DNA parameters

[vbbpinheiro]

Love the interface of ViennaRNA for Julia. I've just installed it and I am still testing all the functions.
For now I seem unable to run FoldCompound using either of the DNA parameters. All RNA parameters work.
I've gone through the code to see if I could pick any obvious glitches but I cannot find any faults there. I looked through the ViennaRNA package and both are there so I don't fully understand why I am being pushed onto "unknown energy parameters" error.

[marcom]

Thank you for the kind words. I forgot to tag a new release after adding support for DNA parameters and updating the README. I just tagged ViennaRNA v0.8.1 and DNA parameters should work now.

I haven't used the DNA parameters much myself yet, so any testing of them is much appreciated.

Something that i haven't investigated much in detail yet is that for the :DNA_Mathews2004 parameters, ViennaRNA outputs the following warnings when loading the parameters:

WARNING: stacking enthalpies not symmetric
WARNING: stacking enthalpies not symmetric
WARNING: stacking enthalpies not symmetric
WARNING: stacking enthalpies not symmetric

Edit: the RNAfold program from ViennaRNA-2.5.1 shows the same behaviour with this parameter set

[vbbpinheiro]

As far as I have tested it, everything is working well.
I get the same warnings you mentioned but the calculations proceed without error.
I ran a few sequences through the algorithm comparing it to the output of UNAfold. Barring some minor differences among the weaker interactions, outputs matched. So, I think all is well now.

[marcom]

Thanks for testing, please let me know if there are any other problems.