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Feature Request: Export to Cadnano #31

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mattaq31 opened this issue Feb 14, 2022 · 5 comments
Open

Feature Request: Export to Cadnano #31

mattaq31 opened this issue Feb 14, 2022 · 5 comments
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enhancement New feature or request

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@mattaq31
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mattaq31 commented Feb 14, 2022

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 thenlevy added the enhancement New feature or request label Feb 23, 2022
@thenlevy
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thenlevy commented Mar 4, 2022

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
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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
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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
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thenlevy commented May 23, 2022

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
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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.

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