You know how when you import PDB structures into Rosetta and relax them Rosetta adds the missing hydrogens? What is the algorithm that does that?
I want to know the mathematical aproach, not the code; does it use rotation vectors and a rotation matrix to find the orientation and position the hydrogens? Does it use another approach?
I beleive this same algorithm is used to add/replace sidechain? it finds the orientation and angles of the side chains and replaces them?
I have a backbone without any oxygens and I want to use this same algorithm to write a script that would add oxygens to a backbone.