.0** targets **NIM 1.9.0**. Releases are validated on
+[TestPyPI](https://test.pypi.org/project/boltz2-python-client/0.6.0/)
+before production publication. Select the matching index when installing.
+See [migration and compatibility](docs/migration-0.6.md).
+
+The source archive (`.tar.gz`) under the release page's **Download files** includes
+the current guides, scripts and notebooks. Relative links in this README refer
+to files in that extracted archive or a matching repository checkout.
+
+## Install
+
+Python 3.10 or newer:
+
+```bash
+# PyPI, after production publication
+python -m pip install boltz2-python-client==0.6.0
+
+# TestPyPI release and dependencies from PyPI
+python -m pip install --index-url https://test.pypi.org/simple/ \
+  --extra-index-url https://pypi.org/simple/ boltz2-python-client==0.6.0
+
+# From this checkout or the extracted source archive
+python -m pip install -e '.[dev,notebooks]'
+```
+
+Optional extras: `notebooks` (Jupyter and visualization), `sagemaker` (boto3),
+`analysis` (NumPy and structure conversion), and `screening` (pandas for CSV and
+DataFrame helpers). The Python client itself needs no GPU;
+a running NIM server performs inference.
+
+## Quick start
+
+Run against a ready local server. This sequence is an input-format example;
+confidence scores do not establish a biological interaction.
+
+```python
+from pathlib import Path
+from boltz2_client import Boltz2SyncClient
+
+client = Boltz2SyncClient(base_url="http://localhost:8000", timeout=600)
+result = client.predict_protein_structure(
+    sequence="MKTVRQERLKSIVRILERSKEPVSGAQLAEELSVSRQVIVQDIAYLRSLGYNIVATPRGYVLAGG",
+    output_dir=Path("results/protein"),
+)
+print(result.confidence_scores)
+```
+
+For notebooks and asynchronous programs, use `Boltz2Client` and `await`:
+
+```python
+from boltz2_client import Boltz2Client, Ligand, Polymer, PredictionRequest
+
+client = Boltz2Client(timeout=600)
+request = PredictionRequest(
+    polymers=[Polymer(id="A", molecule_type="protein", sequence="MTEYKLVVVGACGVGKSALTIQLIQNHFVDEYDPT")],
+    ligands=[Ligand(id="L1", smiles="CC(=O)Oc1ccccc1C(=O)O",
+                    predict_affinity=True, output_affinity_embedding=True)],
+    diffusion_samples=2,
+    max_parallel_samples=1,  # NIM 1.9+: lower peak GPU memory
+)
+result = await client.predict(request, output_dir="results/complex")
+print(result.affinities["L1"].affinity_pic50)
+print(result.affinities["L1"].affinity_embedding)
+```
+
+The second example demonstrates request syntax using a short protein fragment
+and aspirin; it is not a validated binding pair. Use full, appropriate target
+sequences and assess predictions against experimental evidence.
+
+## Endpoints
+
+| Deployment | Configuration | Prediction path |
+|---|---|---|
+| Local/self-hosted | `Boltz2Client(base_url="http://localhost:8000")` | `/biology/mit/boltz2/predict` |
+| NVIDIA hosted | `Boltz2Client(endpoint_type="nvidia_hosted")` | `/v1/biology/mit/boltz2/predict` |
+| SageMaker | `Boltz2Client(endpoint_type="sagemaker", sagemaker_endpoint_name="my-endpoint")` | boto3 `invoke_endpoint` |
+
+For hosted inference, supply the key through `NVIDIA_API_KEY` or `NGC_API_KEY`
+in the process environment (or `api_key` in Python). The default hosted base
+URL is `https://health.api.nvidia.com`. Local inference sends no authorization
