i ran into another problem in my restraint generation: in my model i use the MolecularHierarchy (protein->fragment). to make the restraint work on parts of the protein i introduce 'pseudo-fragments', which are then parents of the respective fragments. however, i now want to access the protein that a specific fragment belongs to. now my code is in the dilemma that there are two parents. i'd like to access the protein particle with the get_parent() function, but i end up with the pseudo-fragment used for restraint generation. can anybody provide my with a solution for 'multiple parents'. i presume one can deal with multiple hierarchies in imp, but i just do not know how...
Two comments:- I was going to post an email about introducing "groups" or some such name which would provide a set of functions for easily defining higher level features (such as a group involving 3 fragments). Each group would be defined by a particle and there would be a standard refined. You could call a function "create_group(Particles)" to create such a group and then pass the resulting particle to ConnectivityRestraint or any other thing which takes a refiner.
You would not easily have the ability to get the set of groups that a particle belongs in (although that could be added) and the group particles themselves would not be atom.Hierarchy particles.
- In your case it sounds like just have a tree like this Protein: - fragment a - fragment 0 - fragment 1 - fragment b - fragment 2 - fragment 3Then to get the protein you just go up in the tree until you get to a hierarchy node of type atom.Hierarchy.PROTEIN.