As SAMSON 0.7.0 is approaching, we would like to highlight a few upcoming features that we feel are bringing us a little closer to our vision of a federating platform for computational nanoscience.
Python scripting is coming to SAMSON 0.7.0, and we are (very) excited about it. Most of the SAMSON API is now exposed in Python, and this will allow you to create models and run simulations, generate movies, perform analysis and reporting, etc., directly from scripts.
What’s more, Python will make 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.
With the growing number of users and developers, we felt that it was important (and, we’ll admit, long overdue) to add a forum to SAMSON Connect. The coming forum will have four main categories: General, SAMSON, Develop, and Connect.
We are especially excited about the Connect category, where users and developers will be able to share SAMSON documents and Python scripts.
Imagine you have built a model of a functionalized nanotube and you would like to share it: you’ll be able to 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 will be able to exchange rich data.
A new documentation center will be released, which will make all the documentation published so far more organized and accessible. An automatic update mechanism will also allow us to very easily release documentation updates, even between two versions of SAMSON.
We will also open the documentation to contributors, so that if you would like to e.g. add a tutorial to the documentation center, 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!
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.
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.
In the example below, the user highlights all atoms within 2 Angstrom of the current selection (“n.t a w 2A of n.s” = “node.type atom within 2 Angstrom of node.selected”), and the Document view shows the corresponding atoms.
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.
That’s all for today’s highlights! Don’t hesitate to comment below to let us know what should be improved, and which features you’d like to have!