You are reading the documentation for version 1.1 of OpenStructure. You may also want to read the documentation for: 1.2 1.3 1.4 1.5 1.6 1.7 1.7.1 1.8 1.9 1.10 1.11 2.0 2.1 2.2 devel

A gentle introduction to OpenStructure

In this tutorial you will be learning by example how to use the OpenStructure framework.

We assume that you already have a version of OpenStructure installed. If not, please refer to Installing OpenStructure From Source.

What will be covered in this tutorial?

This tutorial is aimed at users that would like to get their hands dirty and execute commands in Python and write scripts rather clicking their way through a shiny user interface. The user interface of OpenStructure is in a very early state anyway that you probably won’t go far by clicking your way through...

The tutorial is divided into several parts. The first part of the tutorial is a walk-through of the basic functionality you will be using in your everyday work, followed by an introduction to the mol, img and seq modules.

Getting ready to rumble

The files we will be using in the tutorial are available in the examples folder that comes with OpenStructure. Depending on your platform, the examples are located at a different location:

  • on MacOS X the files are located inside the application bundle. The file browser fill automatically point to the examples.
  • on Linux and Windows PREFIX/share/openstructure/examples, where PREFIX is the path to the directory containing OpenStructure.

Starting DNG

The graphical user interface of OpenStructure is called DNG (Dino/DeepView Next Generation). To start it,

  • on MacOS X double click DNG.app
  • on Windows double click dng.bat inside the PREFIX/bin directory
  • on Linux fire up a terminal change into the OpenStructure installation directory and type ‘bin/dng’. If you have the binary directory in the PATH, typing dng is sufficient.

Interactive Python Shell

Now we will enter commands in the Python Shell (in the screenshot above, the python shell is located at the bottom of the main window). If you want to get more information on any object, function or class, the python help command may be useful. For example:

# get list of methods of EntityView
help(mol.EntityView)
# get help for method Select
help(mol.EntityView.Select)

Continue with part one

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