rdkit-dof 0.1.0__tar.gz

rdkit_dof-0.1.0/.github/workflows/build_test_deploy.yml

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+name: Build, Test, and Deploy
+
+on:
+  push:
+    branches:
+      - main
+  pull_request:
+    branches:
+      - main
+  release:
+    types: [published]
+
+jobs:
+  # ===========================================================================
+  # 1. 构建与测试 (Matrix 测试多系统多版本)
+  # ===========================================================================
+  build-and-test:
+    name: Test on ${{ matrix.os }} (Py ${{ matrix.python-version }})
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false # 如果一个版本失败，不要立即取消其他测试
+      matrix:
+        os: [ubuntu-latest, macos-latest, windows-latest]
+        python-version: ["3.9", "3.10", "3.11"]
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+        with:
+          enable-cache: true
+          cache-suffix: ${{ runner.os }}-${{ matrix.python-version }}
+
+      - name: Set up Python ${{ matrix.python-version }}
+        run: uv python install ${{ matrix.python-version }}
+
+      - name: Install dependencies
+        run: uv sync --all-extras --dev
+
+      - name: Run tests
+        run: uv run pytest
+
+  # ===========================================================================
+  # 2. 部署到 PyPI (仅在 Release 发布时运行)
+  # ===========================================================================
+  deploy:
+    name: Deploy to PyPI
+    runs-on: ubuntu-latest
+    needs: build-and-test
+    if: github.event_name == 'release' && github.event.action == 'published'
+    
+    environment:
+      name: pypi
+      url: https://pypi.org/p/rdkit-dof
+
+    permissions:
+      id-token: write
+      contents: write
+
+    steps:
+      - name: Checkout code
+        uses: actions/checkout@v4
+
+      - name: Install uv
+        uses: astral-sh/setup-uv@v3
+
+      - name: Build distributions
+        run: uv build
+
+      - name: Publish to PyPI
+        run: uv publish
+      
+      - name: Upload artifacts to GitHub Release
+        uses: softprops/action-gh-release@v2
+        with:
+          files: dist/*

