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UC-Davis-molecular-computing / scadnano-python-package

Python scripting library for generating designs readable by scadnano.
https://scadnano.org
MIT License
13 stars 7 forks source link

support Extensions in oxDNA export #240

Closed cgevans closed 1 year ago

cgevans commented 2 years ago

Extensions are currently assumed to be loopouts in the oxDNA export code, causing it to fail.

dave-doty commented 2 years ago

Yeah, sorry, the extension support is very preliminary right now. I need to figure out a good way to do this, and also loopouts, which have a problem we discovered at DNA 28 when there are too many bases in too short a distance and it explodes the oxDNA dynamics simulation.

But I'm hoping this might not be too bad to support. Perhaps a good algorithm is just to draw the extension as a straight line with reasonable inter-base distance, going out perpendicular from the helix, based on the helix roll.

cgevans commented 2 years ago

But I'm hoping this might not be too bad to support. Perhaps a good algorithm is just to draw the extension as a straight line with reasonable inter-base distance, going out perpendicular from the helix, based on the helix roll.

That's what I'm currently playing with, somewhat ineptly, and it doesn't seem too bad: while my current code is doing some things that are clearly wrong in oxview, but they seem to largely correct themselves with a few hundred MC steps. Loopouts seem trickier.