On Wed, Mar 3, 2010 at 4:00 PM, Noel O'Boyle <baoille...@gmail.com> wrote: > On 3 March 2010 14:48, Craig James <craig_ja...@emolecules.com> wrote: >> Noel O'Boyle wrote: >>> >>> Are some of the wedge/hash bonds in typical MOL files unrelated to >>> stereochemistry? That is, are some purely for depiction? If I knew >>> this for sure, I would not retain the wedge/hash bond designations in >>> the input but just work them out from the perceived stereo. >> >> YES. Lots of them. We see this all the time - people use wedge/hash to do >> pseudo-perspective drawings. This is particularly common with metals. >> >> http://www.emolecules.com/image?db=549&id=17252456&width=400&height=400 >> http://www.emolecules.com/image?db=549&id=718320&width=400&height=400 >> >> But I also see it all the time with organic molecules, particularly >> structures that are hard to draw in 2D (semi-cage ring systems that won't >> lay flat). People use hashes and wedges to try to make them look nice, that >> have nothing to do with stereochemistry. > > So...should we retain them or not? I think what I'll do is add an > option to allow users to retain them exactly. However, the default > will be that the wedges/hashes in the output will be solely dependent > on the perceived stereochemistry. *Sigh* This applies to all 2D output > formats.
Having the option to retain them exactly sounds sensible, but that means retaining all of the user-provided markings, right? This almost sounds to me like it's a read setting, not a write one. But then I'm not familiar with the internal flow for processing mols in OB. -greg ------------------------------------------------------------------------------ Download Intel® Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev _______________________________________________ Blueobelisk-discuss mailing list Blueobelisk-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/blueobelisk-discuss
