VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Aug 28 2008 - 17:51:39 CDT

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> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.