I am working on developing my CST file for the protein I'm designing and I have a few questions about some of the additional constraints I've seen in the example CSTs mentioned in the user's manual.
First, when using Algorithm_Info::match_positions, will that apply those restrictions to both atoms specified or just to the second one (assuming the ligand is the first atom)? Obviously, if I'm specifying an interaction between ligand and amino acid, it could only apply to the amino acid, but I would like to constrain one or both residues when specifying interactions between two residues.
Secondly, if I used Template:: Atom_Map: 1 identical: X X, I understand that the first number X is the CST block and the second is the atom within the block - does the matcher interpret that as the same atom in two blocks, or the same residue and maybe different atoms within the residue? Residue seems more usable; same atom seems more likely.