rdkit_dof-0.1.0/.gitignore

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+# ---> JupyterNotebooks
+# gitignore template for Jupyter Notebooks
+# website: http://jupyter.org/
+
+.ipynb_checkpoints
+*/.ipynb_checkpoints/*
+
+# IPython
+profile_default/
+ipython_config.py
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+#   git rm -r .ipynb_checkpoints/
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+*.egg
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+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+cover/
+
+# Translations
+*.mo
+*.pot
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+# Django stuff:
+*.log
+local_settings.py
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+db.sqlite3-journal
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+# Flask stuff:
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+# Sphinx documentation
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+# PyBuilder
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+target/
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+# Jupyter Notebook
+.ipynb_checkpoints
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+# IPython
+profile_default/
+ipython_config.py
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+# pyenv
+#   For a library or package, you might want to ignore these files since the code is
+#   intended to run in multiple environments; otherwise, check them in:
+# .python-version
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+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# UV
+#   Similar to Pipfile.lock, it is generally recommended to include uv.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#uv.lock
+
+# poetry
+#   Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
+#   This is especially recommended for binary packages to ensure reproducibility, and is more
+#   commonly ignored for libraries.
+#   https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
+#poetry.lock
+
+# pdm
+#   Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
+#pdm.lock
+#   pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
+#   in version control.
+#   https://pdm.fming.dev/latest/usage/project/#working-with-version-control
+.pdm.toml
+.pdm-python
+.pdm-build/
+
+# PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/
+
+# pytype static type analyzer
+.pytype/
+
+# Cython debug symbols
+cython_debug/
+
+# PyCharm
+#  JetBrains specific template is maintained in a separate JetBrains.gitignore that can
+#  be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
+#  and can be added to the global gitignore or merged into this file.  For a more nuclear
+#  option (not recommended) you can uncomment the following to ignore the entire idea folder.
+#.idea/
+
+# Ruff stuff:
+.ruff_cache/
+
+# PyPI configuration file
+.pypirc
+
+# ---> VisualStudioCode
+.vscode/*
+!.vscode/settings.json
+!.vscode/tasks.json
+!.vscode/launch.json
+!.vscode/extensions.json
+!.vscode/*.code-snippets
+
+# Local History for Visual Studio Code
+.history/
+
+# Built Visual Studio Code Extensions
+*.vsix
+
+# ---> Windows
+# Windows thumbnail cache files
+Thumbs.db
+Thumbs.db:encryptable
+ehthumbs.db
+ehthumbs_vista.db
+
+# Dump file
+*.stackdump
+
+# Folder config file
+[Dd]esktop.ini
+
+# Recycle Bin used on file shares
+$RECYCLE.BIN/
+
+# Windows Installer files
+*.cab
+*.msi
+*.msix
+*.msm
+*.msp
+
+# Windows shortcuts
+*.lnk
+
+# ---> Linux
+*~
+
+# temporary files which can be created if a process still has a handle open of a deleted file
+.fuse_hidden*
+
+# KDE directory preferences
+.directory
+
+# Linux trash folder which might appear on any partition or disk
+.Trash-*
+
+# .nfs files are created when an open file is removed but is still being accessed
+.nfs*
+
+# ---> macOS
+# General
+.DS_Store
+.AppleDouble
+.LSOverride
+
+# Icon must end with two \r
+Icon
+
+# Thumbnails
+._*
+
+# Files that might appear in the root of a volume
+.DocumentRevisions-V100
+.fseventsd
+.Spotlight-V100
+.TemporaryItems
+.Trashes
+.VolumeIcon.icns
+.com.apple.timemachine.donotpresent
+
+# Directories potentially created on remote AFP share
+.AppleDB
+.AppleDesktop
+Network Trash Folder
+Temporary Items
+.apdisk
+

rdkit_dof-0.1.0/.python-version

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+3.9

rdkit_dof-0.1.0/LICENSE

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+MIT License
+
+Copyright (c) 2025 tmj
+
+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.

