bug in shortcut ungrouping: geometry problem

The code:

            int molIndex = 0;

            debugPrint("Before ungrouping shortcut groups in molecule ",

                    ++molIndex, ": ", mol);

            debugPrintMRV(SELF + "mol in MRV:\n", mol);

            mol.setGUIContracted(false);

            mol.ungroupSgroups(SHORTCUT_GROUPS);

            debugPrint("After ungrouping shortcut groups in molecule ",

                    molIndex, ": ", mol);

            debugPrintMRV(SELF + "molecule ", molIndex, " in MRV:\n", mol);

The debugging output:

Before ungrouping shortcut groups in molecule 3: *[Pd]([H])(Br)(P(C1=CC=CC=C1)(C1=CC=CC=C1)C1=CC=CC=C1)P(C1=CC=CC=C1)(C1=CC=CC=C1)C1=CC=CC=C1.CCOC(=O)\C=C\C1=CC=CC=C1 |c:7,9,14,16,21,23,29,31,36,38,43,45,56,58,t:5,12,19,27,34,41,54,m:0:48.47,C:23.25,4.3,0.0|

MechData.extractMolecules: The remaining atoms are in the same stage.

MechData.extractMolecules: mol in MRV:

<?xml version="1.0"?>

<cml version="ChemAxon file format v5.10.0, generated by v5.11.5">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16" elementType="Pd H Br P P R R R R R R C C R X R" sgroupRef="0 0 0 0 0 sg2 sg3 sg4 sg5 sg6 sg7 sg1 sg1 sg8 0 sg9" x2="-18.205091512033988 -17.116147069006708 -17.116147069006708 -19.294035955061272 -19.294035955061272 -19.294035955061272 -20.834035955061275 -20.382980398088556 -20.834035955061275 -20.382980398088556 -19.294035955061272 -15.647103106806327 -15.647103106806327 -14.698424213860129 -15.647103106806327 -16.595781999752525" y2="2.9609431947980616 4.0498876378253446 1.8719987517707786 1.8719987517707786 4.0498876378253446 5.589887637825345 4.0498876378253446 5.1388320808526275 1.8719987517707781 0.7830543087434951 0.33199875177077853 3.7790679659162256 2.2390679659162256 0.939692949226925 3.0090679659162256 5.030317775181363"/>

      <bondArray>

        <bond atomRefs2="a1 a2" order="1"/>

        <bond atomRefs2="a1 a3" order="1"/>

        <bond atomRefs2="a4 a1" convention="cxn:coord"/>

        <bond atomRefs2="a5 a1" convention="cxn:coord"/>

        <bond atomRefs2="a15 a1" convention="cxn:coord"/>

        <bond atomRefs2="a4 a9" order="1"/>

        <bond atomRefs2="a4 a10" order="1"/>

        <bond atomRefs2="a4 a11" order="1"/>

        <bond atomRefs2="a5 a6" order="1"/>

        <bond atomRefs2="a5 a7" order="1"/>

        <bond atomRefs2="a5 a8" order="1"/>

        <bond atomRefs2="a12 a13" order="2"/>

        <bond atomRefs2="a12 a16" order="1"/>

        <bond atomRefs2="a13 a14" order="1"/>

      </bondArray>

      <molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a12 a13" center="a15"/>

      <molecule id="sg2" role="SuperatomSgroup" title="Ph" molID="m3">

        <atomArray atomID="a17 a18 a19 a20 a21 a22" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-1.686708366723078 -3.0203874885511155 -3.020387488551112 -1.6867083667230744 -0.3530292448950405 -0.3530292448950405" y2="-2.954994332449779 -2.184994332449776 -0.6449943324497749 0.1250056675502229 -0.6449943324497802 -2.1849943324497803"/>

        <bondArray>

          <bond atomRefs2="a17 a18" order="2"/>

          <bond atomRefs2="a17 a22" order="1"/>

          <bond atomRefs2="a18 a19" order="1"/>

          <bond atomRefs2="a19 a20" order="2"/>

          <bond atomRefs2="a20 a21" order="1"/>

          <bond atomRefs2="a21 a22" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg3" role="SuperatomSgroup" title="Ph" molID="m4">

