Easier import for MD

[eackad@…]

If when you tried to load a trajectory file (dcd etc) it asked you into which model (with a list) that would make the whole thing more transparent (and an option to also load the series slider). Especially if it had the typical start, stop, skip options.

[pett]

open MD formats now accept start/step/end keyword arguments (starting at 1, not 0)

[pett]

No option for the series slider yet

[pett]

Okay added a 'slider' option, which defaults to true, to opening MD coordinate files. I'm not entirely sure about the name of the option. For one thing, it could be called 'showSlider'. Another consideration is that in the future we may have a fancier MD interface than a simple slider, so perhaps it should be called 'showTool'. Opinions?

[Elaine Meng]

There are currently subcommands "coordset slider" and "vseries slider" as well as "slider" keyword options of "morph" and "volume morph."

My first impression was that "slider" should be the option since it does exactly the same thing as "coordset slider." However, there is a slight potential ambiguity since the "open" command opens both coordsets (trajectories) and vseries (volume series), but opening the latter automatically opens a slider  anyway, so it would only be needed for the former.

Maybe it could be "slider" now and revisited along with "coordset slider" (i.e. whether synonyms should be added) when the slider balloons into a full-featured tool interface.   I don't feel strongly about any of this, however.

[goddard@…]

I think the open command option name "slider" is better than "showSlider" or "showTool".  Those "show..." options are more descriptive but often our option names aim for concise rather than descriptive.  I think that was my thinking behind the subcommand "coordset slider" instead of the clearer but longer "coordset showSlider".  I don't feel strongly about it.  There are many cases where an option name could be verb+noun but we have chosen just noun or just verb (e,g. measure buriedarea has a "select" option I looked at just today that really means "selectResidues").  I think all 3 are fine but usually the shorter choice if relatively clear is best.

[pett]

Okay, leaving as 'slider' until such time as there is an actual MD tool.