VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu Aug 28 2008 - 15:06:53 CDT

Alejandro,
there are quite a few programs out there that are dedicated text editors
far superior to wordpad/notepad. A couple of examples from the world of
Free software (in no particular order, so as to avoid flamewars):
vim/gvim
emacs
nedit
nano/pico

All of these have a great deal of functionality to make editing text
files easier and more efficient. You should be able to find one or more
of them for whatever platform you use.

Many of the text transformations needed for editing the files associated
with simulation are more efficient to do on the command line using unix
tools such as sed, awk, and grep, or scripting languages such as perl
and python. I highly recommend becoming more familiar with at least some
of these options.
Best,
Peter

Alejandro Ortega wrote:
> Hello everyone,
> First of all, I'm e-mailing this to VMD and NAMD communities because i
> think this problem may affect both of them.
>
> Well, the thing is that creating a simulation requires a lot of TXT
> edition, at least in my personal case. I stay hours and hours editing
> TXT files (The *.params, *.PDB, *.PSF, etc.,) and i think that
> sometimes it is not necessary to do all this job. As a reference, i
> know how to use the "replace" command in notepad, wordpad does not
> have too many extra options, and excel works as well, but it is harder
> to use, is almost the same work than in wordpad or notepad.
>
> I've been thinking in creating one, it is not a great deal, it just
> requires basic knowledge of programming in visual basic or C++, but i
> am running out of time and i really need to edit high amounts of text.
>
>
> In brief, my question is: does someone know a program that is
> specialized in editing TXT files? or does someone has made a program
> specialized for this issue?
> Also, if someone knows a better way to edit large amounts of text
> please let me know.
>
>
> Thank you!
> Cheers,
> Alejandro Ortega.