VMD-L Mailing List

From: Emily Moore (emily.moore_at_utah.edu)
Date: Thu Aug 28 2008 - 18:13:01 CDT

Didn't mean to start anything. :)

I meant csh was simple in the sense that it was straightforward to learn to
use, so Alejandro wouldn't think it was too time consuming to learn. In that
sense, my experience with other sorts of scripting languages has been the
same, that they are fairly straightforward to learn once you decide to do
so. Since csh was the first I was introduced to, I felt I could comment on
it.
As for the relative effectiveness/usefulness of the different scripting
languages I am certainly no expert and cannot comment on that.

~ Emily

On 8/28/08 4:51 PM, "Axel Kohlmeyer" <akohlmey_at_cmm.chem.upenn.edu> wrote:

> On Thu, 28 Aug 2008, Emily Moore wrote:
>
> EM> Alejandro,
> EM>
> EM> I completely agree with Peter. I use vim/emacs for some of my work, but
> for
> EM> editing text files, I use a combination of sed, awk and grep within csh or
> EM> pearl scripts. If you are comfortable in C programming, csh scripts are
> EM> simple, but they're all pretty much the same.
>
> wow. the statement about csh is even more flame bait than
> the vi-vs-emacs vs the rest fights. ;)
>
> haven't you seen: http://www.faqs.org/faqs/unix-faq/shell/csh-whynot/
>
> cheers,
> axel.
>
> EM>
> EM> Good luck.
> EM>
> EM> ~ Emily
> EM>
> EM>
> EM> On 8/28/08 2:06 PM, "Peter Freddolino" <petefred_at_ks.uiuc.edu> wrote:
> EM>
> EM> > Alejandro,
> EM> > there are quite a few programs out there that are dedicated text editors
> EM> > far superior to wordpad/notepad. A couple of examples from the world of
> EM> > Free software (in no particular order, so as to avoid flamewars):
> EM> > vim/gvim
> EM> > emacs
> EM> > nedit
> EM> > nano/pico
> EM> >
> EM> > All of these have a great deal of functionality to make editing text
> EM> > files easier and more efficient. You should be able to find one or more
> EM> > of them for whatever platform you use.
> EM> >
> EM> > Many of the text transformations needed for editing the files associated
> EM> > with simulation are more efficient to do on the command line using unix
> EM> > tools such as sed, awk, and grep, or scripting languages such as perl
> EM> > and python. I highly recommend becoming more familiar with at least some
> EM> > of these options.
> EM> > Best,
> EM> > Peter
> EM> >
> EM> > Alejandro Ortega wrote:
> EM> >> Hello everyone,
> EM> >> First of all, I'm e-mailing this to VMD and NAMD communities because i
> EM> >> think this problem may affect both of them.
> EM> >>
> EM> >> Well, the thing is that creating a simulation requires a lot of TXT
> EM> >> edition, at least in my personal case. I stay hours and hours editing
> EM> >> TXT files (The *.params, *.PDB, *.PSF, etc.,) and i think that
> EM> >> sometimes it is not necessary to do all this job. As a reference, i
> EM> >> know how to use the "replace" command in notepad, wordpad does not
> EM> >> have too many extra options, and excel works as well, but it is harder
> EM> >> to use, is almost the same work than in wordpad or notepad.
> EM> >>
> EM> >> I've been thinking in creating one, it is not a great deal, it just
> EM> >> requires basic knowledge of programming in visual basic or C++, but i
> EM> >> am running out of time and i really need to edit high amounts of text.
> EM> >>
> EM> >>
> EM> >> In brief, my question is: does someone know a program that is
> EM> >> specialized in editing TXT files? or does someone has made a program
> EM> >> specialized for this issue?
> EM> >> Also, if someone knows a better way to edit large amounts of text
> EM> >> please let me know.
> EM> >>
> EM> >>
> EM> >> Thank you!
> EM> >> Cheers,
> EM> >> Alejandro Ortega.
> EM>