        <atomArray atomID="a23 a24 a25 a26 a27 a28" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-14.507380803612463 -13.17370168178443 -13.173701681784433 -14.50738080361247 -15.841059925440497 -15.841059925440497" y2="11.157894648972228 10.387894648972223 8.847894648972224 8.077894648972226 8.847894648972227 10.387894648972226"/>

        <bondArray>

          <bond atomRefs2="a23 a24" order="2"/>

          <bond atomRefs2="a23 a28" order="1"/>

          <bond atomRefs2="a24 a25" order="1"/>

          <bond atomRefs2="a25 a26" order="2"/>

          <bond atomRefs2="a26 a27" order="1"/>

          <bond atomRefs2="a27 a28" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg4" role="SuperatomSgroup" title="Ph" molID="m5">

        <atomArray atomID="a29 a30 a31 a32 a33 a34" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="0.49939990554322833 -0.2706000944567748 -1.810600094456774 -2.5806000944567735 -1.8106000944567668 -0.27060009445677125" y2="11.149675262760486 9.815996140932443 9.815996140932446 11.149675262760486 12.483354384588523 12.48335438458852"/>

        <bondArray>

          <bond atomRefs2="a29 a30" order="2"/>

          <bond atomRefs2="a29 a34" order="1"/>

          <bond atomRefs2="a30 a31" order="1"/>

          <bond atomRefs2="a31 a32" order="2"/>

          <bond atomRefs2="a32 a33" order="1"/>

          <bond atomRefs2="a33 a34" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg5" role="SuperatomSgroup" title="Ph" molID="m6">

        <atomArray atomID="a35 a36 a37 a38 a39 a40" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-14.507380803612463 -13.17370168178443 -13.17370168178443 -14.50738080361247 -15.841059925440504 -15.841059925440504" y2="6.802116876863094 6.032116876863091 4.49211687686309 3.722116876863093 4.492116876863095 6.032116876863094"/>

        <bondArray>

          <bond atomRefs2="a35 a36" order="2"/>

          <bond atomRefs2="a35 a40" order="1"/>

          <bond atomRefs2="a36 a37" order="1"/>

          <bond atomRefs2="a37 a38" order="2"/>

          <bond atomRefs2="a38 a39" order="1"/>

          <bond atomRefs2="a39 a40" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg6" role="SuperatomSgroup" title="Ph" molID="m7">

        <atomArray atomID="a41 a42 a43 a44 a45 a46" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-11.43560018982421 -10.665600189824204 -9.125600189824205 -8.355600189824205 -9.125600189824208 -10.665600189824211" y2="-5.124663832292605 -3.790984710464567 -3.7909847104645706 -5.124663832292605 -6.458342954120642 -6.4583429541206385"/>

        <bondArray>

          <bond atomRefs2="a41 a42" order="2"/>

          <bond atomRefs2="a41 a46" order="1"/>

          <bond atomRefs2="a42 a43" order="1"/>

          <bond atomRefs2="a43 a44" order="2"/>

          <bond atomRefs2="a44 a45" order="1"/>

          <bond atomRefs2="a45 a46" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg7" role="SuperatomSgroup" title="Ph" molID="m8">

        <atomArray atomID="a47 a48 a49 a50 a51 a52" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-1.686708366723078 -3.0203874885511155 -3.0203874885511084 -1.6867083667230744 -0.3530292448950405 -0.3530292448950405" y2="-2.954994332449779 -2.1849943324497767 -0.6449943324497758 0.12500566755022202 -0.6449943324497811 -2.1849943324497803"/>

        <bondArray>

          <bond atomRefs2="a47 a48" order="2"/>

          <bond atomRefs2="a47 a52" order="1"/>

          <bond atomRefs2="a48 a49" order="1"/>

          <bond atomRefs2="a49 a50" order="2"/>

          <bond atomRefs2="a50 a51" order="1"/>

          <bond atomRefs2="a51 a52" order="2"/>

        </bondArray>

      </molecule>

      <molecule id="sg8" role="SuperatomSgroup" title="CO2Et" leftName="EtO2C" molID="m9">

