novomd 1.2.0__tar.gz

novomd-1.2.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 QuantNexus AI
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

novomd-1.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: novomd
+Version: 1.2.0
+Summary: Local-first molecular property calculator. Compute descriptors from SMILES with no server and no API key.
+Author: NovoMCP
+License: MIT
+Project-URL: Homepage, https://github.com/realariharrison/NovoMD
+Project-URL: Documentation, https://github.com/realariharrison/NovoMD#readme
+Project-URL: Repository, https://github.com/realariharrison/NovoMD.git
+Project-URL: Issues, https://github.com/realariharrison/NovoMD/issues
+Keywords: molecular-dynamics,computational-chemistry,cheminformatics,molecular-descriptors,smiles,openmd,rdkit,local-first
+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: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
+Classifier: Framework :: FastAPI
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: numpy<2.0.0,>=1.24.0
+Requires-Dist: scipy>=1.11.0
+Requires-Dist: rdkit>=2023.3.1
+Provides-Extra: server
+Requires-Dist: fastapi>=0.104.0; extra == "server"
+Requires-Dist: uvicorn[standard]>=0.24.0; extra == "server"
+Requires-Dist: pydantic>=2.5.0; extra == "server"
+Requires-Dist: pydantic-settings>=2.1.0; extra == "server"
+Requires-Dist: python-dotenv>=1.0.0; extra == "server"
+Requires-Dist: slowapi>=0.1.9; extra == "server"
+Provides-Extra: dev
+Requires-Dist: pytest>=7.4.0; extra == "dev"
+Requires-Dist: pytest-cov>=4.1.0; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.21.0; extra == "dev"
+Requires-Dist: httpx>=0.25.0; extra == "dev"
+Requires-Dist: flake8>=6.1.0; extra == "dev"
+Requires-Dist: black>=23.9.0; extra == "dev"
+Requires-Dist: isort>=5.12.0; extra == "dev"
+Requires-Dist: mypy>=1.5.0; extra == "dev"
+Requires-Dist: bandit>=1.7.0; extra == "dev"
+Requires-Dist: safety>=2.3.0; extra == "dev"
+Requires-Dist: pre-commit>=3.4.0; extra == "dev"
+Dynamic: license-file
+
+<div align="center">
+
+<img src="docs/novomd-card.png" alt="NovoMD: local-first molecular property calculation" width="820" />
+
+# NovoMD
+
+**local-first molecular property calculation**
+
+[![CI](https://github.com/realariharrison/NovoMD/actions/workflows/ci.yml/badge.svg)](https://github.com/realariharrison/NovoMD/actions/workflows/ci.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-B8704B.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-2D2A26.svg)](https://www.python.org/downloads/)
+
+</div>
+
+NovoMD turns a SMILES string into a set of molecular descriptors. It runs on your own machine, with no account and no API key. Install it as a Python library, call it from the command line, or run it as a REST service.
+
+## What it is, and what it is not
+
+NovoMD computes 32+ outcome-level descriptors from a 3D conformer: geometry, an energy estimate, electrostatics, surface and volume, atom counts, and the coordinates for visualization. The calculation is local and deterministic.
+
+It does not run full molecular dynamics trajectories, docking, binding affinity, or ADMET. The scope is deliberate. For that work, see [Beyond property calculation](#beyond-property-calculation) below.
+
+## Quick start
+
+### Python library
+
+The shortest path. No server, no key.
+
+```bash
+pip install novomd
+```
+
+```python
+from novomd import calculate_properties
+
+props = calculate_properties("CCO")
+print(props["molecular_weight"])     # 46.07
+print(props["radius_of_gyration"])
+```
+
+Process a list in one call. A bad SMILES does not stop the batch; each item carries its own status.
+
+```python
+from novomd import calculate_properties_batch
+
+results = calculate_properties_batch(["CCO", "CC(=O)O", "NOT_VALID"])
+for item in results:
+    if item["status"] == "ok":
+        print(item["smiles"], item["properties"]["molecular_weight"])
+    else:
+        print(item["smiles"], "->", item["error"])
+```
+
+RDKit, NumPy, and SciPy install automatically. Everything runs on your hardware.
