Graphical user interface for SCINE
Project description
Introduction
SCINE Heron is the graphical user interface for all other SCINE modules. It has two main ways of operation.
First, one can explore chemical reactivity immersively and interactively based on first principles. The graphical user interface of SCINE Heron displays a three-dimensional molecular structure and allows users to interact with it. They can induce structural changes with a computer mouse or a haptic device and perceive the effect of their manipulations immediately through visual and/or haptic feedback. For fast electronic structure calculations, we employ currently different semi-empirical methods, which can deliver properties in the millisecond timescale, while providing a qualitatively correct description of the potential energy surface.
Second, one can interact with explorations done by SCINE Chemoton. One can visualize the chemical reaction network without drowning in too much information. For example, one can selectively display reactions with a barrier lower than a certain, user-specified threshold. Furthermore, one can analyze all compounds and reactions discovered, e.g., for reactions, one can visualize the trajectory and study the energy along it. It is also possible to search and visualize all pathways between two given compounds. Any compound discovered by Chemoton can be transferred to the interactive part of the GUI, allowing it to be further studied.
License and Copyright Information
For license and copyright information, see the file LICENSE.txt in this directory.
Installation
Prerequisites
The application requires several third-party and SCINE related Python packages to run. These packages can be installed using the following command:
pip install -r requirements.txt
You may want to create and activate a virtual environment first.
Additional third party packages are used for testing, type checking, and formatting. See requirements-dev.txt and pypi.org for more information. Again, the packages can be installed using:
pip install -r requirements-dev.txt
Installation
Heron can be installed using pip (pip3) once the repository has been cloned:
git clone <heron-repo>
pip install ./heronA non super user can install the package using a virtual environment, or the --user flag.
Usage
Starting the Application
The application can be started by the command:
python3 -m scine_heron
To open a file with molecule directly from the command line, you can use the --file option:
python3 -m scine_heron --file xyz_files/pyridine.xyz
The application is per default in dark mode. If light mode is preferred, you can use the --mode option:
python3 -m scine_heron --mode light
Shortcuts
The application features a range of shortcuts, a few are given here.
- General:
Scrolling Vertically: Mouse Wheel
Scrolling Vertically: Shift + Mouse Wheel
Zooming: Ctrl + Mouse Wheel (in the main molecular viewer also without Ctrl modifier)
Open Database Connection Dialogue: Ctrl + D
- Main Molecular Viewer:
Open File: Ctrl + O
Save Molecule: Ctrl + S
Save Trajectory: Ctrl + Shift + S
Start Real Time Calculation: Ctrl + F (if calculator is available and molecule loaded)
- All Network Views:
Copy ID of Focussed Node: Ctrl + C
Haptic Device
SCINE Heron supports the usage of a haptic device. It allows the user to feel force feedback when manipulating molecules in the main molecular viewer. In order to install and connect a haptic device to SCINE Heron please read the instructions and referenced manuals below.
Haptic Device Install
Connect your haptic device. Download drivers for it and install according to the instructions. Read the official webpage for more information.
Install OpenHaptics SDK. Read the Programmers Guide and API Reference Guide for more information.
Then install the scine_heron_haptic module (see the instructions in the haptics/ subfolder).
How to Cite
When publishing results obtained with Heron, please cite the corresponding release as archived on Zenodo (please use the DOI of the respective release).
Support and Contact
In case you should encounter problems or bugs, please write a short message to scine@phys.chem.ethz.ch.
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