ungroup geometry problem

User 870ab5b546

12-07-2008 21:54:08

The code:





Code:
    public static void ungroupRemapSGroups(Molecule mol) {


        debugPrint("ChemUtils.ungroupRemapSGroups: starting with:\n"


                + mol.toFormat("mrv"));


        Sgroup[] sgroups = mol.getSgroupArray();


        int numSgroups = sgroups.length;


        for (int grpNum = 0; grpNum < numSgroups; grpNum++) {


            SuperatomSgroup sgroup = (SuperatomSgroup) sgroups[grpNum];


            SgroupAtom superatom = sgroup.getSuperAtom();


            String symb = superatom.getSymbol();


            int mapNum = superatom.getAtomMap();


            MolAtom attachPt = sgroup.findAttachAtom();


            debugPrint("ChemUtils.ungroupRemapSGroups: "


                    + "clearing shortcut group " + symb


                    + (mapNum != 0 ? ", setting attachment point "


                            + attachPt.getSymbol()


                            + mol.indexOf(attachPt)


                            + " to map number " + mapNum + "."


                        : ", no map number to set."));


            mol.ungroupSgroup(sgroup);


            if (mapNum >= 0) attachPt.setAtomMap(mapNum);


        }


        mol.aromatize(MoleculeGraph.AROM_GENERAL);


        debugPrint("ChemUtils.ungroupRemapSGroups: returning:\n"


                + mol.toFormat("mrv"));


    } // ungroupRemapSGroups(Molecule)






The purpose is to ungroup a shortcut group, but if the shortcut group is matched, to put the map number on the attachment point.





The problem I am having is that ungroupSgroup() is altering the coordinates of the shortcut group. Below is the output from subjecting two identical or nearly identical structures to this method. In both cases, the geometry of the C atom attached to the Ph group is tortured when the Ph group is ungrouped. (I do not observe this behavior when I ungroup the Ph in the GUI.) Worse, in the second case, the C atom with map number 3 is being given an R configuration, whereas in the first case, it is not. The result is that the two output molecules don't match by a PERFECT search, although they should. Any advice?





Code:
2008-07-12 16:48:04 ChemUtils.ungroupRemapSGroups: starting with:


<?xml version="1.0" ?>


<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"


          elementType="C C C C C C C C C R O O C C C C C C C C O O H R C C C"


          mrvMap="6 7 2 5 1 3 4 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0"


          sgroupRef="0 0 0 0 0 0 0 0 0 sg1 0 0 0 0 0 0 0 0 0 0 0 0 0 sg2 0 0 0"


          x3="-17.801633855590822 -17.119740522257487 -15.828263321533203 -16.35403385559082 -16.223180522257486 -14.439580522257486 -14.990433855590823 -17.588401890031633 -14.859757720419317 -13.350636079230203 -13.350636079230203 -14.220433855590823 -14.73931887850592 -0.9601248056888583 0.4367751943111422 0.9327018884181975 -0.10939811158180213 -1.5062981115818026 -2.002224805688858 -1.178598224384662 0.15341185202598595 -1.8202660434440436 0.9327018884181975 2.4202276609033624 -0.9146931917667391 -2.1772846808831945 1.8805251370906833"


          y3="16.875655052693684 18.10858838602702 18.852713092651367 17.604215052693686 20.47104171936035 18.080401719360353 16.912988386027017 21.284944421043384 21.187057266277982 16.99145727633307 19.169346162387637 15.579309264198981 19.94165753567865 18.211075228881835 17.955675228881837 19.322591247558595 19.165891247558594 19.421291247558592 18.054375228881838 16.74857400473652 16.789904660034182 15.581643377428836 20.412591247558595 18.92400991810071 20.264291247558592 16.892276202114317 18.051925762939455"


          z3="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 1.4073 0.8864 -0.32209999999999994 -1.4073 -0.8864 0.32210000000000005 0.32210000000000005 0.8864 0.32210000000000005 -0.32209999999999994 -0.32209999999999994 1.4073 1.4073 0.8864"


