Challenge 4

Challenge #4: Alignment Points

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STILL UNDER CONSTRUCTION. Identify sets of 6 nucleotides that are watson crick base-paired in helices that can be used as alignment points. An alignment point is defined as (i,j) where i and j are integers such that the residue pairs in the RNA structure (i,j),(i+1,j-1),(i+2,j-2) are watson crick base paired.

Hints: Look at the application pdb2fuzzy to figure out how watson crick base pairs are identified.

Watson-Crick:

std::pair faces;
float hydro=hydroType(i,j,&faces)

if(faces.first==0 && faces.second==0 && hydro > 1){
//watson crick base pair between i and j
}