(Please cc to the list) I think that in these instances you will have to break the symmetry by setting one of the atoms to Xe or so.
- Noel On 15 July 2016 at 20:29, Colin Grambow <colingram...@gmail.com> wrote: > I am attempting to generate all possible structures (under the constraints > of breaking and forming a certain number of bonds) from a single starting > structure without considering the underlying chemistry (at least initially). > This means that if I form a double bond during that generation, then I will > want to include both the cis and the trans structures, and if a double bond > is not involved in going from the starting structure to a product structure, > then I want to ensure that the cis/trans orientation is retained. > > > > I already have code for generating structures based on a list of bonds and > valences, which I then use to construct pybel molecules. The next step is to > generate the 3D geometries of the structures, which is a simple task with > Open Babel, but I want to ensure that the correct ones are generated based > on the stereochemical constraints I mentioned before. > > > > When asking my initial question, I was thinking that I could just generate > all possible stereoisomers and subsequently only select the ones that match > the starting structure based on which bonds were broken/formed, but such a > naïve approach would result in a lot of unnecessary calculations, which I > could avoid if I had the ability to directly create the structure with the > desired stereochemistry. > > > > > > From: Noel O'Boyle [mailto:baoille...@gmail.com] > Sent: Friday, July 15, 2016 2:56 PM > To: cgram <colingram...@gmail.com> > Subject: Re: [Open Babel] Generating all cis-trans stereoisomers > > > > By way of background what is the underlying problem you are trying to solve > here? > > > > On 15 Jul 2016 6:22 p.m., "cgram" <colingram...@gmail.com> wrote: > > Thank you for the answer, I will look into it. > > I have a more general question regarding double bonds. When generating 3D > geometries, is it possible to assign which side of a double bond the > substituents are on? I would like to do this even for double bonds that are > not marked as stereocenters (e.g., if there are two identical substituents > on one side). Perhaps this would be possible by marking bonds as > stereocenters even if they are not and then using some function to assign > which side of the bond the atoms are on (is there a function that enables a > simple assignment like this?) > > > > -- > View this message in context: > http://forums.openbabel.org/Generating-all-cis-trans-stereoisomers-tp4659390p4659393.html > Sent from the General discussion mailing list archive at Nabble.com. > > ------------------------------------------------------------------------------ > What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic > patterns at an interface-level. Reveals which users, apps, and protocols are > consuming the most bandwidth. Provides multi-vendor support for NetFlow, > J-Flow, sFlow and other flows. Make informed decisions using capacity > planning > reports.http://sdm.link/zohodev2dev > _______________________________________________ > OpenBabel-discuss mailing list > OpenBabel-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss ------------------------------------------------------------------------------ What NetFlow Analyzer can do for you? Monitors network bandwidth and traffic patterns at an interface-level. Reveals which users, apps, and protocols are consuming the most bandwidth. Provides multi-vendor support for NetFlow, J-Flow, sFlow and other flows. Make informed decisions using capacity planning reports.http://sdm.link/zohodev2dev _______________________________________________ OpenBabel-discuss mailing list OpenBabel-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
