From: Peter Murray-R. <pm...@ca...> - 2004-05-31 15:53:40
|
At 16:33 31/05/2004 +0200, Egon Willighagen wrote: >On Sunday 16 May 2004 17:30, Peter Murray-Rust wrote: > > If it is known that a given bond is cis or trans (or some other measure of > > stereochemistry such as CMLBondStereo) is there a means that the layout > > algorithm can take this into account? > >AFAIK, not at this moment. I have now solved this in JUMBO in that I can take a CDK layout, find the acyclic double bonds and "flip" about them. The code will be in JUMBO4.4 Of course this will sometimes flip part of a structure on top of itself, but I am prepared to live with this (cis bonds are not likely to be easy to layout anyway). The CDK layout I get is often not as "good" as when I press the clean (broom) button on JCPCDK. Do they use different methods. If so, which should I use? P. >Egon Peter Murray-Rust Unilever Centre for Molecular Informatics Chemistry Department, Cambridge University Lensfield Road, CAMBRIDGE, CB2 1EW, UK Tel: +44-1223-763069 |