[gmx-developers] cmdline parsing / index files

David van der Spoel spoel at xray.bmc.uu.se
Mon Mar 11 17:25:47 CET 2002

On Mon, 11 Mar 2002, Anton Feenstra wrote:

>Couldn't we add a functionality to parse-comon-args to put all not
>recognized entries (like a list of filenames for trjcat or eneconv)
>into an array, which can be retrieved in the program using a function?
>That way we can still do (most of) the cmdline consistency checks that
>we normally have. It should be an option like PCA_MULTIPE_FILES.
>Alternatively, a file option could be multiple, so that we would
>trjcat -f 1.xtc 2.xtc -o all.xtc
>or possibly
>trjcat -f 1.xtc -f 2.xtc -o all.xtc
For files it would have to be added in the filenm bit of parsing I would 

>Another thing is the 'select a group with 413 atoms' message that
>g_anaeig spits out. Couldn't we have a function like select_index()
>that would auto-select the 413 atom group, if there is only one?
>Also it would be great to have the choice to select index groups 
>by their name. Again, not too much work I think, so I might volunteer
>on the same conditions.
And select energies on names in g_energy (using best fit, rather than 
exact fit). THis would make it much easier to run scripts over many files.

Groeten, David.
Dr. David van der Spoel, 	Biomedical center, Dept. of Biochemistry
Husargatan 3, Box 576,  	75123 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://zorn.bmc.uu.se/~spoel

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