Hi,
Sorry for the delay in replying. I kept trying to figure out if there
is a way to do what you want, but I don't think there is yet! You can
loop over atoms/residues/molecules, files, lists, etc. but not
elements of a dataset (which is an oversight on my part!). It's a
great idea and I'll work on getting it implemented ASAP. I've created
an issue on GitHub to track it here:
https://github.com/Amber-MD/cpptraj/issues/1003
Thanks for the suggestion!
-Dan
On Fri, Nov 25, 2022 at 1:13 AM Pietro ARONICA via AMBER
<amber.ambermd.org> wrote:
>
> Dear all,
> I am having a hard time understanding how to use datasets and for loops work in cpptraj.
> I have a pdb named file.pdb. I can calculate using the nativecontacts command all residues in mask1 that are within 6 A of mask2 with a command like this:
>
> nativecontacts :mask1 :mask2 distance 6 resout res.dat
>
> The first column of res.dat contains the residue numbers I am interested in. I have read in this file with
>
> readdata res.dat name resi
>
> What I would like to do at this point is calculate dihedrals of residues that are match the distance criteria I set before, ie those in the first column of res.dat. It is my understanding that resi:1 contains these data points but I do not understand how to extract them or use them.
> In my mind, the for loop would look a little bit like this:
>
> for i in resi:1
> dihedral :($i-1).C :$i.N :$i.CA :$i.C out dihe_$i.dat
> done
>
> It would loop over the elements of the data set, using that number for the mask of the dihedral I want to calculate. I would also want to do some operations on the values.
> However, I am unable to use the dataset in any way like that. If I just use the data set on the command line, it gives this:
>
> > resi:1
> [resi:1]
> Result: 0.000000
>
> which I am unsure how to interpret. I know the data is somewhere within that dataset because if I use writedata it will produce a text file with all the data points as I expect them.
> Can anyone explain to me how data sets are used and accessed and possibly used in for loops?
> Kind regards
> Pietro Aronica
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Received on Wed Nov 30 2022 - 05:30:02 PST
