On 26/02/2012 16:19, Noel O'Boyle wrote: > I've been looking at the opalign which I really like. There's one > issue remaining which I can't quite decide how to handle. > > Basically, if you use --align -s "substructure color" -O myfile.svg > and your input structure is 2D everything is fine. However, if your > input structure is 3D, it does a 3D alignment, but the resulting SVG > is not aligned. > > To get around this, I'm thinking that the op should check the output > format: if it's SVG or PNG(2) then it should align on 2D. Or is this > just a whole can of worms, and a Bad Idea? Maybe there should be a > separate align2d and align3d and leave it to the user to explicitly > save what s/he wants?
I agree with your proposal. Is displaying in 2D after 3D alignment ever any use? Since the image formats automatically* give the molecules 2D coordinates without asking, it would be consistent to do the alignment in 2D also without asking. OpAlign already generates coordinates if the molecule is 0D. * subject to the (undocumented) -xy and -xn options Maybe there could be an extra OBFormat flag which would be set in 2D depiction formats. This would help to maintain their status as plugins. I think there might be some complications when implementing this, which I might be able to help with. Chris ------------------------------------------------------------------------------ Try before you buy = See our experts in action! The most comprehensive online learning library for Microsoft developers is just $99.99! Visual Studio, SharePoint, SQL - plus HTML5, CSS3, MVC3, Metro Style Apps, more. Free future releases when you subscribe now! http://p.sf.net/sfu/learndevnow-dev2 _______________________________________________ OpenBabel-Devel mailing list OpenBabel-Devel@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-devel
