Rewrite of the model layer and restraint layer to cast the model or models as graphs. Restraints or extensions of graphs are achieved via a mapping step that maps small graphs to large ones. Graphs should be serializable, and ideally, at some point, we make them compatible with other model/graph representations of Aimnet2 or Amber. Hydrogens should become default on. Ph level handling is gonna be an afterthought lets start by assuming the Ph is 7.
Rewrite of the model layer and restraint layer to cast the model or models as graphs. Restraints or extensions of graphs are achieved via a mapping step that maps small graphs to large ones. Graphs should be serializable, and ideally, at some point, we make them compatible with other model/graph representations of Aimnet2 or Amber. Hydrogens should become default on. Ph level handling is gonna be an afterthought lets start by assuming the Ph is 7.