RMSD operation in a numpy array of moelcules about rmsd

[larsbratholm]

Use x.reshape(57000,3) to make it the right input format?

[lmegaterium]

I’m currently doing that, but it would be valuable to have element wise RMSD instead of reshaping and “concatenating” all my molecules.

[charnley]

Do you want to rotate each molecule individually or rotate them all in the same space? Because your first comment seems to be answered by Lars (reshape), but your last comment seems to point that you want a RMSD for each molecule.

[lmegaterium]

Thanks for you comment, and sorry for the confusion. I do require in fact RMSD for each molecule.

In my case I have array A which contain 1000 molecules and I need to rotate each molecule and calculate the RMSD against B which also contain 1000 different molecules.

[andersx]

Why don't you just make a double loop? I can't see how this is an issue with the RMSD code?