We are proud to announce that SAMSON 0.7.0 is now available on Windows, Linux and Mac! SAMSON 0.7.0 has tons of new features and improvements, both in its core and through SAMSON Elements, so here’s an overview.
Python scripting
Here it is: Python scripting is now available! Most of the SAMSON API is exposed in Python, and a Jupyter console embedded in SAMSON allows you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.
What’s more, Python makes it even easier to integrate and pipeline SAMSON and SAMSON Elements with well-known packages from diverse fields, e.g. TensorFlow, PyRosetta, RDKit, ASE, etc., to name a few. The possibilities are endless, and that’s why we’re so excited.
For more information about how to use Python in SAMSON, please visit the scripting guide.
Documentation
A new documentation center is now available, which makes all the documentation published so far more organized and accessible. An automatic update mechanism also allows us to very easily release documentation updates, even between two versions of SAMSON.
We also welcome external contributors, so that if you would like to e.g. add a tutorial to the documentation center (for example to explain how to use a SAMSON Element you’re distributing through SAMSON Connect), just ask us and we’ll give you access. Your tutorial might even be featured on the main page of the documentation center, so give it a try!
You may access the documentation center from SAMSON Connect, or directly at https://documentation.samson-connect.net.
Forum
With the growing number of users and developers, now from hundreds of labs and companies, we felt that it became important (and, we’ll admit, long overdue) to add a forum to SAMSON Connect.
The new forum has four main categories: General, SAMSON, Develop, and Connect.
The General category is for announcements, brainstorming, discussing about the community, and practicing writing posts and questions.
The SAMSON category is for everything related to using SAMSON and SAMSON Elements. You may also use this category to showcase your work and request new features.
The Develop category is to get support on developing SAMSON Elements with the SAMSON SDK. Subcategories are based on SAMSON Elements classes: apps, editors, modeling, simulation, etc.
We are especially excited about the Connect category, where users and developers can share SAMSON documents and Python scripts. Imagine you have built a model of a functionalized nanotube and you would like to share it: you can upload your SAMSON document to the forum. What if you don’t know how to build a specific model or perform a specific task? Post a request on the forum to ask for help. Maybe someone will even upload a SAMSON document or a Python script for you. Since SAMSON documents may contain models, properties, etc., and the SAMSON file format is extensible, you can exchange rich data.
You may access the new forum from SAMSON Connect, or directly at https://forum.samson-connect.net.
Inspector
SAMSON 0.7.0 includes an inspector that may be used to visualize and edit node properties, such as PDB properties, simulation parameters, visual characteristics, etc. Properties may be edited for one node only, or for all selected nodes simultaneously.
The Inspector GUI is automatically generated from the descriptors included in the SAMSON Elements, thanks to the new developer functionalities to expose attributes.
Toggle the inspector from the Window menu, or with the CTRL+I or CMD+I shortcut.
Fast filtering and selection
The document view in SAMSON 0.7.0 includes a search widget for fast filtering and selection. Enter a string to show nodes with a matching name, or a Node Specification Language expression for more complex filtering operations, and the Document view automatically adapts as you type. If you want to select the highlighted nodes, just hit Enter.
Here, the user types “ala” to only show the nodes whose name contain “ala” (and their parents). The document view is updated as the user types:
When the user presses the Enter key, the corresponding nodes are selected:
Any Node Specification Language (NSL) expression works. Here, the user selects all side chains (“n.t sc” = “node.type sidechain”):
The current selection is summarized at the bottom of the document view. Click it to access contextual actions:
Paths
A new node type is available: path. A path node may store information about positions, velocities, forces, energies and time. Use the inspector to visualize the path:
You may also double click the path node in the document view to start and stop the animation. You can expect more SAMSON Elements taking advantage of paths in the upcoming weeks.
Orthographic projection
As a growing number of users requested it (for e.g. materials science), we added an orthographic projection mode. Activate it through the context menu of the camera, or the inspector.
Controllable secondary structures renderings
You now have more control on the rendering of secondary structures (arrow shapes, thickness of helices and strands, etc.):
SAMSON Connect
We have added several functionalities to SAMSON Connect.
First, the site now uses AJAX to make it significantly more efficient and improve the user experience. It is now extremely fast to add SAMSON Elements to your SAMSON:
You can now also easily find SAMSON Elements thanks to the search bar:
When you are a developer, you also have access to an improved interface for editing your SAMSON Elements on SAMSON Connect:
New short domain name
Because (we admit) we’re kinda geeky, we have registered a new domain name to make it shorter to communicate on SAMSON Connect: s-c.io.
Feel free to use it when you wanna share SAMSON!
That’s all for today’s highlights! In the coming weeks, we’ll go in more detail about some of the new SAMSON Elements released with SAMSON 0.7.0.
If you already have SAMSON 0.6.0, just start SAMSON and use the auto-update feature. Else, you may download SAMSON 0.7.0 at s-c.io/dl (it’s free!).
Don’t hesitate to comment below to let us know what should be improved, and which features you’d like to have!
