[gmx-developers] multiple file option

[Anton Feenstra]

Marc Lensink wrote:
> 
> Anton Feenstra wrote:
> >
> > Also, we could use these options for programs like gmxcheck,
> > g_rms and g_anaeig, which have options like '-f' and '-f2'
> > or '-s1' and '-s2', which might be changed into a single
> > option that accepts multiple files and issue an error when
> > more than two files are given. This reduces the cmdline option
> > clutter somewhat. Again, given common interest, I'd be willing
> > to implement...
> 
> but how about possible confusion... you don't necessarily know if
> you're comparing file 1 with file 2, or file 2 with file 1. i refer to
> g_confrms, for instance, where you would like to know which structure
> you're fitting onto which structure. with options '-f1' (or '-f') and
> '-f2' such is immediately clear (as in the help it says 'fitting the
> second structure onto the first one).

I don't see that that would necessarily be a problem, first and second
would now refer to first and second on the cmdline. Alternatively, we
could allow the option of specifying multiple files with numbered
options.
So, for example if we would have for g_confrms:
  -f       conf.gro  Input, Mult.  Structure+mass(db): tpr tpb tpa gro
g96 pdb
  -o        fit.pdb  Output        Generic structure: gro g96 pdb
  -n        fit.ndx  Input, Opt., Mult.   Index file
we could allow the user to specify:
# g_confrms -f2 2.gro -n2 2.ndx -f 1.gro -n 1.gro
or, alternatively:
# g_confrms -f 1.gro 2.gro -n 1.ndx 2.ndx
which would then be equivalent. But, in principle I would think
that only the second option should be good enough.


-- 
Groetjes,

Anton
 ________ ___________________________________________________________
|        | Anton Feenstra                                            |
| .      | Dept. of Pharmacochemistry - Free University Amsterdam    |
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