Import of oxDNA Files

[BradyAJohnston]

Adds initial support for importing oxDNA files. Expects a topology and trajectory file to import. The trajectory is often a single frame, where a single topology object will be created. If the trajectory contains multiple frames, then a frames collection containing each frame of the trajectory will be imported, enabling playback of the animation through Molecular Nodes.

Tasks:

• Support old topology
• Support new topology
• properly align with base_normal / base_vector
• multi-frame trajectory import
• trajectory bounding box wrapping

Example trajectory (from here) rendered below, loading in a 5.5 GB trajectory file and 3.8 MB topology file results in ~800 MB .blend file.

origami_trajectory.mp4

The stand ID is labelled as chain_id to fit with the rest of Molecular Nodes. Bases are converted to their numeric representations and stored as res_name. Using the position, base_vector and base_normal you can instance bases on the DNA, either as simple cylinders or their different representations:

A simple Points to Curves node can turn the 'backbones' into the cuves of the DNA.

Build for import oxdna files:

MolecularNodes_oxDNA.zip

[codecov]

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