Python bindings for SAMSON API

The Python Scripting module in SAMSON provides python bindings for SAMSON API and an integrated Python console. It provides you with an access to most of the SAMSON SDK allowing you to access most of SAMSON’s functionality through python scripting.

Python bindings for the SAMSON API are done in the same structure as the SAMSON SDK. The Software Development Kit (SDK) of SAMSON is composed of a set of libraries gathered in several library groups (SDK Organization). This documentation has links to the SAMSON SDK which you can check out for comparison and some additional information.

Note

This version of Python bindings is for SAMSON SDK 2023 R1.

The Python console in SAMSON comes with an integrated Jupyter Qt Console.

Python bindings are done thanks to pybind11 (pybind11 license).

Guide

The following guides demonstrate the usage of Python bindings for SAMSON API.

Guide

• Getting started
  • Importing samson module
  • Getting help
  • Saving history
  • Running scripts
• Working with documents and nodes
  • Documents
  • Moving around
  • Working with nodes
• Importing and exporting
• Running actions
  • Running actions by name
  • Running actions by UUID
  • Selecting nodes using runCommand and NSL
• Selecting nodes
  • Select using actions
  • Select using NSL
  • Select via nodes
  • Clear selection
  • Selection examples
• Getting nodes
• Colorizing nodes
  • Apply color
  • Apply color scheme
  • List of color schemes
  • Apply a color scheme with a color palette
• Visualizing
  • Applying visual models
  • Applying visual presets
• Making operations undoable
• Building
  • Creating a structural model
  • Creating an atom
  • Creating covalent bonds
  • Adding hydrogens
  • Minimizing systems
  • Examples
• Presenting and animating
  • What is a presentation
  • How to create a presentation
  • How to create an animation
  • Exporting a movie
  • List of available animations
• Units
  • SBQuantity
  • Type
• Examples
  • Building a decane molecule
  • Creation of a carbon nanotube fabric: replication, modification of positions
  • Compute RMSD between two molecules
  • Compute bond lengths along paths
  • Compute interatomic distances along path
  • Presentation: play path
  • Export trajectory frames

API documentation

Below the Python Scripting API description is subdivided into groups that correspond to the SDK Organization.

API

• Facade
  • SAMSON
• Data Model
  • Asset
  • Color Scheme
  • Data Graph
  • Document
  • Palette
  • SBQuantity
  • Type
  • Visualization
• Modeling
  • Dynamical Model
  • Element
  • Interaction Model
  • Model
  • Property Model
  • Structural Model
  • Visual Model
• Simulation
  • Neighbor Search
  • Simulator
  • State Updater
• GUI
  • Action
• Core
  • Class
  • Container
  • Reference

• Changelog
• All versions