fractaldna

Python routines for generating simple models of DNA

FractalDNA is being converted to a package, it is under active developmemt

This repository is an offshoot of my thesis work, where I simulate the impact of ionising radiation on DNA. For this, I need to model and visualise very large DNA structures

Modelling DNA geometries computationally can be done very crudely based on a few DNA motifs and a fractal geometry. It provides a memory efficient way of ensuring that an appropriate density of DNA is placed in a sample volume. The idea is to use a fractal as a seed for a collection of turned and straight geometries, and then place repeating turned and straight DNA segments inside these geometries.

Here you can see the idea being applied to the first few iterations of a Hilbert curve.

The project is divided into three sections, each with their own Readme:

• hilbert3d provides routines for generating 3D fractals from L-systems.
• simpledna has some routines for generating simple turned and straight DNA models.
• vis contains some Python routines that work in Blender to visualise the whole DNA structure.

This project is currently in a beta form, I'm working on documentation and the ability to generate videos of DNA procedurally in Blender from Python scripts. Though at the moment you can get some decent still results from the visualisation tools:

Also, a shout out to the blender DNA example by George Lydecker where I first saw Blender being used to render DNA, and whose example code inspired some of what is here. (https://github.com/glydeck/MoloculeParser)