stereo flags

User 870ab5b546

31-10-2006 19:26:06

I have this code:





Code:
        Molecule origMol = (Molecule) mol.clone();


        int origNumBonds = origMol.getBondCount();


        mol.hydrogenize(true);


        for (int bIndex = 0; bIndex<origNumBonds; bIndex++) {


            MolBond mb = (MolBond) mol.getEdge(bIndex);


            int stereo = mb.getFlags() & MolBond.STEREO_MASK;


            MolBond origmb = (MolBond) origMol.getEdge(bIndex);


            int origStereo = origmb.getFlags() & MolBond.STEREO_MASK;


            if (stereo != origStereo) {


                System.out.println("ChemUtils.addImplicitH: "


                        + "resetting a " + mb.getAtom1().getSymbol()


                        + "-" + mb.getAtom2().getSymbol() 


                        + " bond from stereo " + stereo


                        + " back to original stereo " + origStereo);


                mb.setFlags(origmb.getFlags());


            } // if stereo has been changed by hydrogenizing   


        } // for each original bond in mol








I find that hydrogenize() has changed stereo from 0 to 64 for *every* bond in mol. Any reason why?

ChemAxon 25dcd765a3

03-11-2006 16:00:12

I may misunderstand something, but I think I miss the problem.





I have done the following under marvin 4_1_2:


Code:
java SmomeTest 1.mrv



Nothing is written.





All the best


Andras

User 870ab5b546

08-11-2006 02:55:45

Hm, I can't seem to reproduce the behavior now. OK, I'll write again if I have trouble again.

User eec9d4ad39

10-11-2006 18:15:24

I have just updated to MarvinView 4.1.2, and noticed some error in


terms of (R)/(S) configurations in my files. At first I thought that


my SMILES strings were incorrect, but now I believe that the problems


lies with your viewer.





I am using the following example (CAS 40715-31-9):





c1c(O)ccc2[C@@]3([H])CC[C@]4(C)C(=O)CO[C@@]4([H])[C@]3([H])CCc12





This SMILES string shows me the correct 3D structure in Accelrys, but


the (incorrect) mirror-image in MarvinView. As far as I can tell, this


problem has occurred just recently with my installation of the update.

ChemAxon 43e6884a7a

11-11-2006 18:11:35

That is a bug. We will fix that asap. Thanks.

ChemAxon 43e6884a7a

12-11-2006 10:00:42

(However it works in MarvinSpace)