On Thu, Sep 06, 2012 at 09:16:59AM +0200, Dorothee Geppert wrote: > I have just started to explore the many capabilities of CDK. An important > issue for me is the handling of stereochemistry while converting between > different file formats. > When I have created a CDK Molecule by parsing a Smile with stereochemistry, > is it possible to generate 2d coordinates with wedged bonds from this?
Not readily, but in principle, as I reread an earlier answer on this by Egon. I think I will open both a CDK and a JCP issue for it. He wrote (2012-May-26 on cdk-devel): > But for JChemPaint, or any 2D visualization, you indeed need > converting atom parity like stereochemistry to wedge bond based > stereochemistry. Mind you, JChemPaint can easily visualize R,S > stereochemistry indicators, but I guess you are thinking of wedge > bonds here. > There is code for converting stuff, but I am not familiar with the API > and the exact functionality implemented... that would need to be > summarized first. Either from parities to wedge bond, or from wedge > bonds to parities is available, but I am not sure about the state... > I briefly checked the keyword list [0], but cannot find it there... I > don't have the Eclipse with the CDK sources open, so will have to look > later, if you haven't found it by then... > Egon > 0.http://pele.farmbio.uu.se/nightly-1.4.x/keywords.html ralf ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
