cnotebook 1.2.0__py3-none-any.whl → 2.1.1__py3-none-any.whl

cnotebook-1.2.0.dist-info/METADATA

@@ -1,280 +0,0 @@
-Metadata-Version: 2.4
-Name: cnotebook
-Version: 1.2.0
-Summary: Chemistry visualization in Jupyter Notebooks with the OpenEye Toolkits
-Author-email: Scott Arne Johnson <scott.arne.johnson@gmail.com>
-License-Expression: MIT
-Project-URL: Homepage, https://github.com/scott-arne/cnotebook
-Project-URL: Bug Reports, https://github.com/scott-arne/cnotebook/issues
-Project-URL: Source, https://github.com/scott-arne/cnotebook
-Project-URL: Documentation, https://github.com/scott-arne/cnotebook#readme
-Project-URL: Changelog, https://github.com/scott-arne/cnotebook/blob/master/CHANGELOG.md
-Keywords: chemistry,cheminformatics,computational-chemistry,molecular-visualization,jupyter,marimo,openeye,scientific-computing
-Classifier: Development Status :: 5 - Production/Stable
-Classifier: Intended Audience :: Science/Research
-Classifier: Intended Audience :: Developers
-Classifier: Topic :: Scientific/Engineering :: Chemistry
-Classifier: Topic :: Scientific/Engineering :: Visualization
-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 :: Only
-Classifier: Operating System :: OS Independent
-Classifier: Framework :: Jupyter
-Classifier: Framework :: IPython
-Requires-Python: >=3.11
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: pandas>=2.2.0
-Requires-Dist: oepandas>=2.0.0
-Requires-Dist: openeye-toolkits>=2025.2.1
-Provides-Extra: dev
-Requires-Dist: invoke; extra == "dev"
-Requires-Dist: build; extra == "dev"
-Requires-Dist: pytest; extra == "dev"
-Provides-Extra: test
-Requires-Dist: pytest; extra == "test"
-Requires-Dist: pytest-cov; extra == "test"
-Dynamic: license-file
-
-# CNotebook
-
-[![Python 3.11+](https://img.shields.io/badge/python-3.11+-blue.svg)](https://www.python.org/downloads/)
-[![OpenEye Toolkits](https://img.shields.io/badge/OpenEye-2025.2.1+-green.svg)](https://www.eyesopen.com/toolkits)
-[![Pandas 2.2+](https://img.shields.io/badge/pandas-2.2+-orange.svg)](https://pandas.pydata.org/)
-
-
-**Author:** Scott Arne Johnson ([scott.arne.johnson@gmail.com](mailto:scott.arne.johnson@gmail.com))
-
-CNotebook provides ergonomic chemistry visualization in Jupyter Notebooks and Marimo with the OpenEye Toolkits. Simply import the package and your molecular data will be automatically rendered as beautiful chemical structures - no additional configuration required!
-
-## 🚀 Quick Start
-
-### Installation
-
-```bash
-pip install cnotebook
-```
-
-**Prerequisites:** Requires OpenEye Toolkits and oepandas to be installed and properly licensed.
-
-### Basic Usage
-
-```python
-import cnotebook
-from openeye import oechem
-
-# Create a molecule
-mol = oechem.OEGraphMol()
-oechem.OESmilesToMol(mol, "n1cnccc1")
-
-# Display it - automatically renders as a chemical structure!
-mol
-```
-
-That's it! CNotebook automatically registers formatters so that OpenEye molecule objects display as chemical structures instead of cryptic text representations.
-
-## Features
-
-### Automatic Rendering
-- **Zero Configuration**: Just import and go - molecules automatically render as structures
-- **Multiple Formats**: Supports both Jupyter Notebooks and Marimo environments
-- **Smart Detection**: Automatically detects your notebook environment
-
-### Molecule Support
-- **OEMol Objects**: Direct rendering of `oechem.OEMolBase` derived objects
-- **OE2DMolDisplay**: Advanced rendering with custom depiction options
-- **Pandas Integration**: Seamless rendering in DataFrames with oepandas
-
-### Visualization Options
-- **Multiple Formats**: PNG (default) or SVG output
-- **Customizable Sizing**: Configurable width, height, and scaling
-- **Grid Layouts**: Multi-molecule grid displays
-- **Substructure Highlighting**: SMARTS pattern highlighting
-- **Molecular Alignment**: Align molecules to reference structures
-
-### Pandas Integration
-- **DataFrame Rendering**: Automatic molecule column detection and rendering
-- **Column Highlighting**: Highlight different patterns per row
-- **Alignment Tools**: Align molecular depictions in DataFrames
-- **Fingerprint Similarity**: Visual similarity coloring
-- **Property Calculation**: Chemistry-aware DataFrame operations
-
-## Environment Support
-
-### Jupyter Notebooks
-CNotebook automatically integrates with Jupyter when imported:
-
-```python
-import cnotebook
-import pandas as pd
-from openeye import oechem
-
-# Molecules will automatically render in cells
-mol = oechem.OEGraphMol()
