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Modified bases energy parameters. #23
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At the moment this isn't available, but it shouldn't be too hard to add. I will try and add some basic functionality for this in the next few days. |
I have an initial implementation, you can try it out like this: Add the branch
and try some modified bases using ViennaRNA
fc = FoldCompound("AAACCCUUU")
partfn(fc) # -0.0025467473022687203 kcal mol^-1
ViennaRNA.sc_mod_pseudouridine!(fc, [7,8,9]) # modify positions 7, 8, 9
partfn(fc) # -0.004713416050703315 kcal mol^-1 Let me know how it goes. Note that this is all just very lightly tested at this moment. |
I tried it, and got the same output you did, thanks! |
It does seem to work, though I've noticed it works in the REPL but not in Jupyter or Pluto.jl. Is that expected? |
With Pluto you have to have something like this at the top of your notebook to disable Pluto's package manager and be able to use a branch of a package: begin
import Pkg
Pkg.activate("./")
Pkg.add(url="https://github.com/marcom/ViennaRNA.jl", rev="sc_mod-functions")
end Note the directory The Pluto wiki has some more information: https://github.com/fonsp/Pluto.jl/wiki/%F0%9F%8E%81-Package-management |
Package management under Jupyter should work more like normal Julia. You can check which Julia environment is active with: import Pkg
Pkg.status() and use |
Thanks, I'll look around a little more. I'm still getting the
So I think the right version is installed, just something else is going wrong. Thanks for your help, so far, though! Edit: got it working, needed to get rid of my old Manifest.toml and Project.toml and restart Julia. |
I have just released v0.11.2 of ViennaRNA.jl with the support for modified bases included, so feel free to switch over to the normal version of the package again. |
Is it currently possible to use the modified base energy parameters built in to Vienna 2.6?
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