+header. Hosted deployments may lag the container release; enable version-specific
+options only when that endpoint supports them.
+
+SageMaker requires the `sagemaker` extra and configured AWS credentials/region.
+See the [SageMaker connection example](docs/deployment.md#existing-sagemaker-endpoint).
+Use asynchronous clients in Jupyter; the synchronous wrapper uses `asyncio.run()`.
+
+## CLI
+
+```bash
+boltz2 health
+boltz2 protein ACDEFGHIKLMNPQRSTVWY --output-dir results/protein
+boltz2 protein ACDEFGHIKLMNPQRSTVWY --diffusion-samples 2 --max-parallel-samples 1
+boltz2 ligand ACDEFGHIKLMNPQRSTVWY --smiles CC --predict-affinity --output-affinity-embedding
+boltz2 advanced --config-file examples/data/nim_1_9_request.json --output-dir results/advanced
+boltz2 --endpoint-type nvidia_hosted protein ACDEFGHIKLMNPQRSTVWY
+boltz2 --multi-endpoint --base-url http://gpu1:8000,http://gpu2:8000 protein ACDEFGHIKLMNPQRSTVWY
+```
+
+These short sequences/ligands illustrate syntax. `boltz2 --help` lists all
+commands, including covalent constraints, YAML, MSA conversion and screening.
+
+## Results and matrices
+
+`predict()` saves every structure as `structure_0.cif`, `structure_1.cif`, etc.,
+plus `prediction_response.json` (complete response), `prediction_metadata.json`
+(scores, affinities, embeddings and runtime metrics), and `affinities.json` when
+present. Use `save_structures=False` or CLI `--no-save` to suppress client output.
+Use separate output directories for separate predictions to avoid overwriting files.
+
+**NIM 1.9 does not return full PAE/PDE matrices in JSON.** `write_full_pae=True`
+and `write_full_pde=True` create NPZ files on the server under
+`$NIM_OUTPUT_PATH/prediction_*/pae/` and `.../pde/`. `result.pae` and `result.pde`
+remain `None`. Mount the server output directory to retrieve these artifacts.
+Aggregate `complex_pde_scores` and `complex_ipde_scores` remain in the response.
+See [outputs](docs/outputs.md) for loading matrices and retaining results.
+
+## Deploy a local server
+
+Follow [local deployment](docs/deployment.md), including GPU/driver prerequisites,
+NGC login, cache and output mounts. The pinned image is
+`nvcr.io/nim/mit/boltz2:1.9.0`. The deployment script checks GPU access before
+starting a container:
+
+```bash
+# Set NGC_API_KEY (or NVIDIA_API_KEY) in the environment first.
+export LOCAL_NIM_CACHE="$HOME/.cache/nim"
+export LOCAL_NIM_OUTPUT="$HOME/boltz2-output"
+bash scripts/start_local_nim.sh
+```
+
+## Guides and examples
+
+Start with the [protein prediction notebook](examples/notebooks/01_protein_prediction.ipynb)
+and [example index](examples/README.md). Guides:
+
+- [Parameters](docs/parameters.md), [migration](docs/migration-0.6.md), [outputs](docs/outputs.md)
+- [Affinity](docs/affinity_prediction.md), [covalent complexes](docs/covalent_complex.md)
+- [MSA search](docs/msa_search.md), [A3M multimer pairing](docs/a3m_to_multimer_msa.md)
+- [YAML subset](docs/yaml.md), [async usage](docs/async.md)
+- [Multiple endpoints](docs/multi_endpoint.md), [virtual screening](docs/virtual_screening.md)
+- [Validation and release procedure](docs/development.md), [changelog](CHANGELOG.md)
+
+## License
+
+[MIT](LICENSE). Third-party assets retain their [licenses](licenses/README.md).
+NVIDIA NIM container and model terms are separate from the Python client license.