rdkit_dof-0.1.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: rdkit-dof
+Version: 0.1.0
+Summary: RDKit molecule drawing with Depth of Field (DOF) effects.
+Project-URL: Homepage, https://github.com/gentle1999/rdkit-dof
+Project-URL: Bug Tracker, https://github.com/gentle1999/rdkit-dof/issues
+Project-URL: Repository, https://github.com/gentle1999/rdkit-dof.git
+Author-email: Miao-Jiong Tang <mj_t@zju.edu.cn>
+License: MIT
+License-File: LICENSE
+Keywords: DOF,cheminformatics,chemistry,drawing,molecule,rdkit,visualization
+Classifier: Development Status :: 4 - Beta
+Classifier: Intended Audience :: Developers
+Classifier: Intended Audience :: Science/Research
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Classifier: Programming Language :: Python :: 3
+Classifier: Programming Language :: Python :: 3.9
+Classifier: Programming Language :: Python :: 3.10
+Classifier: Programming Language :: Python :: 3.11
+Classifier: Topic :: Scientific/Engineering :: Chemistry
+Classifier: Topic :: Scientific/Engineering :: Visualization
+Classifier: Typing :: Typed
+Requires-Python: >=3.9
+Requires-Dist: pydantic-settings>=2.11.0
+Requires-Dist: pydantic>=2.12.5
+Requires-Dist: rdkit>=2023.9.6
+Description-Content-Type: text/markdown
+
+# rdkit-dof
+
+[![license](https://img.shields.io/badge/license-MIT-green)](LICENSE)
+
+[简体中文](README_zh.md)
+
+`rdkit-dof` is a Python toolkit that uses RDKit to generate beautiful 2D images of molecules with a "Depth of Field" (DOF) or "fog" effect. Based on the molecule's 3D conformation, atoms and bonds farther from the viewer are drawn with higher transparency and lower saturation, creating a sense of visual depth in the 2D image.
+
+## Comparison
+
+To better showcase the effect of `rdkit-dof`, we have compared it with RDKit's default drawing function.
+
+### Single Molecule Comparison
+
+|                        Default RDKit                        |                  rdkit-dof Effect                   |
+| :---------------------------------------------------------: | :-------------------------------------------------: |
+| ![Paclitaxel Default](assets/comparison_single_default.svg) | ![Paclitaxel DOF](assets/comparison_single_dof.svg) |
+
+### Grid Mode Comparison
+
+|                    Default RDKit                    |              rdkit-dof Effect               |
+| :-------------------------------------------------: | :-----------------------------------------: |
+| ![Grid Default](assets/comparison_grid_default.svg) | ![Grid DOF](assets/comparison_grid_dof.svg) |
+
+## Tech Stack
+
+- **Core:** Python 3.9+
+- **Cheminformatics:** RDKit
+- **Image Processing:** Pillow
+- **Configuration:** Pydantic
+
+## Installation
+
+```bash
+pip install rdkit-dof
+```
+
+## Usage
+
+Here is a basic example of how to generate an image with a depth-of-field effect for a molecule.
+
+```python
+from rdkit import Chem
+from rdkit.Chem.rdDistGeom import EmbedMolecule
+from rdkit.Chem.rdForceFieldHelpers import MMFFOptimizeMolecule
+from rdkit_dof import MolToDofImage, dofconfig
+
+# 1. Create an RDKit molecule object and generate a 3D conformation
+smiles = "CC1=C2[C@@]([C@]([C@H]([C@@H]3[C@]4([C@H](OC4)C[C@@H]([C@]3(C(=O)[C@@H]2OC(=O)C)C)O)OC(=O)C)OC(=O)c5ccccc5)(C[C@@H]1OC(=O)[C@H](O)[C@@H](NC(=O)c6ccccc6)c7ccccc7)C)C"
+mol = Chem.MolFromSmiles(smiles)
+mol = Chem.AddHs(mol)
+EmbedMolecule(mol, randomSeed=42)
+MMFFOptimizeMolecule(mol)
+
+# 2. (Optional) Switch to a preset theme
+dofconfig.use_style("default")
+
+# 3. Call the core function to generate the image (returns SVG text)
+svg_data = MolToDofImage(
+    mol,
+    size=(1000, 800),
+    legend="Paclitaxel (Taxol)",
+    use_svg=True,
+    return_image=False, # Set to False to get raw data (str or bytes)
+)
+
+# 4. Save to a file
+with open("paclitaxel.svg", "w") as f:
+    f.write(svg_data)
+
+print("Image saved to paclitaxel.svg")
+
+# 5. (Optional) Display the image (in a Jupyter Notebook)
+svg_img = MolToDofImage(
+    mol,
+    size=(1000, 800),
+    legend="Paclitaxel (Taxol)",
+    use_svg=True,
+    return_image=True, # Set to True to get an IPython/Pillow image object
+)
+svg_img # Display the image
+```
+
+## API
+
+This toolkit provides two core drawing functions:
+
+### `MolToDofImage`
+
+Generates a DOF image for a single molecule.
+
+```python
+MolToDofImage(
+    mol: Chem.Mol,
