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RDkit in Samson


I've posted about Samson a couple of times and it just keeps getting better and better.

SAMSON is a novel software platform for computational nanoscience. Rapidly build models of nanotubes, proteins, and complex nanosystems. Run interactive simulations to simulate chemical reactions, bend graphene sheets, (un)fold proteins. SAMSON's generic architecture makes it suitable for material science, life science, physics, electronics, chemistry, and even education. SAMSON is developed by the NANO-D group at INRIA, and means "Software for Adaptive Modeling and Simulation Of Nanosystems.

A recent blog post highlights the use of RDKit in Samson.

In this post I will present you the RDKit-SMILES Manager module that I integrated in the SAMSON platform. As some of you know, RDKit is an open source toolkit for cheminformatics which is widely used in the bioinformatics research. One of its features is the conversion of molecules from their SMILES code to a 2D and 3D structures. Thanks to the new SAMSON Element, it is now possible to use these features in the SAMSON platform. SMILES code files (.smi) or text files (.txt) containing several SMILES codes can be read using the import button.

The new module allows you to import a file containing SMILES strings, generate 2D depictions, and by right-clicking on these images, you can open, generate the 3D structure in SAMSON or save the image as png or svg.


It is also possible to run substructure searching using SMARTS.

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