VMD-L Mailing List

From: bo liu (liubo.njuer_at_gmail.com)
Date: Fri Aug 29 2008 - 03:17:57 CDT

Hi Alejandro,

UltraEdit would be the best choice for you under Windows,
Under linux, as mentioned by others, plenty of choices.

I don't know exactly what tast you are dealing with,
if you are preparing input files for NAMD simulations,
Tcl scripting plus VMD built-in commands can do almost everything.
it pays off if you spend sometime to learn Tcl scripting.

Cheers!

2008/8/29 Emily Moore <emily.moore_at_utah.edu>

> 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>
>
> 

-- 
-Liu bo
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Computational Biochemistry&Biophysics, Nano-bio systems: MD method;
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