Hi, I have run into a potential 'for loop' bottleneck. Let me outline: The following array describes bonds (connections) in a benzene molecule b = [[0, 0, 0, 1, 1, 1, 2, 2, 2, 3, 3, 3, 4, 4, 4, 5, 5, 5, 6, 7, 8, 9, 10, 11], [5, 6, 1, 0, 2, 7, 3, 8, 1, 4, 9, 2, 10, 5, 3, 4, 11, 0, 0, 1, 2, 3, 4, 5]] ie. bond 0 connects atoms 0 and 5, bond 1 connects atom 0 and 6, etc. In practical examples, the list can be much larger (N > 100.000 connections. Suppose atoms with indices a = [1,2,3,7,8] are deleted, then all bonds connecting those atoms must be deleted. I achieve this doing i_0 = numpy.in1d(b[0], a) i_1 = numpy.in1d(b[1], a) b_i = numpy.where(i_0 | i_1)[0] b = b[:,~(i_0 | i_1)] If you find this approach lacking, feel free to comment. This results in the following updated bond list b = [[0, 0, 4, 4, 5, 5, 5, 6, 10, 11] [5, 6, 10, 5, 4, 11, 0, 0, 4, 5]] This list is however not correct: Since atoms [1,2,3,7,8] have been deleted, the remaining atoms with indices larger than the deleted atoms must be decremented. I do this as follows: for i in a: b = numpy.where(b > i, bonds-1, bonds) (*) yielding the correct result b = [[0, 0, 1, 1, 2, 2, 2, 3, 5, 6], [2, 3, 5, 2, 1, 6, 0, 0, 1, 2]] The Python for loop in (*) may easily contain 50.000 iteration. Is there a smart way to utilize numpy functionality to avoid this? Thanks and best regards, Mads -- +---------------------------------------------------------+ | Mads Ipsen | +----------------------+----------------------------------+ | Gåsebæksvej 7, 4. tv | phone: +45-29716388 | | DK-2500 Valby | email: mads.ipsen@gmail.com | | Denmark | map : www.tinyurl.com/ns52fpa | +----------------------+----------------------------------+