-oechem.OESmilesToMol(mol, "CCO")
-mol  # Displays as chemical structure
-```
-
-### Marimo
-CNotebook provides seamless Marimo integration:
-
-```python
-import marimo as mo
-import cnotebook
-from openeye import oechem
-
-# Create and display molecules
-mol = oechem.OEGraphMol()
-oechem.OESmilesToMol(mol, "c1ccccc1")
-mol  # Automatically renders as PNG for Marimo compatibility
-```
-
-## Advanced Usage
-
-### Rendering Configuration
-
-```python
-# Access global rendering context
-ctx = cnotebook.cnotebook_context.get()
-
-# Customize rendering options
-ctx.width = 300
-ctx.height = 300
-ctx.image_format = "svg"  # Use SVG instead of PNG
-ctx.max_width = 600      # Prevent oversized molecules
-
-# Reset to defaults
-ctx.reset()
-```
-
-### Molecule Grids
-
-```python
-# Display multiple molecules in a grid
-molecules = [mol1, mol2, mol3, mol4]
-cnotebook.render_molecule_grid(
-    molecules,
-    ncols=2,
-    smarts="c1ccccc1",  # Highlight benzene rings
-    scale=0.8
-)
-```
-
-### Pandas DataFrame Integration
-
-```python
-import oepandas as oepd
-import pandas as pd
-
-# Create DataFrame with SMILES
-df = pd.DataFrame({
-    "Name": ["Benzene", "Pyridine", "Pyrimidine"],
-    "SMILES": ["c1ccccc1", "c1cnccc1", "n1cnccc1"]
-})
-
-# Convert to molecules
-df.as_molecule("SMILES", inplace=True)
-
-# DataFrame automatically renders molecules as structures
-df  # Molecule column shows chemical structures!
-
-# Add substructure highlighting
-df.SMILES.highlight("c1ccccc1")  # Highlight aromatic rings
-df
-
-# Align molecules to a reference
-df.SMILES.align_depictions("first")  # Align to first molecule
-df
-```
-
-### Substructure Highlighting
-
-```python
-# Highlight SMARTS patterns
-df["Pattern"] = ["cc", "cnc", "ncn"]
-df.highlight_using_column("Molecule", "Pattern", inplace=True)
-df  # Shows molecules with different highlights per row
-```
-
-### Fingerprint Similarity
-
-```python
-# Color molecules by fingerprint similarity
-reference_mol = oechem.OEGraphMol()
-oechem.OESmilesToMol(reference_mol, "c1ccc(N)cc1")
-
-df.fingerprint_similarity("Molecule", reference_mol, inplace=True)
-df  # Shows similarity coloring and Tanimoto coefficients
-```
-
-## Demo Notebooks
-
-Explore comprehensive examples in the `demos/` directory:
-
-### [Small_Molecules.ipynb](demos/Small_Molecules.ipynb)
-**Complete CNotebook Tutorial** - Comprehensive guide covering:
-- Basic molecule rendering and display options
-- OE2DMolDisplay objects with custom styling
-- Molecule grid layouts with highlighting
-- Advanced rendering configuration
-- Pandas DataFrame integration with oepandas
-- Substructure highlighting and SMARTS patterns
-- Column-based highlighting with different patterns per row
-- Molecular alignment techniques
-- Fingerprint similarity visualization
-- Empty and invalid molecule handling
-
-### [SVGs.ipynb](demos/SVGs.ipynb)
-**SVG Rendering Guide** - Learn how to:
-- Switch from PNG to SVG output format
-- Benefits and trade-offs of SVG vs PNG
-- High-quality crisp molecular graphics
-- SVG compatibility considerations
-
-## Configuration Options
-
-### Global Context Settings
-
-```python
-ctx = cnotebook.cnotebook_context.get()
-
-# Image dimensions
-ctx.width = 250          # Default width in pixels
-ctx.height = 250         # Default height in pixels
-ctx.max_width = 1200     # Maximum width (prevents oversized molecules)
-ctx.max_height = 800     # Maximum height
-
-# Output format
-ctx.image_format = "png"  # or "svg"
-
-# Display options
-ctx.scale = 1.0          # Scaling factor
-```
-
-### Environment-Specific Behavior
-
-- **Jupyter**: Supports both PNG and SVG formats
-- **Marimo**: Automatically uses PNG format for compatibility
-- **Console**: Falls back to string representations
-
-## Contributing
-
-We welcome contributions! Please ensure your code:
-- Follows existing code style and conventions
-- Includes appropriate tests
-- Works with both Jupyter and Marimo environments
-- Maintains compatibility with OpenEye Toolkits
-
-## License
-
-This project is licensed under the MIT License. See the [LICENSE](LICENSE) file for details.
-
-## Issues & Support
-
-For bug reports, feature requests, or general support, please open an issue on GitHub or contact the author at [scott.arne.johnson@gmail.com](mailto:scott.arne.johnson@gmail.com).
-
----
-
-*CNotebook makes chemical data visualization effortless. Import once, visualize everywhere!* 🧬✨

cnotebook-1.2.0.dist-info/RECORD

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