Scripting guide

Getting started

• Setting up Python Scripting
• Documentation
• Troubleshooting
• Version changes

Developer tutorials

• Creation of Python bindings for a SAMSON Extension

User tutorials

• Introduction
  • Working with the module
  • Getting help
  • Working with nodes in data graph
  • Importing and exporting
  • Making history: holding
  • Getting active Document, Camera and Layer
  • Saving history
  • Running scripts
• Units
  • Quantity sub-module
    • Unit systems
      • SI units (International System of Units)
      • atomic units
      • dalton
      • electronvolt
      • kilocaloriePerMole
      • Examples
    • Conversion between different unit systems
      • Examples
  • Type sub-module
    • Examples
• SAMSON Python Scripting samples on github
• Visualization and exploration of data
  • matplotlib
  • R ggplot
  • seaborn
  • bokeh
• Colorization
• Using the Camera and producing animations
  • Rotation of a molecule
  • Moving along the path
• Computation of the RMSD
• Creation of a nanotube fabric: replication, modification of positions
• Using ASE in SAMSON
  • Optimization of a water molecule using BFGS
  • Nitrogen on copper
  • Usage of the SAMSON’s Interaction Model
• Using MDAnalysis in SAMSON
  • Analyzing trajectories
  • Superposition of structure
• Using MDTraj in SAMSON
  • Analyzing trajectories
  • Superposition of structure
• System preparation with HTMD