+
+### Command line
+
+```bash
+novomd props "CCO"
+novomd props "CC(=O)OC1=CC=CC=C1C(=O)O" --compact
+novomd batch molecules.smi --out results.csv
+```
+
+`batch` reads a `.smi` file (one SMILES per line) and writes a CSV, TSV, or JSON table.
+
+### From an AI assistant (MCP)
+
+NovoMD exposes a [Model Context Protocol](https://modelcontextprotocol.io/) endpoint, so assistants like Claude can query molecular properties directly.
+
+**Endpoint:** `https://quantnexusai-novomd.hf.space/gradio_api/mcp/sse`
+
+Add it as a custom connector in Claude (Settings, then Integrations), or point any MCP-compatible client at the same URL. Then ask:
+
+- "Calculate the molecular properties of aspirin (CC(=O)OC1=CC=CC=C1C(=O)O)."
+- "What is the dipole moment of caffeine?"
+
+The endpoint works with Claude (web and desktop), Cursor, Continue.dev, and any client that speaks the [MCP specification](https://modelcontextprotocol.io/).
+
+### REST service (Docker)
+
+For networked or containerized use, run the same core behind FastAPI.
+
+```bash
+# pre-built image
+docker run -d -p 8010:8010 \
+  -e NOVOMD_API_KEY="your-secure-api-key" \
+  --name novomd \
+  ghcr.io/realariharrison/novomd:latest
+
+curl http://localhost:8010/health
+```
+
+Or from source:
+
+```bash
+pip install "novomd[server]"
+uvicorn main:app --host 0.0.0.0 --port 8010
+```
+
+## What you get
+
+32+ descriptors, calculated from an embedded 3D structure:
+
+- **Geometry** (7): radius of gyration, asphericity, eccentricity, inertia shape factor, span, principal moments of inertia
+- **Energy** (6): conformer energy, van der Waals, electrostatic, torsion strain, angle strain, optimization delta
+- **Electrostatics** (6): dipole moment, total charge, max and min partial charge, charge span, electrostatic potential
+- **Surface and volume** (4): SASA, molecular volume, globularity, surface-to-volume ratio
+- **Atom counts** (2): total atoms, heavy atoms
+- **Visualization** (5+): full atomic coordinates, atom types, bond connectivity
+
+Energy values are estimates from the conformer, not from a force-field simulation. The descriptors are derived from real 3D coordinates, not mocked.
+
+## Library reference
+
+```python
+from novomd import calculate_properties, calculate_properties_batch
+
+# one molecule -> descriptor dict
+calculate_properties("CCO", add_hydrogens=True, optimize_3d=True)
+
+# many molecules -> list of {smiles, status, properties | error}
+calculate_properties_batch(["CCO", "C"], max_batch_size=1000)
+```
+
+Both raise `InvalidSMILESError` for unparseable input and `RDKitNotAvailableError` if RDKit is missing. The batch function isolates per-item failures instead of raising.
+
+## REST API
+
+All endpoints except `/health` require an API key in the `X-API-Key` header.
+
+| Endpoint | Method | Description |
+|----------|--------|-------------|
+| `/health` | GET | Health check (no auth) |
+| `/status` | GET | Service status and capabilities |
+| `/smiles-to-omd` | POST | Convert SMILES to OpenMD with 32+ properties |
+| `/batch` | POST | Calculate properties for many SMILES in one call |
+| `/atom2md` | POST | Convert PDB to OpenMD format |
+| `/force-fields` | GET | List available force fields |
+| `/force-field-types/{ff}` | GET | Atom types for a force field |
+
+```bash
+curl -X POST http://localhost:8010/batch \
+  -H "Content-Type: application/json" \
+  -H "X-API-Key: your-api-key" \
+  -d '{"molecules": ["CCO", "CC(=O)O", "NOT_VALID"]}'
+```
+
+```json
+{
+  "count": 3,
+  "succeeded": 2,
+  "failed": 1,
+  "results": [
+    {"smiles": "CCO", "status": "ok", "properties": {"molecular_weight": 46.07, "...": "..."}},
+    {"smiles": "CC(=O)O", "status": "ok", "properties": {"...": "..."}},
+    {"smiles": "NOT_VALID", "status": "error", "error": "Invalid SMILES string: 'NOT_VALID'"}
+  ]
+}
+```
+
+Batches are capped at 1,000 molecules per request and share the service rate limit.
