On Tue, Dec 6, 2022 at 1:14 AM Pietro ARONICA <pietroa.bii.a-star.edu.sg> wrote:
> I ended up using multidihedral for my analysis. I did have to do it in a roundabout way, though, because it uses internal numbering to define the residues for which torsions are calculated rather the actual pdb numbering one might access with the mask :;
> Is there any plan to add that functionality?
I changed it so you can specify a mask expression for 'resrange', e.g.
'multdihedral resrange <mask>' (version 6.16.4 -
https://github.com/Amber-MD/cpptraj/pull/1008) - see if that works for
you.
-Dan
> Cheers
> Pietro
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, December 1, 2022 1:30 AM
> To: Pietro ARONICA <pietroa.bii.a-star.edu.sg>; AMBER Mailing List <amber.ambermd.org>
> Subject: Re: [AMBER] Cpptraj for loops and dataset operations
>
> This email is from a sender external to A*STAR. If you are unsure of the content, please check the source before you respond.
>
>
> 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 Tue Dec 06 2022 - 08:30:03 PST
