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Scripting guide

Script everything in SAMSON thanks to the integrated Python console and SAMSON API accessible through Python.

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

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