>> When are there ever no 2D coordinates? > > e.g. SMILES input.
Depiction to SVG will automatically generate 2D coordinates. Now you may not like them, but the -gen2d flag should give you the same 2D coordinates and depiction as not specifying this. > Yes it does and yes there are. The attached was generated by pumping the > SMILES through indigo, saving the SDF with 2D coordinates, using OB to > generate the SVG and then post-processing the SVG to make the labels > legible. So it seems for this molecule, that Indigo is giving better 2D depiction than Open Babel and that you have an inelegant but workable workflow? Certainly, getting the bug reports of 2D depiction issues is helpful. At the moment, it's not clear to me where the problem is in the OB code.. it seems it's being a bit too lenient in allowing collisions. Best regards, -Geoff ------------------------------------------------------------------------------ Learn Graph Databases - Download FREE O'Reilly Book "Graph Databases" is the definitive new guide to graph databases and their applications. Written by three acclaimed leaders in the field, this first edition is now available. Download your free book today! http://p.sf.net/sfu/NeoTech _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