        <atomArray atomID="a53 a54 a55 a56 a57" elementType="C C O C O" attachmentPoint="1 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0" x2="-1.5464783161991846 -1.546478316199181 -2.3164783161991807 -2.3164783161991807 -2.316478316199184" y2="-1.7651035074064767 -4.432461751062549 -3.0987826292345115 -5.766140872890585 -0.43142438557844187"/>

        <bondArray>

          <bond atomRefs2="a55 a53" order="1"/>

          <bond atomRefs2="a53 a57" order="2"/>

          <bond atomRefs2="a56 a54" order="1"/>

          <bond atomRefs2="a54 a55" order="1"/>

        </bondArray>

      </molecule>

      <molecule id="sg9" role="SuperatomSgroup" title="Ph" molID="m10">

        <atomArray atomID="a58 a59 a60 a61 a62 a63" elementType="C C C C C C" attachmentPoint="1 0 0 0 0 0" sgroupAttachmentPoint="1 0 0 0 0 0" x2="-17.145527326560092 -17.1455273265601 -18.47920644838814 -19.812885570216174 -19.812885570216164 -18.479206448388126" y2="21.240640544268167 19.70064054426817 18.930640544268172 19.70064054426818 21.24064054426817 22.010640544268167"/>

        <bondArray>

          <bond atomRefs2="a58 a59" order="2"/>

          <bond atomRefs2="a58 a63" order="1"/>

          <bond atomRefs2="a59 a60" order="1"/>

          <bond atomRefs2="a60 a61" order="2"/>

          <bond atomRefs2="a61 a62" order="1"/>

          <bond atomRefs2="a62 a63" order="2"/>

        </bondArray>

      </molecule>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>





After ungrouping shortcut groups in molecule 3: *[Pd]([H])(Br)(P(C1=CC=CC=C1)(C1=CC=CC=C1)C1=CC=CC=C1)P(C1=CC=CC=C1)(C1=CC=CC=C1)C1=CC=CC=C1.CCOC(=O)C=CC1=CC=CC=C1 |c:7,9,14,16,21,23,29,31,36,38,43,45,56,58,t:5,12,19,27,34,41,54,m:0:48.47,C:23.25,4.3,0.0|

MechData.extractFlows: molecule 3 in MRV:

