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thenlevy / ensnano

ENSnano, a 3D graphical application for DNA nanostructures.
GNU General Public License v3.0
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Feature Request: Export to Cadnano #31

Open mattaq31 opened 2 years ago

mattaq31 commented 2 years ago

Hi,

First of all, this tool is great, all the combined 2D/3D features make it a significant improvement over Cadnano! Thanks for open-sourcing this for the community!

I have a feature request - Importing Cadnano files into ENSnano works well, but there doesn't seem to be a way to export back out to the Cadnano json format. This would be especially useful when running Cando (http://cando-dna-origami.org) simulations, which only work with a Cadnano file input. Perhaps you could also implement this to export 1 file per grid in a single system?

Many thanks!

thenlevy commented 2 years ago

Hi, Thank you for your kind words about ENSnano.

The Cadnano's file format is really different from ENSnano's, and writing an export procedure will require a bit of work. We may eventually implement it but it is quite low in our priority list right now. In the meantime we recommend instead to use the export to OxDNA for simulations

thenlevy commented 2 years ago

Hi, Little update on that topic, I'm thinking about implementing a direct export to the CanDo file format. This seems easier than an export to cadnano, and will allow simulations in CanDo

mattaq31 commented 2 years ago

That would be really helpful too! Do you think it would be possible to check the file if there are structures in the exported file that CanDo would find illegal?

thenlevy commented 2 years ago

I don't know about structures that are illegal in CanDo. The CanDo file format does not mention that https://cando-dna-origami.org/cndo-file-converter/

Do you have a link to some documentation that would describe what an illegal structure is in CanDo ?

mattaq31 commented 2 years ago

I don't know if there is any documentation, but I know from previous attempts, that if you attempt to uploaded a cadnano file with single-stranded elements the simulation typically crashes. Probably if you export directly to CanDo format you would be able to skip any issues with conversion from cadnano to cando - which would be even better.