Stephane Redon – Page 2 – SAMSON Documentation

What’s new in SAMSON 2020 R3

The new SAMSON 2020 R3 release brings numerous new features and improvements throughout the core of SAMSON, so let’s dive right in! Cloud computing One of the most exciting features of SAMSON 2020 R3 is the introduction of cloud computing capabilities. In many design situations, a personal computer might have too little processing power to perform advanced calculations (e.g. high-throughput screening, some molecular dynamics simulations, etc.). In agreement with our vision of democratizing molecular design, we are introducing the possibility to…

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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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Building carbon nanotube models with SAMSON

In this quick tutorial, we will show you how to easily generate carbon nanotube (CNT) models within SAMSON. Nanotube creator First, make sure you have the Nanotube creator SAMSON Extension that you can find on the SAMSON Extensions web page. If you need help with installing new SAMSON Extensions to your SAMSON installation, please visit User guide: Adding Extensions from SAMSON Connect. If you need help with installing SAMSON itself, please visit User guide: Installing SAMSON. Note: you can check whether you have…

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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 firstLineParser(line);
	firstLineParser >> numberOfAtoms;

	if (!numberOfAtoms) {

		std::ofstream output("output.txt");
		output << "No atoms" << std::endl;
		output.close();
		return 0;

	}

	// read the coordinates of the atoms and update the barycenter

	double x = 0.0;
	double y = 0.0;
	double z = 0.0;

	while (std::getline(input, line)) {

		std::stringstream lineParser(line);

		double currentX = 0.0;
		double currentY = 0.0;
		double currentZ = 0.0;

		lineParser >> currentX >> currentY >> currentZ;

		x += currentX;
		y += currentY;
		z += currentZ;

	}

	x /= (double)numberOfAtoms;
	y /= (double)numberOfAtoms;
	z /= (double)numberOfAtoms;

	std::ofstream output("output.txt");
	output << x << "A " << y << "A " << z << "A" << std::endl;

	return 0;

}

#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 firstLineParser(line);

firstLineParser >> numberOfAtoms;

if (!numberOfAtoms) {

std::ofstream output("output.txt");

output << "No atoms" << std::endl;

output.close();

return 0;

}

// read the coordinates of the atoms and update the barycenter

double x = 0.0;

double y = 0.0;

double z = 0.0;

while (std::getline(input, line)) {

std::stringstream lineParser(line);

double currentX = 0.0;

double currentY = 0.0;

double currentZ = 0.0;

lineParser >> currentX >> currentY >> currentZ;

x += currentX;

y += currentY;

z += currentZ;

}

x /= (double)numberOfAtoms;

y /= (double)numberOfAtoms;

z /= (double)numberOfAtoms;

std::ofstream output("output.txt");

output << x << "A " << y << "A " << z << "A" << std::endl;

return 0;

}

This program opens a text file named input.txt containing atoms coordinates and creates a file named output.txt that contains the coordinates of the barycenter of the atoms (or the string “No atoms” if the initial file…

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Snapping, cloning and extracting with selection editors

Please refer to the updated documentation: User guide: Selecting and User guide: Moving objects. The guide below is for the SAMSON version older than 0.8.0. The new version of selection editors now includes the possibility of snapping to atoms and nodes, as well as cloning and extracting structural nodes. Selection editors (point, lasso and rectangle selection) can be found in the Editors toolbar and the Edit menu: Activate snapping by clicking twice a selection editor (or use the corresponding shortcut twice): …

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