Examples

This section collects practical examples of using the SAMSON Python API. The examples are grouped by task so you can quickly find a workflow that is close to what you want to script.

If you would like your examples to be featured here, please contact us.

Animations

• Presentation: play path
• Create animations and movies without presentations

Building systems

• Building a decane molecule
• Create atoms on a sphere
• Creation of a carbon nanotube fabric: replication, modification of positions

Colorization and visualization

• Colorize atoms by position
• Colorize atoms by velocity along path
• Visualize coarse-grained systems
• Colorize connected components by molecular weight

Exporting

• Export trajectory frames

Processing

• Compute RMSD between two molecules
• Compute bond lengths along paths
• Compute interatomic distances along path

Selections

• Select atoms and bonds by location
• Select connected components by molecular weight

Simulation

• Examples of usage of ASE package

Apps and GUIs

• Embedded app: a simple GUI with buttons
• Select connected components by molecular weight