>> >> so i implemented option 1, which seems to do what i want (the >> restraint acting closest two spheres). >> to check that the code actually does the right thing (score the single >> shortest distance between (f3,f5,f7) and (f0,f1,f2)) i tried to return >> the connected pairs (=ONE pair for my desired restraint, not FIVE >> restraints for the undesired behavior). sadly, >> connrest.get_connected_pairs() returns my newly generated particles, >> which specify the interacting fragments. is there any way to return >> the actually interacting LowestRefined particles? otherwise, i cannot >> check that the code does the right thing (and the information is >> useful for me)... > > Good point. The easiest way around is for me to add add a method to the > LowestRefinedPairScore that returns the actual pair given an input pair. > Makes the verification two steps, but it is just verification, so being > slightly annoying seems fine to me. I'll do that later today. >
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...
thanks
frido
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Dr. Friedrich Foerster Max-Planck Institut fuer Biochemie Am Klopferspitz 18 D-82152 Martinsried
Tel: +49 89 8578 2651 Fax: +49 89 8578 2641
foerster@biochem.mpg.de
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