+    size: Optional[tuple[int, int]] = None,
+    legend: str = "",
+    use_svg: bool = True,
+    return_image: bool = True,
+    *,
+    settings: Optional[DofDrawSettings] = None,
+    **kwargs: Any,
+) -> Union["SVG", str, Image.Image, bytes]
+```
+
+- **`mol`**: RDKit molecule object, which must contain a 3D conformation.
+- **`size`**: Image dimensions `(width, height)`.
+- **`legend`**: Legend text below the image.
+- **`use_svg`**: `True` returns SVG, `False` returns PNG.
+- **`return_image`**: `True` returns an IPython/Pillow image object, `False` returns raw data (string for SVG, bytes for PNG).
+- **`settings`**: A `DofDrawSettings` instance for local configuration.
+- **`**kwargs`**: Other RDKit `MolDrawOptions` parameters.
+
+### `MolGridToDofImage`
+
+Generates a DOF image for a grid of molecules, with parameters similar to RDKit's `MolsToGridImage`.
+
+```python
+MolGridToDofImage(
+    mols: Sequence[Union[Chem.Mol, Chem.RWMol, None]],
+    molsPerRow: int = 3,
+    subImgSize: tuple[int, int] = (300, 300),
+    legends: Optional[Sequence[Union[str, None]]] = None,
+    use_svg: bool = True,
+    return_image: bool = True,
+    *,
+    settings: Optional[DofDrawSettings] = None,
+    **kwargs: Any,
+) -> Union["SVG", str, Image.Image, bytes]
+```
+
+## Configuration
+
+You can customize the drawing style via a global `dofconfig` object or environment variables (`.env`).
+
+### Global Config Object
+
+Modify the properties of the `rdkit_dof.dofconfig` object directly in your code.
+
+```python
+from rdkit_dof import dofconfig
+
+# Use a preset style
+dofconfig.use_style("nature") # Options: 'default', 'nature', 'jacs', 'dark'
+
+# Customize colors and effects
+dofconfig.fog_color = (0.1, 0.1, 0.1) # Background fog color (RGB, 0-1)
+dofconfig.min_alpha = 0.3             # Minimum alpha for the farthest atoms
+dofconfig.default_size = (500, 500)   # Default image size
+
+# Override colors for specific atoms (atomic number -> RGB)
+dofconfig.atom_colors[8] = (1.0, 0.2, 0.2) # Set Oxygen to bright red
+```
+
+### Environment Variables
+
+You can also customize the drawing style by setting environment variables. All configuration properties have a corresponding environment variable, named `MOL_DOF_` plus the property name (in upper snake case).
+
+For example, to set `fog_color` to dark gray (RGB 0.1, 0.1, 0.1) and `min_alpha` to 0.2, you can add this to your `.env` file:
+
+```env
+# Set fog color to dark gray
+MOL_DOF_FOG_COLOR=[0.1, 0.1, 0.1]
+# Adjust minimum alpha
+MOL_DOF_MIN_ALPHA=0.2
+```
+
+### Main Configuration Properties
+
+| Property         | Description                                              | Default (Light Theme)   |
+| ---------------- | -------------------------------------------------------- | ----------------------- |
+| `preset_style`   | Name of the preset style                                 | `"default"`             |
+| `fog_color`      | Fog/background color (RGB, 0-1)                          | `(0.95, 0.95, 0.95)`    |
+| `min_alpha`      | Minimum alpha for the farthest atoms                     | `0.4`                   |
+| `default_size`   | Default image size `(width, height)` for `MolToDofImage` | `(800, 800)`            |
+| `enable_ipython` | Whether to enable IPython image display                  | `True`                  |
+| `atom_colors`    | Atom color map `(dict[int, tuple])`                      | Based on `preset_style` |
+
+## Running the Examples
+
+The script `scripts/_generate_comparison_images.py` is a complete example for generating all the images in this document. You can run it to reproduce them:
+
+```bash
+# Generate comparison images
+python scripts/_generate_comparison_images.py
+```
+
+## Compatibility
+
+- **OS:** This project is OS-independent and runs on Linux, macOS, and Windows.
+- **Python Version:** Requires Python 3.9 or higher.
+- **RDKit Version:** Recommended to use `2023.09` or higher.
+
+## Contribution Guide
+
+Contributions of any kind are welcome!
+
+1. Fork the repository.
+2. Create your feature branch (`git checkout -b feature/AmazingFeature`).
+3. Commit your changes (`git commit -m 'Add some AmazingFeature'`).
+4. Push to the branch (`git push origin feature/AmazingFeature`).
+5. Open a Pull Request.
+
+## License
+
+This project is distributed under the MIT License. See the [LICENSE](LICENSE) file for details.