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membrane-systems / PCAlipids

Scripts for PCA and related analyses of lipid motions
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Order of atoms in two trajectories #19

Open markussmiettinen opened 3 years ago

markussmiettinen commented 3 years ago

When one compares the trajectories from two different force fields, the atoms might have different order.

Currently the pearson tool assumes the atoms to be in the same order.

It is somewhat tedious to reorder atoms in the trajectories themselves.

It would be useful to be able to tell pearson with an optional input file, how the two atom orders differ.

pbuslaev commented 3 years ago

Hi @markussmiettinen! Thanks for bringing this up. I think that we need to add an option -order not only to pearson tool, but to others as well, since the wrong atom order will affect all the comparison results.

As I see it now, the best way to do so, is to use some library with universal naming, like those used in NMRlipids (e.g. these ones). I will start working on that later.