          />


      <bondArray>


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


        <bond atomRefs2="a2 a3" order="1" />


        <bond atomRefs2="a1 a4" order="1" />


        <bond atomRefs2="a4 a5" order="1" />


        <bond atomRefs2="a5 a3" order="1" />


        <bond atomRefs2="a3 a6" order="1" />


        <bond atomRefs2="a6 a7" order="1" />


        <bond atomRefs2="a7 a4" order="1" />


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


        <bond atomRefs2="a5 a9" order="1" />


        <bond atomRefs2="a6 a11" order="1" />


        <bond atomRefs2="a7 a12" order="2" />


        <bond atomRefs2="a3 a13" order="1" />


        <bond atomRefs2="a14 a15" order="1" />


        <bond atomRefs2="a14 a19" order="1" />


        <bond atomRefs2="a15 a16" order="1" />


        <bond atomRefs2="a16 a17" order="1" />


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


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


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


        <bond atomRefs2="a15 a21" order="1" />


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


        <bond atomRefs2="a20 a22" order="2" />


        <bond atomRefs2="a16 a23" order="1" />


        <bond atomRefs2="a14 a25" order="1" />


        <bond atomRefs2="a14 a26" order="1" />


        <bond atomRefs2="a15 a27" order="1" />


        <bond atomRefs2="a16 a24" order="1" />


        <bond atomRefs2="a6 a10" order="1" />


      </bondArray>


      <molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">


        <atomArray


            atomID="a28 a29 a30 a31 a32 a33"


            elementType="C C C C C C"


            attachmentPoint="1 0 0 0 0 0"


            x3="-13.616512548427243 -12.894622462173087 -11.480487984511763 -10.758873911286287 -11.480487984511765 -12.89462246217309"


            y3="19.491926003990464 18.280627340201388 18.27889472078708 19.491926003990468 20.704957287193857 20.703224667779548"


            z3="-3.631633523608078E-10 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


            />


        <bondArray>


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


          <bond atomRefs2="a28 a33" order="1" />


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


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


          <bond atomRefs2="a31 a32" order="1" />


          <bond atomRefs2="a32 a33" order="2" />


        </bondArray>


      </molecule>


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


        <atomArray


            atomID="a34 a35 a36 a37 a38 a39"


            elementType="C C C C C C"


            attachmentPoint="1 0 0 0 0 0"


            x3="2.457237470646243 3.179127556900399 4.593262034561723 5.314876107787199 4.593262034561722 3.179127556900397"


            y3="21.56130008846312 20.350001424674044 20.348268805259735 21.561300088463124 22.774331371666513 22.772598752252204"


            z3="-3.631633523608078E-10 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


            />


        <bondArray>


          <bond atomRefs2="a34 a35" order="2" />


          <bond atomRefs2="a34 a39" order="1" />


          <bond atomRefs2="a35 a36" order="1" />


          <bond atomRefs2="a36 a37" order="2" />


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


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


        </bondArray>


      </molecule>


    </molecule>


  </MChemicalStruct>


</MDocument>





ChemUtils.ungroupRemapSGroups: clearing shortcut group Ph, no map number to set.


ChemUtils.ungroupRemapSGroups: clearing shortcut group Ph, no map number to set.


ChemUtils.ungroupRemapSGroups: returning:


<?xml version="1.0" ?>


<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"


          elementType="C C C C C C C C C C O O C C C C C C C C O O H C C C C C C C C C C C C C C"


          mrvMap="6 7 2 5 1 3 4 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"


          x3="-17.801633855590822 -17.119740522257487 -15.828263321533203 -16.35403385559082 -16.223180522257486 -14.439580522257486 -14.990433855590823 -17.588401890031633 -14.859757720419317 -13.616512548427243 -13.350636079230203 -14.220433855590823 -14.73931887850592 -0.9601248056888583 0.4367751943111422 0.9327018884181975 -0.10939811158180213 -1.5062981115818026 -2.002224805688858 -1.178598224384662 0.15341185202598595 -1.8202660434440436 0.9327018884181975 2.457237470646243 -0.9146931917667391 -2.1772846808831945 1.8805251370906833 -12.894622462173087 -11.480487984511763 -10.758873911286287 -11.480487984511765 -12.89462246217309 3.179127556900399 4.593262034561723 5.314876107787199 4.593262034561722 3.179127556900397"