+
+### Notebooks
+
+| Notebook | Topic |
+|----------|-------|
+| [01_getting_started.ipynb](examples/01_getting_started.ipynb) | Basic usage and conversion |
+| [02_molecular_properties.ipynb](examples/02_molecular_properties.ipynb) | Property analysis with pandas and matplotlib |
+| [03_visualization.ipynb](examples/03_visualization.ipynb) | 3D visualization with plotly and py3Dmol |
+| [04_batch_processing.ipynb](examples/04_batch_processing.ipynb) | One-call batch, library and endpoint |
+
+## Beyond property calculation
+
+NovoMD computes molecular descriptors locally. It does not run full MD trajectories, docking, ADMET, or compliance.
+
+For those, the same team builds NovoMCP, a computational engine for AI-native discovery: 122M enriched compounds, docking and FEP pipelines, ADMET and compliance scoring, and an immutable audit trail on every step. NovoMD is open and always will be. NovoMCP is the production layer for work that outgrows it.
+
+Learn more: [novomcp.com](https://novomcp.com)
+
+## Force fields
+
+`AMBER14`, `AMBER99SB`, `CHARMM36`, `OPLS-AA/M`, `GROMOS 54A7`. Property values are conformer-derived and force-field-independent; the force field affects only the OpenMD output.
+
+## Configuration
+
+Set these in a `.env` file or as environment variables (REST service only).
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `NOVOMD_API_KEY` | API authentication key (required) | - |
+| `PORT` | Server port | 8010 |
+| `HOST` | Server host | 0.0.0.0 |
+| `LOG_LEVEL` | DEBUG, INFO, WARNING, ERROR | INFO |
+| `CORS_ORIGINS` | Comma-separated origins, or "*" for all | localhost:3000,localhost:8080 |
+| `RATE_LIMIT` | e.g. "100/minute", "1000/hour" | 100/minute |
+
+## Development
+
+```bash
+pip install -e ".[dev,server]"   # core + server + dev tools
+pre-commit install
+
+pytest tests/ -v
+pytest tests/ --cov=novomd --cov=main --cov-report=term-missing
+
+black . && isort . && flake8 .
+mypy novomd main.py auth.py config.py
+bandit -r . -x ./tests
+```
+
+```
+NovoMD/
+├── novomd/              # importable library (framework-free core)
+│   ├── core.py          # property calculation
+│   ├── batch.py         # batch with per-item error isolation
+│   ├── conversion.py    # PDB to OpenMD
+│   ├── cli.py           # `novomd` command
+│   └── exceptions.py
+├── main.py              # FastAPI service (imports the core)
+├── config.py            # configuration
+├── auth.py              # API-key authentication
+├── tests/               # unit + integration tests
+├── examples/            # Jupyter notebooks
+└── .github/workflows/   # CI and PyPI publish
+```
+
+## Security
+
+NovoMD runs locally by default; no molecular data leaves your machine. For the REST service, use a strong `NOVOMD_API_KEY`, deploy behind TLS, and restrict `CORS_ORIGINS`. To report a vulnerability, see [SECURITY.md](SECURITY.md).
+
+## Contributing
+
+Contributions are welcome. See [CONTRIBUTING.md](CONTRIBUTING.md).
+
+- **Issues**: [GitHub Issues](https://github.com/realariharrison/NovoMD/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/realariharrison/NovoMD/discussions)
+
+## License
+
+MIT. See [LICENSE](LICENSE).
+
+Built with [FastAPI](https://fastapi.tiangolo.com/) and [RDKit](https://www.rdkit.org/).
