Accessing the data graph in Python

To efficiently manipulate nodes (atoms, bonds, side chains, molecules, etc.), use node indexers returned by the SAMSON.getNodes function applied to a Node Specification Language (NSL) expression. For example, SAMSON.getNodes(‘node.type atom’) returns an indexer containing all atoms in the active document.…

Creating a nanopore

To build a carbon nanopore, draw a graphene sheet and a nanotube, remove some atoms and use the Brenner reactive force field during interactive minimization to meld them. The Brenner potential (Brenner et al., Journal of Physics: Condensed Matter, Volume…

Create molecules using Python

To create molecules, Python bindings give you access to all modeling capabilities from SAMSON’s C++ core. Add atoms, bonds, molecules, crystals, automatically find covalent bonds, add hydrogens, etc., and minimize. All in a few lines. Use the Code Editor to…

Triggering GUI commands using Python

To trigger any GUI command in Python, call the SAMSON.runCommand function on the command name. Use this directly in the Python console (Ctrl / Cmd + 8), or in Python scripts to automate tasks using the Code Editor (Ctrl /…

Using appearance presets

To quickly change the look of objects when rendering with Cycles in SAMSON (Trace mode, shortcut F9), first apply a material, then apply an appearance preset in the Inspector.

Building with atoms and fragments

To build molecules, use A to add atoms and fragments, B to edit bonds, and C to edit charges. Combine this with interactive minimization (shortcut Z) to build physically-based structures.

Creating Python Apps with GUIs

To create a Python app with a GUI, use PySide to add widgets and connect their signals (“clicked”, etc.) to slots (Python functions). Here is the complete code (65 lines) of a simple app with two buttons to add and…

Illustrative style in two steps

To show molecules in the Goodsell Illustrative style in two steps, go to Visualization menu > Visual model > Visual Preset and choose Illustrative, then go to Visualization menu > Presets and choose Illustrative as well. The first step will…

Rotating fragments around bonds

To rotate a molecular fragment around a bond, use the Local Move Editor (shortcut M) and just click on the bond. The editor will automatically select the shortest fragment and will show the move widgets. Combine this with interactive minimization…