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/boltz2_client/__init__.py

@@ -26,7 +26,7 @@ Example:
     >>> print(f"Confidence: {result.confidence_scores[0]:.3f}")
 """
 
-__version__ = "0.5.2.post1"
+__version__ = "0.6.0"
 __author__ = "NVIDIA Corporation"
 __email__ = "bionemo-support@nvidia.com"
 

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/boltz2_client/cli/__init__.py

@@ -56,7 +56,7 @@ def print_warning(message: str):
 @click.group()
 @click.version_option(_pkg_version, "-V", "--version", prog_name="boltz2",
                       message="%(prog)s %(version)s")
-@click.option('--base-url', default='http://localhost:8000', help='Service base URL (can be comma-separated for multiple endpoints)')
+@click.option('--base-url', default=None, help='Service base URL (can be comma-separated for multiple endpoints)')
 @click.option('--api-key', help='API key for NVIDIA hosted endpoints (or set NVIDIA_API_KEY env var)')
 @click.option('--endpoint-type',
               type=click.Choice(['local', 'nvidia_hosted', 'sagemaker']),
@@ -109,6 +109,9 @@ def cli(ctx, base_url: str, api_key: Optional[str], endpoint_type: str,
     export SAGEMAKER_ENDPOINT_NAME=my-boltz2-endpoint
     boltz2 --endpoint-type sagemaker protein "MKTVRQERLK..."
     """
+    if base_url is not None and not base_url.strip():
+        raise click.BadParameter("must not be empty", param_hint="--base-url")
+    base_url = base_url or ("https://health.api.nvidia.com" if endpoint_type == "nvidia_hosted" else "http://localhost:8000")
     ctx.ensure_object(dict)
     ctx.obj['base_url'] = base_url
     ctx.obj['api_key'] = api_key

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/boltz2_client/cli/info.py

@@ -28,18 +28,7 @@ def health(ctx):
         try:
             # Handle NVIDIA hosted endpoints specially
             if ctx.obj['endpoint_type'] == 'nvidia_hosted':
-                print_warning("Health checks are not supported on NVIDIA hosted endpoints")
-                print_info("NVIDIA hosted endpoints use managed infrastructure with built-in health monitoring")
-                print_success("NVIDIA endpoint is considered healthy if you can make predictions")
-                
-                if ctx.obj['verbose']:
-                    console.print("\nService Info:", style="bold")
-                    console.print(f"  Base URL: {ctx.obj['base_url']}")
-                    console.print(f"  Endpoint Type: {ctx.obj['endpoint_type']}")
-                    console.print(f"  API Key: {'✅ Set via environment' if ctx.obj.get('api_key') is None else '✅ Provided via CLI'}")
-                    console.print(f"  Note: To verify connectivity, try running a prediction command")
-                    
-                print_info("To test connectivity, try: boltz2 --endpoint-type nvidia_hosted protein \"SEQUENCE\" --no-save")
+                raise click.ClickException("NVIDIA hosted inference has no readiness API; verify availability with a prediction.")
             else:
                 # Local endpoint - use normal health check
                 client = create_client(ctx)
@@ -64,11 +53,12 @@ def health(ctx):
                         for key, value in health_status.details.items():
                             console.print(f"  {key}: {value}")
                         
+        except click.ClickException:
+            raise
         except Exception as e:
-            if ctx.obj['endpoint_type'] not in ('nvidia_hosted',):
-                print_error(f"Health check failed: {e}")
-                raise click.Abort()
-    
+            print_error(f"Health check failed: {e}")
+            raise click.Abort()
+
     asyncio.run(check_health())
 
 

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/boltz2_client/cli/msa.py

@@ -559,9 +559,9 @@ def convert_msa_command(ctx, a3m_files: Tuple[str, ...], chain_ids: str,
 @click.option('--diffusion-samples', type=click.IntRange(1, 25), default=1,
               help='Number of diffusion samples/structures (1-25, default: 1)')
 @click.option('--write-full-pae', is_flag=True, default=False,
-              help='Output full PAE (Predicted Aligned Error) matrix')
+              help='Write PAE NPZ files on the NIM 1.9+ server')
 @click.option('--write-full-pde', is_flag=True, default=False,
-              help='Output full PDE (Predicted Distance Error) matrix')
+              help='Write PDE NPZ files on the NIM 1.9+ server')
 @click.option('--output-format', type=click.Choice(['cif', 'pdb']), default='cif',
               help='Output structure format: cif (default) or pdb')
 @click.pass_context
@@ -825,7 +825,10 @@ def multimer_msa_command(ctx, a3m_files: Tuple[str, ...], chain_ids: str,
                 if response.ptm_scores:
                     print_info(f"pTM: {response.ptm_scores[0]:.4f}")
             
-            # Save PAE matrix if available
+            if write_full_pae or write_full_pde:
+                print_info("NIM 1.9+ matrix files are under server NIM_OUTPUT_PATH; JSON pae/pde fields are null.")
+
+            # Save legacy inline PAE matrix if available
             if write_full_pae and response.pae:
                 pae_path = output_path.with_suffix('.pae.json')
                 pae_path.write_text(json.dumps({'pae': response.pae}, indent=2))

