Slat Generator API

Name

Slat Generator API: Utility scripts for working in the aSAM and kSAM

Description

The Slat Generator API is a set of utility scripts to facilitate work with the abstract Slat Assembly Model (aSAM) and kinetic Slat Assembly Model (kSAM). They can be used to generate and work with systems used by the SlatTAS and RodSim simulators.

The Slat Generator API is a set of Python scripts and functions designed to facilitate the generation, simulation, viewing, and analysis of slat assembly systems. It is evolving, and therefore changing, extremely quickly so it is likely to have many bugs and broken pieces of functionality. Its main components are the following:

• slat_generator.py: A set of classes and functions shared by most scripts and used to abstractly represent, generate, manipulate, and output slats, gadgets, etc.

• SlatSystem.py, SlatAssembly.py, SlatType.py, PyTASTileTypeLight.py: A set of classes to represent slat systems, assemblies, and types

• slat_ribbon_generator.py: A script for generating slat systems that self-assemble ``ribbons, allowing for the setting of parameters such as cooperativity, slat count, motifs, etc.

• slat_simulator_wrapper.py: A script that can be used to drive the RodSim simulator by setting all necessary input parameters via the command line. It allows for batches of simulations to be run and performs tasks such as pattern matching of input file names.

• slat-assembly-drawer.py: A script that can read xml files containing slat assemblies (e.g. those output by RodSim) and output PDF and/or SVG files showing images of the assemblies.

• slat-Sierpinski-triangle-generator.py: A script for generating slat systems that self-assemble the Sierpinski triangle pattern, allowing for the setting of parameters such as cooperativity, slat count, motifs, etc.

The scripts can be downloaded via the following link:

Slat Generator API files Note that the latest version can be found at the bottom of the list.