<?xml version="1.0"?>

<cml version="ChemAxon file format v5.10.0, generated by v5.11.5">

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray atomID="a1 a2 a3 a4 a5 a6 a7 a8 a9 a10 a11 a12 a13 a14 a15 a16 a17 a18 a19 a20 a21 a22 a23 a24 a25 a26 a27 a28 a29 a30 a31 a32 a33 a34 a35 a36 a37 a38 a39 a40 a41 a42 a43 a44 a45 a46 a47 a48 a49 a50 a51 a52 a53 a54 a55" elementType="Pd H Br P P C C C C C C C C C X C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C C O C O C C C C C" sgroupRef="0 0 0 0 0 0 0 0 0 0 0 sg1 sg1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0" x2="-18.205091512033988 -17.116147069006708 -17.116147069006708 -19.294035955061272 -19.294035955061272 -1.686708366723078 -14.507380803612463 0.49939990554322833 -14.507380803612463 -11.43560018982421 -1.686708366723078 -15.647103106806327 -15.647103106806327 -1.5464783161991846 -15.647103106806327 -17.145527326560092 -3.0203874885511155 -3.020387488551112 -1.6867083667230744 -0.3530292448950405 -0.3530292448950405 -13.17370168178443 -13.173701681784433 -14.50738080361247 -15.841059925440497 -15.841059925440497 -0.2706000944567748 -1.810600094456774 -2.5806000944567735 -1.8106000944567668 -0.27060009445677125 -13.17370168178443 -13.17370168178443 -14.50738080361247 -15.841059925440504 -15.841059925440504 -10.665600189824204 -9.125600189824205 -8.355600189824205 -9.125600189824208 -10.665600189824211 -3.0203874885511155 -3.0203874885511084 -1.6867083667230744 -0.3530292448950405 -0.3530292448950405 -1.546478316199181 -2.3164783161991807 -2.3164783161991807 -2.316478316199184 -17.1455273265601 -18.47920644838814 -19.812885570216174 -19.812885570216164 -18.479206448388126" y2="2.9609431947980616 4.0498876378253446 1.8719987517707786 1.8719987517707786 4.0498876378253446 -2.954994332449779 11.157894648972228 11.149675262760486 6.802116876863094 -5.124663832292605 -2.954994332449779 3.7790679659162256 2.2390679659162256 -1.7651035074064767 3.0090679659162256 21.240640544268167 -2.184994332449776 -0.6449943324497749 0.1250056675502229 -0.6449943324497802 -2.1849943324497803 10.387894648972223 8.847894648972224 8.077894648972226 8.847894648972227 10.387894648972226 9.815996140932443 9.815996140932446 11.149675262760486 12.483354384588523 12.48335438458852 6.032116876863091 4.49211687686309 3.722116876863093 4.492116876863095 6.032116876863094 -3.790984710464567 -3.7909847104645706 -5.124663832292605 -6.458342954120642 -6.4583429541206385 -2.1849943324497767 -0.6449943324497758 0.12500566755022202 -0.6449943324497811 -2.1849943324497803 -4.432461751062549 -3.0987826292345115 -5.766140872890585 -0.43142438557844187 19.70064054426817 18.930640544268172 19.70064054426818 21.24064054426817 22.010640544268167"/>