{boltz2_python_client-0.5.2.post1 → boltz2_python_client-0.6.0}/boltz2_client/cli/predict.py

@@ -38,6 +38,7 @@ def create_client(ctx):
               help='Number of sampling steps (10-1000, default: 50)')
 @click.option('--diffusion-samples', default=1, type=click.IntRange(1, 25),
               help='Number of diffusion samples (1-25, default: 1)')
+@click.option('--max-parallel-samples', default=None, type=click.IntRange(1, 25), help='Concurrent diffusion samples (NIM 1.9+)')
 @click.option('--step-scale', default=1.638, type=click.FloatRange(0.5, 5.0),
               help='Step scale for diffusion sampling (0.5-5.0, default: 1.638)')
 @click.option('--msa-file', multiple=True, type=(str, click.Choice(['a3m', 'csv', 'fasta'])),
@@ -45,16 +46,16 @@ def create_client(ctx):
 @click.option('--output-dir', type=click.Path(), default='.', help='Directory to save output files (structure_0.cif, prediction_metadata.json). Default: current directory')
 @click.option('--no-save', is_flag=True, help='Do not save structure files')
 @click.option('--write-full-pae', is_flag=True, default=False,
-              help='Output full PAE (Predicted Aligned Error) matrix as JSON')
+              help='Write PAE NPZ files under NIM_OUTPUT_PATH on the NIM 1.9+ server')
 @click.option('--write-full-pde', is_flag=True, default=False,
-              help='Output full PDE (Predicted Distance Error) matrix as JSON')
+              help='Write PDE NPZ files under NIM_OUTPUT_PATH on the NIM 1.9+ server')
 @click.option('--output-format', type=click.Choice(['cif', 'pdb']), default='cif',
               help='Output structure format: cif (default) or pdb')
 @click.pass_context
 def protein(ctx, sequence: str, polymer_id: str, recycling_steps: int, sampling_steps: int,
            diffusion_samples: int, step_scale: float, msa_file: List[Tuple[str, str]], 
            output_dir: str, no_save: bool, write_full_pae: bool, write_full_pde: bool,
-           output_format: str):
+           output_format: str, max_parallel_samples: Optional[int]):
     """
     Predict protein structure with optional MSA guidance.
     
@@ -118,6 +119,7 @@ def protein(ctx, sequence: str, polymer_id: str, recycling_steps: int, sampling_
                 recycling_steps=recycling_steps,
                 sampling_steps=sampling_steps,
                 diffusion_samples=diffusion_samples,
+                max_parallel_samples=max_parallel_samples,
                 step_scale=step_scale,
                 write_full_pae=write_full_pae,
                 write_full_pde=write_full_pde
@@ -164,8 +166,11 @@ def protein(ctx, sequence: str, polymer_id: str, recycling_steps: int, sampling_
                             convert_cif_to_pdb(cif_path, pdb_path)
                             print_info(f"Converted to PDB: {pdb_path}")
             
-            # Save PAE matrix if requested and available
-            if write_full_pae and result.pae:
+            if write_full_pae or write_full_pde:
+                print_info("NIM 1.9+ writes matrices under server NIM_OUTPUT_PATH/prediction_*/{pae,pde}/. The JSON pae/pde fields are null; mount the server output directory to access NPZ files.")
+
+            # Save legacy inline matrices if available
+            if not no_save and write_full_pae and result.pae:
                 import json
                 pae_path = Path(output_dir) / f"structure_{polymer_id}.pae.json"
                 pae_path.write_text(json.dumps({'pae': result.pae}, indent=2))
@@ -173,7 +178,7 @@ def protein(ctx, sequence: str, polymer_id: str, recycling_steps: int, sampling_
                 print_info(f"PAE matrix saved to: {pae_path} (shape: {pae_shape})")
             
