SAMSON

In this part, you will learn how to use SAMSON, from its fundamentals to more advanced tasks.

Basics

Let's start with some basics: the structure of the main interface, then SAMSON Elements.

Interface

The SAMSON interface is composed of six parts, visible in the image below:

Interface.png
The SAMSON interface
  1. The menu bar gives you access to the main commands
  2. The toolbars give you fast access to the most used commands
  3. The viewport shows a three-dimensional representation of the document
  4. The document view shows a representation of the structure of the document
  5. The history gives you a list of performed actions
  6. The status bar may provide messages


The SAMSON interface is automatically constructed from your SAMSON Elements.

SAMSON Elements

SAMSON Elements are modules for SAMSON that you add from SAMSON Connect. The first time you start SAMSON, some default SAMSON Elements are automatically installed.

SAMSON Elements may contain apps, editors, importers, exporters, interaction models, visual models, and state updaters.

Apps

Apps may provide any type of functionality. For example, an app may be a connector to an external executable or web service, may wrap previously developed code to integrate its functionality with SAMSON and other SAMSON Elements, or provide entirely new functionality based on the SAMSON Application Programming Interface. When SAMSON loads an app from a SAMSON Element during startup, it includes it in the App menu and the App toolbar. To start using an app, click on it from either the App menu or the App toolbar.

Apps.png
A few Apps in SAMSON

Editors

Editors are one of the main ways to interact with documents. Editors receive user events (e.g. mouse and keyboard events) and use these events to provide potentially complex editing functionality. For example, an editor may be a rectangle selection tool, a nanotube generator that lets users create a new nanotube model in a few clicks, a tool for deforming molecular structures while preserving local rigidity, a tool to apply a rigid-body transform to a model, etc. At startup, SAMSON positions editors in the Edit menu and the Editors toolbar.

Important: only one editor is active at any time.

GeneratingANanotube.png
A nanotube generator editor

Importers

Importers are dedicated to parsing files. An importer may be e.g. a PDB parser, an electron density parser, etc. Whenever an importer is loaded at startup, SAMSON adds it to the list of available importers, used in particular when opening a new file from the File menu.

Exporters

Exporters are classes dedicated to exporting content from the document to files. An exporter may be e.g. a PDB exporter, an XYZ exporter, etc. Whenever an exporter is loaded at startup, SAMSON adds it to the list of available exporters, used in particular when saving to a file from the File menu.

Interaction models

Interaction models are one of the five categories of models in SAMSON. They are responsible for computing energies and forces and are used in SAMSON to perform various modeling and simulation tasks. An interaction model could be e.g. a spring model, an elastic network model, an extended Hückel model, etc. When an interaction model is loaded at startup, SAMSON stores it in a list of available interaction models, used in particular when adding a simulator from the Simulation menu.

Visual models

Visual models are one of the five categories of models in SAMSON. They provide visual representations in the viewport. A visual model may be e.g. a secondary structure representation applicable to protein models, an electron density isosurface, a volume rendering of an electrostatics field, etc. When a visual model is loaded at startup, SAMSON stores it in a list of available visual models, used in particular when adding a visual model from the Visualization menu.

State updaters

State updaters implement methods used to advance states during simulations. State updaters may be e.g. minimization algorithms, Monte Carlo methods, molecular dynamics algorithms, etc. When a state updater is loaded at startup, SAMSON stores it in a list of available state updaters, used in particular when adding a simulator from the Simulation menu.