stereo flags

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?

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

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

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.

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

(However it works in MarvinSpace)