Sec struct

[sreisser]

Hi, this uses output of ANNOTATE to minimize and draw secondary structures: 1) minimize on dotbracket, draw dotbracket 2) minimize on stack+pair, draw stack+pair 3) minimize on dotbracket, draw stack+pair For trajectories (multiple frames), interactions are color-coded by population. It's also possible to use VARNA or RNAstructure svg as template positions for the residues.

I changed the output in ANNOTATE to read residue IDs and nucleotides from the sequence (added an extra line).

Code might still a bit messy but should be working now. It draws most of the structures I tried fine, including pseudoknots, however can get messy with large structures with many interactions. Let me know if you have suggestions (also esthetic ones) or have a specific molecule that's not working.

Cheers, have a good weekend Sabine

[sbottaro]

Hi @sreisser, thanks! this looks great. It seems that RMSD tests fail - is it because you changed to backbone-only RMSD? Should we add a flag so that the user can choose whether to use BB-only or heavy-atoms?

[codecov-io]

Codecov Report

Merging #32 into master will decrease coverage by 12.67%. The diff coverage is 1.9%.

@@             Coverage Diff             @@
##           master      #32       +/-   ##
===========================================
- Coverage   79.82%   67.14%   -12.68%     
===========================================
  Files          13       13               
  Lines        1621     1936      +315     
===========================================
+ Hits         1294     1300        +6     
- Misses        327      636      +309

Impacted Files	Coverage Δ
barnaba/functions.py	57.67% <1.9%> (-32.66%)	:arrow_down:

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[GiovanniBussi]

@sreisser is it possible to add a regtest for this?

[sreisser]

Hi @sbottaro,

yes sorry I forgot to reverse that. Yes I think it would be useful to have an option for BB-only, to be able to better compare different sequences.

Cheers Sabine

2018-05-19 14:47 GMT+02:00 Sandro notifications@github.com:

Hi @sreisser https://github.com/sreisser, thanks! this looks great. It seems that RMSD tests fail - is it because you changed to backbone-only RMSD? Should we add a flag so that the user can choose whether to use BB-only or heavy-atoms?

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/srnas/barnaba/pull/32#issuecomment-390402735, or mute the thread https://github.com/notifications/unsubscribe-auth/APiEqPn0bH1bfWazuEfcVMAuGY945RTFks5t0BRugaJpZM4UFA0d .

[sbottaro]

Yes, that's a good idea. I open a new issue now.