Hi,
I've implemented this in the GitHub version of cpptraj
(
https://github.com/Amber-MD/cpptraj) as of version 6.16.1. There is a
new for loop keyword called 'indata' which will allow you to loop over
elements of a data set. For your example you would use something like:
readdata res.dat name resi intcols 1
for i indata resi:1
h = $i - 1
dihedral :$h.C :$i.N :$i.CA :$i.C out dihe_$i.dat
done
If you don't want to have to define the dihedrals explicitly you could
use multidihedral, e.g.
readdata res.dat name resi intcols 1
for i indata resi:1
multidihedral phi resrange $i out dihe_$i.dat
done
Hope this helps. Let me know how it works for you! Thanks again for
the suggestion.
-Dan
On Wed, Nov 30, 2022 at 8:07 AM Daniel Roe <daniel.r.roe.gmail.com> wrote:
>
> 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 - 10:00:03 PST