+
+## Citation
+
+```bibtex
+@software{novomd2025,
+  title = {NovoMD: Local-First Molecular Property Calculation},
+  author = {NovoMCP},
+  year = {2025},
+  url = {https://github.com/realariharrison/NovoMD}
+}
+```
+
+---
+
+<div align="center">
+
+Built by the NovoMCP team
+
+</div>

novomd-1.2.0/README.md

@@ -0,0 +1,261 @@
+<div align="center">
+
+<img src="docs/novomd-card.png" alt="NovoMD: local-first molecular property calculation" width="820" />
+
+# NovoMD
+
+**local-first molecular property calculation**
+
+[![CI](https://github.com/realariharrison/NovoMD/actions/workflows/ci.yml/badge.svg)](https://github.com/realariharrison/NovoMD/actions/workflows/ci.yml)
+[![License: MIT](https://img.shields.io/badge/License-MIT-B8704B.svg)](LICENSE)
+[![Python 3.10+](https://img.shields.io/badge/python-3.10+-2D2A26.svg)](https://www.python.org/downloads/)
+
+</div>
+
+NovoMD turns a SMILES string into a set of molecular descriptors. It runs on your own machine, with no account and no API key. Install it as a Python library, call it from the command line, or run it as a REST service.
+
+## What it is, and what it is not
+
+NovoMD computes 32+ outcome-level descriptors from a 3D conformer: geometry, an energy estimate, electrostatics, surface and volume, atom counts, and the coordinates for visualization. The calculation is local and deterministic.
+
+It does not run full molecular dynamics trajectories, docking, binding affinity, or ADMET. The scope is deliberate. For that work, see [Beyond property calculation](#beyond-property-calculation) below.
+
+## Quick start
+
+### Python library
+
+The shortest path. No server, no key.
+
+```bash
+pip install novomd
+```
+
+```python
+from novomd import calculate_properties
+
+props = calculate_properties("CCO")
+print(props["molecular_weight"])     # 46.07
+print(props["radius_of_gyration"])
+```
+
+Process a list in one call. A bad SMILES does not stop the batch; each item carries its own status.
+
+```python
+from novomd import calculate_properties_batch
+
+results = calculate_properties_batch(["CCO", "CC(=O)O", "NOT_VALID"])
+for item in results:
+    if item["status"] == "ok":
+        print(item["smiles"], item["properties"]["molecular_weight"])
+    else:
+        print(item["smiles"], "->", item["error"])
+```
+
+RDKit, NumPy, and SciPy install automatically. Everything runs on your hardware.
+
+### Command line
+
+```bash
+novomd props "CCO"
+novomd props "CC(=O)OC1=CC=CC=C1C(=O)O" --compact
+novomd batch molecules.smi --out results.csv
+```
+
+`batch` reads a `.smi` file (one SMILES per line) and writes a CSV, TSV, or JSON table.
+
+### From an AI assistant (MCP)
+
+NovoMD exposes a [Model Context Protocol](https://modelcontextprotocol.io/) endpoint, so assistants like Claude can query molecular properties directly.
+
+**Endpoint:** `https://quantnexusai-novomd.hf.space/gradio_api/mcp/sse`
+
+Add it as a custom connector in Claude (Settings, then Integrations), or point any MCP-compatible client at the same URL. Then ask:
+
+- "Calculate the molecular properties of aspirin (CC(=O)OC1=CC=CC=C1C(=O)O)."
+- "What is the dipole moment of caffeine?"
+
+The endpoint works with Claude (web and desktop), Cursor, Continue.dev, and any client that speaks the [MCP specification](https://modelcontextprotocol.io/).
+
+### REST service (Docker)
+
+For networked or containerized use, run the same core behind FastAPI.
+
+```bash
+# pre-built image
+docker run -d -p 8010:8010 \
+  -e NOVOMD_API_KEY="your-secure-api-key" \
+  --name novomd \
+  ghcr.io/realariharrison/novomd:latest
+
+curl http://localhost:8010/health
+```
+
+Or from source:
+
+```bash
+pip install "novomd[server]"
+uvicorn main:app --host 0.0.0.0 --port 8010
+```
+
+## What you get
+
+32+ descriptors, calculated from an embedded 3D structure:
+
+- **Geometry** (7): radius of gyration, asphericity, eccentricity, inertia shape factor, span, principal moments of inertia
+- **Energy** (6): conformer energy, van der Waals, electrostatic, torsion strain, angle strain, optimization delta
+- **Electrostatics** (6): dipole moment, total charge, max and min partial charge, charge span, electrostatic potential
+- **Surface and volume** (4): SASA, molecular volume, globularity, surface-to-volume ratio
+- **Atom counts** (2): total atoms, heavy atoms
+- **Visualization** (5+): full atomic coordinates, atom types, bond connectivity
+
+Energy values are estimates from the conformer, not from a force-field simulation. The descriptors are derived from real 3D coordinates, not mocked.
