CNotebook

Getting Started

  • Installation
    • Requirements
    • Installing CNotebook
    • Installing Optional Dependencies
    • OpenEye Toolkits License
    • Verifying Installation
  • Quick Start
    • Basic Molecule Rendering
    • Working with DataFrames
    • Using MolGrid
    • Customizing Rendering
    • Environment Support
    • Next Steps

User Guide

  • Basic Rendering
    • Molecules
    • Query Molecules
    • Display Objects
    • Design Units
    • Substructure Highlighting
    • Rendering Contexts
      • Global Context
      • Local Contexts
    • Environment-Specific Behavior
  • DataFrame Integration
    • Pandas Integration
      • Prerequisites
      • Creating Molecule Columns
      • Creating Query Columns
      • Substructure Highlighting
      • Molecular Alignment
      • Fingerprint Similarity
    • Polars Integration
      • Prerequisites
      • Creating Molecule Columns
      • Reading Molecule Files
      • Substructure Highlighting
      • Molecular Alignment
      • Fingerprint Similarity
    • MolGrid from DataFrames
    • Best Practices
  • MolGrid: Interactive Molecule Grids
    • Overview
    • Basic Usage
      • Creating a Simple Grid
    • Selection
      • Enabling Selection
      • Selection Methods
      • Retrieving Selections
      • Exporting Selections
    • Customizing the Display
      • Image Settings
      • Pagination
      • Title Display
    • Search and Filtering
      • Text Search
      • SMARTS Mode (Substructure Search)
    • Info Button and Tooltips
      • Configuring Displayed Data
      • Disabling the Info Button
    • DataFrame Integration
      • Pandas
      • Automatic Field Detection
    • Viewing Clusters
    • API Reference
      • MolGrid Class
        • MolGrid
      • molgrid Function
        • molgrid()
  • C3D Interactive 3D Viewer
    • Quick Start
    • Adding Molecules
    • Adding Design Units
    • Disabled Molecules
    • View Presets
    • Custom Styles
    • Surfaces, Maps, and Isosurfaces
    • Zoom Targets
    • UI Configuration
    • Background Color
    • Builder API
    • HTML Export
  • Advanced Rendering

API Reference

  • API Reference
    • cnotebook
      • LevelSpecificFormatter
        • LevelSpecificFormatter.NORMAL_FORMAT
        • LevelSpecificFormatter.DEBUG_FORMAT
        • LevelSpecificFormatter.__init__()
        • LevelSpecificFormatter.format()
      • enable_debugging()
      • CNotebookEnvInfo
        • CNotebookEnvInfo.__init__()
        • CNotebookEnvInfo.pandas_available
        • CNotebookEnvInfo.pandas_version
        • CNotebookEnvInfo.polars_available
        • CNotebookEnvInfo.polars_version
        • CNotebookEnvInfo.ipython_available
        • CNotebookEnvInfo.ipython_version
        • CNotebookEnvInfo.marimo_available
        • CNotebookEnvInfo.marimo_version
        • CNotebookEnvInfo.molgrid_available
        • CNotebookEnvInfo.c3d_available
        • CNotebookEnvInfo.is_jupyter_notebook
        • CNotebookEnvInfo.is_marimo_notebook
      • get_env()
      • display()
      • Package Overview
      • Usage
      • Module Attributes
        • cnotebook_context
      • Environment Detection
    • molgrid
      • Usage Examples
        • Basic Grid
        • Grid with DataFrame
        • Retrieving Selections
    • C3D Module
      • C3D Class
        • C3D
      • Conversion Utilities
    • context
      • CNotebookContext Class
      • Usage
      • Configuration Options
        • Image Dimensions
        • Output Format
        • Scaling
    • render
      • Rendering Functions
      • Key Functions
        • oemol_to_html
        • render_molecule
    • pandas_ext
      • Pandas DataFrame Accessor
      • Usage
      • DataFrame Methods
        • DataFrame.chem.as_molecule()
        • DataFrame.chem.highlight_using_column()
        • DataFrame.chem.fingerprint_similarity()
        • DataFrame.chem.molgrid()
        • DataFrame.chem.set_render_options()
      • Series Methods
        • Series.chem.highlight()
        • Series.chem.align_depictions()
        • Series.chem.set_render_options()
        • Series.chem.molgrid()
    • polars_ext
      • Polars DataFrame Accessor
      • Usage
      • DataFrame Methods
      • Series Methods
    • Module Overview
      • Core Modules
      • Visualization
      • DataFrame Extensions
CNotebook
  • Search

© Copyright 2024, Scott Arne Johnson.

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