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I'm trying to compare the output of 2 different algorithms of RNA structure prediction (my implementation of Nussinov vs RNA-mfold algorithm) using the RNAdistance algorithm that is part of ViennaRNA package. I'm getting a distance score of 38 between Nussinov prediction and the actual NMR structure, and a score of 14 between the m-fold algorithm and the NMR structure and I'm trying to understand whether it is a big difference.

In order to do that I have to look at the scoring table that is used by RNAdistance and found the following score table in the source code:

RIVATE CostMatrix  UsualCost =
{

/*    Null,       U,        P,        H,        B,        I,        M,        S,        E,        R     */

   {        0,        1,        2,        2,        2,        2,        2,        1,        1, DIST_INF},   /* Null replaced */
   {        1,        0,        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* U    replaced */
   {        2,        1,        0, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF},   /* P    replaced */
   {        2, DIST_INF, DIST_INF,        0,        2,        2,        2, DIST_INF, DIST_INF, DIST_INF},   /* H    replaced */
   {        2, DIST_INF, DIST_INF,        2,        0,        1,        2, DIST_INF, DIST_INF, DIST_INF},   /* B    replaced */
   {        2, DIST_INF, DIST_INF,        2,        1,        0,        2, DIST_INF, DIST_INF, DIST_INF},   /* I    replaced */
   {        2, DIST_INF, DIST_INF,        2,        2,        2,        0, DIST_INF, DIST_INF, DIST_INF},   /* M    replaced */
   {        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF, DIST_INF},   /* S    replaced */
   {        1, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0, DIST_INF},   /* E    replaced */
   { DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF, DIST_INF,        0},   /* R    replaced */

};

I also found the enter link description herefollowing explanation, but I do not understand what is the meaning of the table letters: U,P,H,B,I,MS,E,R ?

What is the meaning of the score of [H,B] = 2 for example? If anyone can explain the table it will be a great help in my project, thank you!

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Ok, the answer was right here and I missed it, posting it in case anyone else will do the same mistake as me in the future.

U = unpaired
P = paired
H = hairpin
B = bulge
I = internal loop
M = multiloop
S = stem (or stack)
E = external loop
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