For molecular modelers, translating complex designs into precise atomic-level structures can be a major challenge. How do you fine-tune atomic properties, automate structural edits, or create intricate geometries with ease? If you’ve ever faced this struggle, SAMSON’s Simple Script Extension may hold the answer.
The Simple Script Extension empowers users to modify multiple atomic properties like positions, visibility, and element types through scripting. Using mathematical expressions and powerful logical operators, it transforms molecular modeling processes into structured, automated workflows, thereby saving time and enhancing precision. One particularly illuminating example is the creation of nanoscale designs—like a graphene-based Batman batarang! 🎨🦇 Let’s explore how this tool can simplify molecular manipulation while opening vast creative opportunities.
Key Capabilities of the Simple Script Extension
At its core, this extension provides a scripting framework where you can manipulate an active molecular document. Using predefined variables and math-based logic, you can achieve tasks such as:
- Adjusting atomic positions with precision.
- Controlling visibility of selected atomic groups.
- Assigning new properties like chain IDs, charges, or element IDs.
- Using logical expressions to create conditional changes based on atomic attributes.
Getting Started with the Scripting Language
The extension supports variables for nodes and atoms as well as mathematical operations. Here’s a small list of possible manipulations using variables:
a.x,a.y,a.z: Atomic positions.a.element: Name of the element, e.g.,'Carbon'.n.selectionFlag: Select or deselect a node based on conditions.
The scripting syntax follows C-like logic, incorporating standard operators (+, -, *, /), functions (sin, cos, log), and control structures (if-then-else, for-loops, switch-case). You can even include comments for better script organization.
Example: Creating a Sinusoidal Graphene Sheet
Consider altering the z-coordinates of all atoms in a graphene sheet using sine-based logic:
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a.z := sin(a.x * π / 12); |
This simple script creates an elegant sinusoidal pattern, as demonstrated in the animation below:
Design Complex Structures, Like Nano-Batarangs!
Moving beyond simple changes, let’s look at creative applications, like crafting nano-batarangs. By utilizing conditional logic and intricate mathematical setups, you can generate nanoscale versions of Batman’s iconic batarang shape within a graphene sheet. Below is a visual illustration:
Here’s a snippet of the script that governs the shape by modifying visibility and selection flags based on specific conditions:
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// Top of the head if (abs(x) <= 0.5 && y <= 2.25) { n.selectionFlag := 1; a.visibilityFlag := 1; } else { n.selectionFlag := 0; a.visibilityFlag := 0; } |
This is only a teaser of what the Simple Script Extension can achieve. Whether it’s educational demonstrations, testing hypotheses, or visualizing complex geometries, the possibilities are vast.
Why Molecular Modelers Should Use It
The greatest pain for modelers is often the manual repetition of structural modifications. With this extension, you:
- Automate tedious molecular edits via customizable scripts.
- Leverage mathematical logic to ensure consistent precision.
- Experiment with creative molecular designs effortlessly.
Ready to start scripting and elevate your molecular modeling capabilities? Visit SAMSON’s documentation for the Simple Script Extension here.
Note: SAMSON and all SAMSON Extensions are free for non-commercial use. Download SAMSON at https://www.samson-connect.net.