             # Save PDE matrix if requested and available
-            if write_full_pde and result.pde:
+            if not no_save and write_full_pde and result.pde:
                 import json
                 pde_path = Path(output_dir) / f"structure_{polymer_id}.pde.json"
                 pde_path.write_text(json.dumps({'pde': result.pde}, indent=2))
@@ -197,6 +202,7 @@ def protein(ctx, sequence: str, polymer_id: str, recycling_steps: int, sampling_
 @click.option('--recycling-steps', default=3, type=click.IntRange(1, 10))
 @click.option('--sampling-steps', default=50, type=click.IntRange(10, 1000))
 @click.option('--predict-affinity', is_flag=True, help='Enable affinity prediction for the ligand')
+@click.option('--output-affinity-embedding', is_flag=True, help='Return affinity embeddings; requires --predict-affinity (NIM 1.8+)')
 @click.option('--sampling-steps-affinity', default=200, type=click.IntRange(10, 1000), help='Sampling steps for affinity prediction (default: 200)')
 @click.option('--diffusion-samples-affinity', default=5, type=click.IntRange(1, 10), help='Diffusion samples for affinity prediction (default: 5)')
 @click.option('--affinity-mw-correction', is_flag=True, help='Apply molecular weight correction to affinity prediction')
@@ -210,7 +216,7 @@ def ligand(ctx, protein_sequence: str, smiles: Optional[str], ccd: Optional[str]
           recycling_steps: int, sampling_steps: int, predict_affinity: bool,
           sampling_steps_affinity: int, diffusion_samples_affinity: int, 
           affinity_mw_correction: bool, msa_file: List[Tuple[str, str]], 
-          output_dir: str, no_save: bool):
+          output_dir: str, no_save: bool, output_affinity_embedding: bool):
     """
     Predict protein-ligand complex structure with optional MSA guidance.
     
@@ -284,10 +290,11 @@ def ligand(ctx, protein_sequence: str, smiles: Optional[str], ccd: Optional[str]
                     recycling_steps=recycling_steps,
                     sampling_steps=sampling_steps,
                     predict_affinity=predict_affinity,
+                    output_affinity_embedding=output_affinity_embedding,
                     sampling_steps_affinity=sampling_steps_affinity,
                     diffusion_samples_affinity=diffusion_samples_affinity,
                     affinity_mw_correction=affinity_mw_correction,
-                    save_structures=False,
+                    save_structures=not no_save,
                     msa_files=msa_files if msa_files else None,
                     output_dir=Path(output_dir),
                     progress_callback=progress_callback
@@ -323,16 +330,16 @@ def ligand(ctx, protein_sequence: str, smiles: Optional[str], ccd: Optional[str]
                 
                 # Interpretation
                 if affinity.affinity_probability_binary[0] > 0.7:
-                    print_success("Strong binding predicted (>70% probability)")
+                    print_success("High predicted binder likelihood (>70% probability)")
                 elif affinity.affinity_probability_binary[0] > 0.5:
-                    print_info("Moderate binding predicted (>50% probability)")
+                    print_info("Predicted binder likelihood above 50%")
                 else:
-                    print_info("Weak binding predicted (<50% probability)")
+                    print_info("Predicted binder likelihood at or below 50%")
             
             # Save results
             if not no_save:
                 output_path = Path(output_dir)
-                output_path.mkdir(exist_ok=True)
+                output_path.mkdir(parents=True, exist_ok=True)
                 
                 # Save structure
                 structure_file = output_path / "structure_0.cif"
@@ -732,7 +739,7 @@ def yaml_config(ctx, yaml_file: str, msa_dir: Optional[str], recycling_steps: in
     """
     Run prediction from YAML configuration file (official Boltz format).
     
-    This command supports the official Boltz YAML configuration format as used
+    This command supports the supported Boltz YAML configuration subset as used
     in the original Boltz repository examples.
     
     YAML_FILE: Path to YAML configuration file
@@ -845,7 +852,7 @@ def yaml_config(ctx, yaml_file: str, msa_dir: Optional[str], recycling_steps: in
                             if polymer_idx < len(request.polymers):
                                 request.polymers[polymer_idx].msa = {"default": {format_type: msa_record}}
                         else:
-                            print_warning(f"MSA file not found: {msa_path}")
+                            raise ValueError(f"MSA file not found: {msa_path}")
                 
                 # Override with CLI parameters
                 request.recycling_steps = recycling_steps