On Tue, Jan 15, 2013 at 11:32 AM, Simon Norberg <[email protected]> wrote: > >> Avogadro uses OpenBabel for this (http://openbabel.org). It supports >> batch conversions for files using the (o)babel program. If you have >> Avogadro installed, this is most likely installed on your system too. >> >> babel mysmiles.smi foo.png -m >> >> The -m option turns the multi-molecule file into seperate png files >> (foo1.png, foo2.png, ...). There is also support for SVG output. >> >> Hope this helps, >> Tim > Hi Tim, > Thansk for the hint, but I guess I didn’t specify what i meant with nice > looking images Avogadro generates well enough, the image i want to > create is a image of a 3d molecule. Similar to what you export from > avogadro when you choose to export a PNG. > OpenBabel is only able to generate 2d text based image AFAIK. One > possibility i have tested is to use OpenBabel to generate a .pdb file > and then use raster3D to generate a 3d molecule image. > The image raster3d generate isn’t as nice as avogadros, and i have a > hard time to render a atom of constant size. I want to have a Carbon > atom to be the same size in pixels regardless of generating a simple CO > or a more complex molecule. I dont know if avogadro supports this > either, but at least if i could hack a python script i might be able to > fix it myself in avogadro. > Avogadro doesn't have that level of control from the command line, the Python bindings might be enough to allow you to accomplish what you need (and I remember Tim writing some blog posts about doing similar things there).
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