      <bondArray>

        <bond atomRefs2="a1 a2" order="1"/>

        <bond atomRefs2="a1 a3" order="1"/>

        <bond atomRefs2="a4 a1" convention="cxn:coord"/>

        <bond atomRefs2="a5 a1" convention="cxn:coord"/>

        <bond atomRefs2="a15 a1" convention="cxn:coord"/>

        <bond atomRefs2="a4 a9" order="1"/>

        <bond atomRefs2="a4 a10" order="1"/>

        <bond atomRefs2="a4 a11" order="1"/>

        <bond atomRefs2="a5 a6" order="1"/>

        <bond atomRefs2="a5 a7" order="1"/>

        <bond atomRefs2="a5 a8" order="1"/>

        <bond atomRefs2="a12 a13" order="2"/>

        <bond atomRefs2="a12 a16" order="1"/>

        <bond atomRefs2="a13 a14" order="1"/>

        <bond atomRefs2="a6 a17" order="2"/>

        <bond atomRefs2="a6 a21" order="1"/>

        <bond atomRefs2="a17 a18" order="1"/>

        <bond atomRefs2="a18 a19" order="2"/>

        <bond atomRefs2="a19 a20" order="1"/>

        <bond atomRefs2="a20 a21" order="2"/>

        <bond atomRefs2="a7 a22" order="2"/>

        <bond atomRefs2="a7 a26" order="1"/>

        <bond atomRefs2="a22 a23" order="1"/>

        <bond atomRefs2="a23 a24" order="2"/>

        <bond atomRefs2="a24 a25" order="1"/>

        <bond atomRefs2="a25 a26" order="2"/>

        <bond atomRefs2="a8 a27" order="2"/>

        <bond atomRefs2="a8 a31" order="1"/>

        <bond atomRefs2="a27 a28" order="1"/>

        <bond atomRefs2="a28 a29" order="2"/>

        <bond atomRefs2="a29 a30" order="1"/>

        <bond atomRefs2="a30 a31" order="2"/>

        <bond atomRefs2="a9 a32" order="2"/>

        <bond atomRefs2="a9 a36" order="1"/>

        <bond atomRefs2="a32 a33" order="1"/>

        <bond atomRefs2="a33 a34" order="2"/>

        <bond atomRefs2="a34 a35" order="1"/>

        <bond atomRefs2="a35 a36" order="2"/>

        <bond atomRefs2="a10 a37" order="2"/>

        <bond atomRefs2="a10 a41" order="1"/>

        <bond atomRefs2="a37 a38" order="1"/>

        <bond atomRefs2="a38 a39" order="2"/>

        <bond atomRefs2="a39 a40" order="1"/>

        <bond atomRefs2="a40 a41" order="2"/>

        <bond atomRefs2="a11 a42" order="2"/>

        <bond atomRefs2="a11 a46" order="1"/>

        <bond atomRefs2="a42 a43" order="1"/>

        <bond atomRefs2="a43 a44" order="2"/>

        <bond atomRefs2="a44 a45" order="1"/>

        <bond atomRefs2="a45 a46" order="2"/>

        <bond atomRefs2="a48 a14" order="1"/>

        <bond atomRefs2="a14 a50" order="2"/>

        <bond atomRefs2="a49 a47" order="1"/>

        <bond atomRefs2="a47 a48" order="1"/>

        <bond atomRefs2="a16 a51" order="2"/>

        <bond atomRefs2="a16 a55" order="1"/>

        <bond atomRefs2="a51 a52" order="1"/>

        <bond atomRefs2="a52 a53" order="2"/>

        <bond atomRefs2="a53 a54" order="1"/>

        <bond atomRefs2="a54 a55" order="2"/>

      </bondArray>

      <molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a12 a13" center="a15"/>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

First look at the MRV before ungrouping, and note the trans stereochemistry of the cinnamate group.  Now look at the MRV after ungrouping.  In addition to the crazy positions of the atoms after the ungrouping, the location of the cinnamate Ph group relative to the C=C double bond is creating a problem; the C-Ph bond is nearly collinear with the C=C bond.  If you now look at the CXSMILES after ungrouping, you can see that Marvin is now interpreting the double bond as having an unspecified geometry.  This change is causing the compound not to match to the same structure before the shortcut groups were ungrouped.  

It is absolutely essential that shortcut ungrouping be accomplished without changing the stereochemistry of the compound.  Please fix.

Hi Bob,

I tried your example code and it doesn't do the ungroupping at all.

Changing

mol.setGUIContracted(false);

 

 

to 

mol.setGUIContracted(true);

 

 

solved the problem and proper coordinates are generated.

Regards,

Erika

 

I don't understand why you say that the example code didn't do the ungrouping at all.  Before executing setGUIContracted(false) and ungroupSgroups(Sgroup.ST_SUPERATOM), the MRV shows multiple SuperatomSgroups.  Afterwards, it shows none. 

Anyway, I need setGUIContracted(false) in the code, because I need the sources and sinks of any electron-flow arrows associated with the superatoms to be associated with the superatoms' attachment points before I get rid of the superatoms; see this discussion.  

Hi Bob, 

I can't reproduce your problem.

See the attached code. After setGUI and ungroup the stereo2 information and the cxsmiles don't change.

Can you help me reproducing the issue?

Peter

Change molecule.setGUIContracted(true) to molecule.setGUIContracted(false).  

I've set up a JSP page here that demonstrates the problem using your code (but it has a Marvin interface for playing around).

bobgr wrote:

Change molecule.setGUIContracted(true) to molecule.setGUIContracted(false).

Yes, that did the trick. 

We'll investigate the issue and get back to you soon. 

Hi Bob,

I have started to work on this issue, and I have a question. As I understood from other forum topics, first setGUIContracted(true) should invoke because of some electron flow arrow. My question is that, before you call setGUIContracted(true), are the Cis/Trans information OK?

setGUIContracted(false) does not update the coordinates of the atoms, so they get back their original. If you call mol.expandSgroups() instead of setGUIContracted(false) and the trans stereo chemistry will remain.

Best Regards,

Peter

Before I call setGUIContracted(true), the atom coordinates of the molecule are set by whatever the user drew in the GUI.  So if the user drew the molecule correctly (which I did in the example I gave you), the answer is yes.

        importedMolecule = MolImporter.importMol(respMRV);

        mols = importedMolecule.convertToFrags();

        for (Molecule mol : mols) {

            mol.setGUIContracted(true);

I investigated the file you have attached, MRV debug before ungroup. I found that the coordinates of the atoms in the shortcut S-groups are the same as get after the ungroup. It's not the invocation of setGUIContracted(false) or ungroupSgroups() that made this with the coordinates.

