Hi Egon, Totally agree. However, when explicite hydrogens have been added the it=false gives the wrong result.
Peter -----Original Message----- From: Egon Willighagen [mailto:egon.willigha...@gmail.com] Sent: Friday, December 19, 2008 2:11 PM To: Peter Maas Cc: cdk-user@lists.sourceforge.net Subject: Re: [Cdk-user] rotatable bonds Hi Peter, On Fri, Dec 19, 2008 at 2:03 PM, Peter Maas <peter.m...@specs.net> wrote: > This issue came up more often. > I think it is advised always to add explicite hydrogens when calculating > qsar properties. > At one point somebody checked all cases to make sure hydrogens were removed > when this was really needed. I think in the case of rotable bonds this > should also be done. Otherwise the parameter "include terminals"= false > won't work properly. OK, so, we should expect (it=include terminals): ethane: RotB=1, it=false -> 0 butane: RotB=3, it=false -> 1 Correct? Egon -- ---- http://chem-bla-ics.blogspot.com/ ------------------------------------------------------------------------------ _______________________________________________ Cdk-user mailing list Cdk-user@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/cdk-user
