[phenixbb] Gap between R and Rfree

Nathaniel Echols NEchols at lbl.gov
Thu Feb 25 14:50:54 PST 2010

On Feb 25, 2010, at 2:01 PM, Simon Kolstoe wrote:
> oh yes please Pavel (command line polygon/statistics overview) - could the output be a pdf or ps rather than just starting up the GUI?

Not sure if you found this already, but the GUI can save the image as PNG, which can be converted into pretty much anything.  Doing this automatically from the command line is certainly possible - the code is relatively modular and was written with this in mind - but it's actually a fair amount of work, because the image is ultimately drawn directly by wxPython (i.e. it isn't simply an image embedded in the window).  (Plain text output, on the other hand, is very simple.)  I would actually prefer to switch entirely to a scalable, device-independent format such as PS or PDF (which the GUI could then display), but it will take a while for this to migrate up my to-do list.

The simple text output like the histograms Pavel shows are much easier to do, probably just a matter of pulling together code fragments.  I'm pretty sure I could produce graphical output for these entirely on the command line (see the PDB Statistics GUI for an example of what they'd look like), since the drawing of these is handled by a separate module.  But this isn't going to save much time over feeding the raw numbers into Excel and making your own graphs.


Nathaniel Echols
Lawrence Berkeley Lab
NEchols at lbl.gov

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