To demonstrate this, I plot the coordinates of the atoms using gnuplot (both shortcut atoms (green) and atoms in shortcut S-groups (red)). The result pdf is attached.

Best Regards,

Peter

Let's refer to the attached JSP page, ungroupTest.jsp.  I have also attached the necessary resources.  (I had to add the .txt attachment to their names so this forum would upload them.)

Please explain why the molecule that is loaded into the Marvin applet in ungroupTest.jsp has its geometry altered so poorly when the user presses the Ungroup button underneath the applet.  Note that ungrouping, either before or after expansion, in the Marvin applet works just fine.

Can you please attach ungroupTest.jsp as text as well? We can't download it now.

Superatom (Shortcut) S-groups have three states: expanded, when all of their atoms are in the molecule; contracted, when only the superatom is part of the molecule, and the so-called GUIContracted state, which is an "expanded-like" state but the coordinates of the atoms are not re-calculated. 

Your molecule is in GUIContracted state, when it is imported from mrv using our API. However, importing it to MarvinSketch, its state will be contracted, as Marvin contracts it. This is an important difference, because method Molecule.ungroupSgroups() expands, and therefore recalculates the coordates of the atoms in shortcut, only when the sgroup is in contracted state.

Hence, I recommend you to call Molecule.expandSgroups() or Molecule.contractSgroups() before ungroup.

It is not clear from the information you provided us how the coordinates in the mrv file before ungroup were generate. Can you attach the mrv of the structure you have drawn as well as the whole process you done with it before ungroup?

Thanks!

Sorry for the delay.  I was out of the country and without my laptop.  Here it is.

Have yout tried the solution I recommended? Is it suitable for you?

Please attach the mrv file you have drawn as well as the the whole process that were done on the original file. Using them we can investigate if we have a bug or not.

Thanks!

You can find the MRV in the code in the file I attached with my previous comment.

The mrv file in ungroupTest.jsp is the same that was attached in the first post. The coordinates of the atoms, as I wrote before are wrong in this file.

You can try Molecule.expandSgroups() or Molecule.contractSgroups() before ungroup. Or try to regenerate, redraw your file.

From these information unfortunately we don't know what went wrong with the mrv file.

pszakacs wrote:

The mrv file in ungroupTest.jsp is the same that was attached in the first post. The coordinates of the atoms, as I wrote before are wrong in this file. You can try Molecule.expandSgroups() or Molecule.contractSgroups() before ungroup. Or try to regenerate, redraw your file. From these information unfortunately we don't know what went wrong with the mrv file.

What do you mean, "the coordinates of the atoms ... are wrong in this file?"  I drew the structure in Marvin (using the Ph and CO2Et shortcut groups), went to Edit -> Source, copied the MRV code there, and pasted it into ungroupTest.jsp, just so I could avoid having to draw the structure every time.  Even if I delete the structure and redraw it, the same error occurs.  How could the coordinates be wrong?

I was able to work around the problem in my main code by running mol.setGUIContracted(false) before getting the electron-flow arrow termini, then running mol.setGUIContracted(true) before running mol.ungroupSgroups(SHORTCUT_GROUPS).  But it seems like a waste of processor time to have to run mol.setGUIContracted(true) before ungrouping the shortcut groups.

Hi Bob,

we have found what is wrong, ungroupSgroups(int sgroupType) behaves differently than uggroupSgroups(). We will notify you when the fix will be available.

Best regards,

Zsuzsa

Hi Bob,

The bug is fixed and will be available in Marvin 6.3.

Best regards,
Domi

Köszönöm.  

Can you confirm that this fix is available in JChem 6.3?

Hi Bob,

yes, the fix is available in version 6.3.

Please let us know if it's still not working as expected.

BRs,

Peter