+
+## Library reference
+
+```python
+from novomd import calculate_properties, calculate_properties_batch
+
+# one molecule -> descriptor dict
+calculate_properties("CCO", add_hydrogens=True, optimize_3d=True)
+
+# many molecules -> list of {smiles, status, properties | error}
+calculate_properties_batch(["CCO", "C"], max_batch_size=1000)
+```
+
+Both raise `InvalidSMILESError` for unparseable input and `RDKitNotAvailableError` if RDKit is missing. The batch function isolates per-item failures instead of raising.
+
+## REST API
+
+All endpoints except `/health` require an API key in the `X-API-Key` header.
+
+| Endpoint | Method | Description |
+|----------|--------|-------------|
+| `/health` | GET | Health check (no auth) |
+| `/status` | GET | Service status and capabilities |
+| `/smiles-to-omd` | POST | Convert SMILES to OpenMD with 32+ properties |
+| `/batch` | POST | Calculate properties for many SMILES in one call |
+| `/atom2md` | POST | Convert PDB to OpenMD format |
+| `/force-fields` | GET | List available force fields |
+| `/force-field-types/{ff}` | GET | Atom types for a force field |
+
+```bash
+curl -X POST http://localhost:8010/batch \
+  -H "Content-Type: application/json" \
+  -H "X-API-Key: your-api-key" \
+  -d '{"molecules": ["CCO", "CC(=O)O", "NOT_VALID"]}'
+```
+
+```json
+{
+  "count": 3,
+  "succeeded": 2,
+  "failed": 1,
+  "results": [
+    {"smiles": "CCO", "status": "ok", "properties": {"molecular_weight": 46.07, "...": "..."}},
+    {"smiles": "CC(=O)O", "status": "ok", "properties": {"...": "..."}},
+    {"smiles": "NOT_VALID", "status": "error", "error": "Invalid SMILES string: 'NOT_VALID'"}
+  ]
+}
+```
+
+Batches are capped at 1,000 molecules per request and share the service rate limit.
+
+### Notebooks
+
+| Notebook | Topic |
+|----------|-------|
+| [01_getting_started.ipynb](examples/01_getting_started.ipynb) | Basic usage and conversion |
+| [02_molecular_properties.ipynb](examples/02_molecular_properties.ipynb) | Property analysis with pandas and matplotlib |
+| [03_visualization.ipynb](examples/03_visualization.ipynb) | 3D visualization with plotly and py3Dmol |
+| [04_batch_processing.ipynb](examples/04_batch_processing.ipynb) | One-call batch, library and endpoint |
+
+## Beyond property calculation
+
+NovoMD computes molecular descriptors locally. It does not run full MD trajectories, docking, ADMET, or compliance.
+
+For those, the same team builds NovoMCP, a computational engine for AI-native discovery: 122M enriched compounds, docking and FEP pipelines, ADMET and compliance scoring, and an immutable audit trail on every step. NovoMD is open and always will be. NovoMCP is the production layer for work that outgrows it.
+
+Learn more: [novomcp.com](https://novomcp.com)
+
+## Force fields
+
+`AMBER14`, `AMBER99SB`, `CHARMM36`, `OPLS-AA/M`, `GROMOS 54A7`. Property values are conformer-derived and force-field-independent; the force field affects only the OpenMD output.
+
+## Configuration
+
+Set these in a `.env` file or as environment variables (REST service only).
