Convert xyz into zmatrix11/6/2023 ![]() From the xyz parameters, I need to find the distance between atoms, angle and dihedral between atoms. ![]() Sin and cos terms of vector components have immediate representation on the unit circle of the angular offsets being produced as you apply the chain of ops to the decomposed matrix and are important to understanding what is going on.I want to make a python script that will load an xyz file. ![]() Missing the cosine term and not checking for the cos0 case (both things outlined in the paper I linked) will have many invalid fringes, when that happens the terms to look up in the matrix change, so this can’t be solved with a single triplet that goes end to end for each row.Īnd for the sake of understanding I find the extended explanation (again in paper linked) tends to be easier to visualize. Past a certain point or sign drift will transfer (it can’t be accounted for post facto, it needs to be factored in before atan2s). Solid piece of help, but a couple notes worth making IMO:įunctionally speaking that will drift on cos0 cases.Į.G: cmds.rotate(20, 90, 0, b) will (I think) drift off on the Z, and 0,90,20 will drift on X. For some combinations those operations would be invalid, so one check to prevent a divide by zero is required mid-way to choose how to do the next steps.ĭoing it in a computationally optimal way is a different matter, it’s a tricky operation to pack in a truly efficient cycle count and it will usually require clever use of intrinsics to pack, mask and unpack quadruplets in the most effective manner. ![]() In less pompous sounding words: It takes the axes in the matrix as vectors, puts their terms (x, y, z) on the unit circle (trigonometry component), and figures out bit by bit, in reverse, how much of an angle is needed to produce that axis. It largely boils down to trig derivative angles from vectors being offset and projected on cardinal axes in order (rot order matters), and, since it’s not a unequivocal operation end to end, managing the branching possibilities of the polynomial to produce deterministic results. ![]() This is one of the most approachable and complete papers on the subject: The math behind it you could have just googled for to be honest. ![]()
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