Author: Stephane Redon

What’s new in SAMSON 2020, the open molecular modeling platform?

To get SAMSON, sign up on SAMSON Connect (it’s free!) and download it now!   In line with our vision of a platform democratizing access to molecular modeling, SAMSON 2020 significantly improves the user experience and brings numerous, game-changing functionalities.   As easy as “ABC” We’ve wanted to offer this in SAMSON for years, and it’s finally here: a powerful yet easy-to-use Molecular builder. A is for “Atoms” and “Assets” Of course, we made it possible to build using individual atoms:…

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A new major release of SAMSON, the integrated platform for molecular modeling

We are excited to share a new major release of SAMSON, the integrated platform for molecular modeling. Here is a quick overview of the main novelties. A streamlined user interface We have completely redesigned SAMSON’s interface to make it easier to learn and use. Toolbars are gone, menu widgets are in: Easily find what you need The Search box on the top right of the menu bar lets you quickly find commands, editors and apps: Furthermore, menus, command groups and…

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Programming a path generator

  In this tutorial, we are going to create an editor such that a user can create paths in the viewport. First, use the SAMSON Element Generator to create a new SAMSON Element called Path containing: An Editor class called Editor (full name: SEPathEditor). This class will make it possible for the user to add new nodes to the path. A Visual Model class called VisualModel (full name: SEPathVisualModel). This will be the main class used to represent a path…

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Docking libraries of ligands with AutoDock Vina Extended

In this tutorial, we will see how to dock libraries of ligands into proteins and rank them with AutoDock Vina Extended SAMSON Element. The AutoDock Vina Extended SAMSON Element wraps the popular protein-ligand docking program AutoDock Vina (O. Trott, A. J. Olson, AutoDock Vina: improving the speed and accuracy of docking with a new scoring function, efficient optimization and multithreading, Journal of Computational Chemistry 31 (2010) 455-461). Requirements SAMSON, version 0.7.0 or higher AutoDock Vina Extended SAMSON Element Before starting the…

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Building nanotubes models with SAMSON

In this quick tutorial, you will learn how to easily generate nanotube models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Element that you can find in SAMSON Elements: If you need help with installing new SAMSON Elements to your SAMSON installation, please visit User guide: Adding Elements from SAMSON Connect. If you need help with installing SAMSON itself, please visit User guide: Installing SAMSON. Note: you can check whether you have this SAMSON Element…

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Integrating external programs

In this tutorial, we show how to call an external executable from SAMSON, in order to perform calculations based on selected atoms in the document. Setting up the external executable Implement the following program, and compile it to produce an executable called Barycenter: #include <sstream> #include <fstream> #include <string> #include <iostream>   int main() {   unsigned int numberOfAtoms;   // open the file   std::ifstream input("input.txt");   // read the number of atoms   std::string line; std::getline(input, line); std::stringstream…

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Creating novel visualizations

Please, refer to the updated version: Developer guide: Creating visualizations. This tutorial shows you how to create a new visual model that shows the van der Waals representation of a group of atoms. Setting up the SAMSON Element Use the SAMSON SDK Element Generator to create a new SAMSON Element called VanDerWaals, containing a visual model called SEVanDerWaalsVisualModel. We refer to the tutorial on generating the SAMSON Element for a reminder on how to use the SAMSON Element Generator. Setting up…

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Importing and exporting data

Please, refer to the updated version: Developer guide: Importing data Developer guide: Exporting data In this tutorial, we create an importer and an exporter for the .xyz format. Start by creating a new SAMSON Element called XYZ with the SAMSON SDK Element Generator, and add an importer class (called SEXYZImporter) and an exporter class (SEXYZExporter). We refer to the tutorial on generating the SAMSON Element for a reminder on how to use the SAMSON Element Generator. Despite what the names…

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Handling units and dimensional analysis

Please, refer to the updated tutorial: Developer guide: Handling units. In this tutorial, we explore a bit more the role of units in SAMSON by developing an app that performs energy conversions. We refer you to the SDK documentation for an extensive description of the units mechanism in SAMSON. Setting up the SAMSON Element and its interface Use the SAMSON SDK Element Generator to create a new SAMSON Element called EnergyConverter, containing an app called SEEnergyConverterApp. We refer to the…

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Programming new apps

Please, refer to the updated version: Developer guide: Programming new apps. In this tutorial, you will learn how to program an App that shakes atoms in a document when the user presses a button. Generating the SAMSON Element First, use the SAMSON SDK Element Generator to create a new SAMSON Element containing one app class. We refer to the tutorial on generating the SAMSON Element for a reminder on how to use the SAMSON Element Generator. Call the SAMSON Element…

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