+
+| Variable | Description | Default |
+|----------|-------------|---------|
+| `NOVOMD_API_KEY` | API authentication key (required) | - |
+| `PORT` | Server port | 8010 |
+| `HOST` | Server host | 0.0.0.0 |
+| `LOG_LEVEL` | DEBUG, INFO, WARNING, ERROR | INFO |
+| `CORS_ORIGINS` | Comma-separated origins, or "*" for all | localhost:3000,localhost:8080 |
+| `RATE_LIMIT` | e.g. "100/minute", "1000/hour" | 100/minute |
+
+## Development
+
+```bash
+pip install -e ".[dev,server]"   # core + server + dev tools
+pre-commit install
+
+pytest tests/ -v
+pytest tests/ --cov=novomd --cov=main --cov-report=term-missing
+
+black . && isort . && flake8 .
+mypy novomd main.py auth.py config.py
+bandit -r . -x ./tests
+```
+
+```
+NovoMD/
+├── novomd/              # importable library (framework-free core)
+│   ├── core.py          # property calculation
+│   ├── batch.py         # batch with per-item error isolation
+│   ├── conversion.py    # PDB to OpenMD
+│   ├── cli.py           # `novomd` command
+│   └── exceptions.py
+├── main.py              # FastAPI service (imports the core)
+├── config.py            # configuration
+├── auth.py              # API-key authentication
+├── tests/               # unit + integration tests
+├── examples/            # Jupyter notebooks
+└── .github/workflows/   # CI and PyPI publish
+```
+
+## Security
+
+NovoMD runs locally by default; no molecular data leaves your machine. For the REST service, use a strong `NOVOMD_API_KEY`, deploy behind TLS, and restrict `CORS_ORIGINS`. To report a vulnerability, see [SECURITY.md](SECURITY.md).
+
+## Contributing
+
+Contributions are welcome. See [CONTRIBUTING.md](CONTRIBUTING.md).
+
+- **Issues**: [GitHub Issues](https://github.com/realariharrison/NovoMD/issues)
+- **Discussions**: [GitHub Discussions](https://github.com/realariharrison/NovoMD/discussions)
+
+## License
+
+MIT. See [LICENSE](LICENSE).
+
+Built with [FastAPI](https://fastapi.tiangolo.com/) and [RDKit](https://www.rdkit.org/).
+
+## Citation
+
+```bibtex
+@software{novomd2025,
+  title = {NovoMD: Local-First Molecular Property Calculation},
+  author = {NovoMCP},
+  year = {2025},
+  url = {https://github.com/realariharrison/NovoMD}
+}
+```
+
+---
+
+<div align="center">
+
+Built by the NovoMCP team
+
+</div>

novomd-1.2.0/novomd/__about__.py

@@ -0,0 +1,3 @@
+"""Single source of truth for the package version."""
+
+__version__ = "1.2.0"

novomd-1.2.0/novomd/__init__.py

@@ -0,0 +1,42 @@
+"""NovoMD: a local-first molecular property calculator.
+
+Compute molecular descriptors on your own hardware, no server and no API key::
+
+    from novomd import calculate_properties
+    props = calculate_properties("CCO")
+    print(props["molecular_weight"])
+
+The same core powers the optional REST service (``pip install novomd[server]``).
+"""
+
+from __future__ import annotations
+
+from .__about__ import __version__
+from .batch import MAX_BATCH_SIZE, calculate_properties_batch
+from .conversion import get_atom_type, pdb_to_omd
+from .core import (
+    RDKIT_AVAILABLE,
+    calculate_all_molecular_properties,
+    calculate_partial_charges,
+    calculate_properties,
+    extract_coordinates_from_pdb,
+    smiles_to_pdb,
+)
+from .exceptions import InvalidSMILESError, NovoMDError, RDKitNotAvailableError
+
+__all__ = [
+    "__version__",
+    "RDKIT_AVAILABLE",
+    "calculate_properties",
+    "calculate_properties_batch",
+    "MAX_BATCH_SIZE",
+    "calculate_all_molecular_properties",
+    "calculate_partial_charges",
+    "extract_coordinates_from_pdb",
+    "smiles_to_pdb",
+    "get_atom_type",
+    "pdb_to_omd",
+    "NovoMDError",
+    "InvalidSMILESError",
+    "RDKitNotAvailableError",
+]