On Mon, Aug 16, 2010 at 7:12 AM, James Davidson <[email protected]> wrote: > >> You're doing it correctly; no worries there. The problem is >> that most pieces of chemical drawing software generate 2D >> coordinates for molecules such that a C-C single bond is 1.0A >> long. The RDKit, on the other hand, sets the C-C single bond >> to be 1.5A long. The consequence is a depiction with a core >> that's smaller than it should be. > > I was using ISISDraw for sketching the core motif. It seems that the > single-bond length (from the Origdraw settings) is ~ 0.825 A (!)
that's seems peculiar, but I guess there's some rationale behind it. > So I modified the scalar to 1.818 (1.5/0.825) in your code and it works > beautifully! Glad to hear it. >> It should be possible to specify the scale used in the RDKit >> depictions so that these contortions are not necessary. I >> will put a feature request in for this and get it in the next version. > > Thanks for this - I certainly think this would be a worthwhile feature. > What I may implement in the meantime is running through all the bonds of > type SINGLE in the core molecule, taking the average, then using > 1.5/(average) as the scalar to protect against differing user settings! I checked the changes in this weekend. From python you can now provide a "bondLength" argument to set the value that's used while generating depictions. The default value for this is -1, which means "don't mess with the default". -greg ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-dev2dev _______________________________________________ Rdkit-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
