Seconding Jaime; I use this trick in mesh manipulations a lot as well. There are a lot of graph-type manipulations you can express effectively in numpy using np.unique and related functionality. On Sun, Feb 2, 2014 at 11:57 PM, Jaime Fernández del Río < jaime.frio@gmail.com> wrote:

Cannot test right now, but np.unique(b, return_inverse=True)[1].reshape(2, -1) should do what you are after, I think. On Feb 2, 2014 11:58 AM, "Mads Ipsen"

wrote: 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 | +----------------------+----------------------------------+ _______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion

_______________________________________________ NumPy-Discussion mailing list NumPy-Discussion@scipy.org http://mail.scipy.org/mailman/listinfo/numpy-discussion