Protein

• Graphein - Residue Graph Tutorial
  • Config
  • High-level API
    • Edge Functions
    • Features & Metadata
  • Low-Level API
    • Pre-Processing
    • Building the Graph
• Graphein - Atom Graph Tutorial
  • Config
  • Config for Atom-level Graphs
  • High-level API
• Constructing Graphs from AlphaFold Protein Structure Database
  • Downloading Structures
  • Constructing the Graph
  • Adding Edges
• Secondary Structure Graphs & Chain Graphs
  • Secondary Structure Graphs
    • MultiGraph
  • Chain Graph
    • Multigraph
    • Weighted Graph
• Constructing Subgraphs in Graphein
  • Subsetting with a list of nodes
  • Spatial Subgraphing
  • Subgraphing based on Residue Types
  • Subgraphing based on Chains
  • Subgraphing to Protein Surface
  • Subgraphing based on Secondary Structure
  • Subgraphing based on sequence positions
  • Subgraphs based on bond types
  • K-hop subgraphs
  • Subgraphing based on Atom Types
  • High-level function
• Creating Protein Meshes in Graphein & 3D Visualisation
  • High-level API
    • Config
    • Building a mesh
  • Modifying Mesh Parameters
  • Using PyMol for 3D Visualisation
• Protein Graph Analytics
  • Constructing a graph for analysis
  • Residue Composition
  • Graph Summary Statistics
  • Degree Distribution
  • Edge Type Distribution
  • Scatter Matrix
• Interactive Visualisation with Plotly
  • Creating graphs
  • Distance Matrix and Contact Map
  • Distance Landscape
  • Plot 3D Structure
    • Interactive
    • Static Plots
  • Asteroid Plot
    • Parameters