          y3="16.875655052693684 18.10858838602702 18.852713092651367 17.604215052693686 20.47104171936035 18.080401719360353 16.912988386027017 21.284944421043384 21.187057266277982 19.491926003990464 19.169346162387637 15.579309264198981 19.94165753567865 18.211075228881835 17.955675228881837 19.322591247558595 19.165891247558594 19.421291247558592 18.054375228881838 16.74857400473652 16.789904660034182 15.581643377428836 20.412591247558595 21.56130008846312 20.264291247558592 16.892276202114317 18.051925762939455 18.280627340201388 18.27889472078708 19.491926003990468 20.704957287193857 20.703224667779548 20.350001424674044 20.348268805259735 21.561300088463124 22.774331371666513 22.772598752252204"


          z3="0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 0.0 -3.631633523608078E-10 0.0 0.0 0.0 1.4073 0.8864 -0.32209999999999994 -1.4073 -0.8864 0.32210000000000005 0.32210000000000005 0.8864 0.32210000000000005 -0.32209999999999994 -3.631633523608078E-10 1.4073 1.4073 0.8864 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


          />


      <bondArray>


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


        <bond atomRefs2="a2 a3" order="1" />


        <bond atomRefs2="a1 a4" order="1" />


        <bond atomRefs2="a4 a5" order="1" />


        <bond atomRefs2="a5 a3" order="1" />


        <bond atomRefs2="a3 a6" order="1" />


        <bond atomRefs2="a6 a7" order="1" />


        <bond atomRefs2="a7 a4" order="1" />


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


        <bond atomRefs2="a5 a9" order="1" />


        <bond atomRefs2="a6 a11" order="1" />


        <bond atomRefs2="a7 a12" order="2" />


        <bond atomRefs2="a3 a13" order="1" />


        <bond atomRefs2="a14 a15" order="1" />


        <bond atomRefs2="a14 a19" order="1" />


        <bond atomRefs2="a15 a16" order="1" />


        <bond atomRefs2="a16 a17" order="1" />


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


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


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


        <bond atomRefs2="a15 a21" order="1" />


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


        <bond atomRefs2="a20 a22" order="2" />


        <bond atomRefs2="a16 a23" order="1" />


        <bond atomRefs2="a14 a25" order="1" />


        <bond atomRefs2="a14 a26" order="1" />


        <bond atomRefs2="a15 a27" order="1" />


        <bond atomRefs2="a16 a24" order="1" />


        <bond atomRefs2="a6 a10" order="1" />


        <bond atomRefs2="a10 a28" order="A" />


        <bond atomRefs2="a10 a32" order="A" />


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


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


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


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


        <bond atomRefs2="a24 a33" order="A" />


        <bond atomRefs2="a24 a37" order="A" />


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


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


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


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


      </bondArray>


    </molecule>


  </MChemicalStruct>


</MDocument>





ChemUtils.ungroupRemapSGroups: starting with:


<?xml version="1.0" ?>


<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"


          elementType="C C C C C C C C C R O O C C C C C C C C O O H R C C C"


          mrvMap="6 7 2 5 1 3 4 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0"


          sgroupRef="0 0 0 0 0 0 0 0 0 sg1 0 0 0 0 0 0 0 0 0 0 0 0 0 sg2 0 0 0"


          x3="-18.774792851747844 -18.09289951841451 -16.801422317690225 -17.327192851747842 -17.196339518414508 -15.412739518414508 -15.963592851747844 -18.561560886188655 -15.832916716576339 -14.323795075387228 -14.323795075387224 -15.193592851747844 -15.712477874662941 -1.9332838018458807 -0.5363838018458802 -0.04045710773882494 -1.0825571077388245 -2.479457107738825 -2.9753838018458802 -2.1517572205416844 -0.8197471441310364 -2.793425039601066 -0.04045710773882494 1.44706866474634 -1.8878521879237615 -3.150443677040217 0.9073661409336609"


          y3="17.232299911108697 18.465233244442032 19.20935795106638 17.9608599111087 20.827686577775363 18.437046577775366 17.26963324444203 21.641589279458397 21.543702124692995 17.34810213474808 19.52599102080265 15.935954122613994 20.298302394093664 18.56772008729685 18.31232008729685 19.679236105973608 19.522536105973607 19.777936105973605 18.41102008729685 17.10521886315153 17.146549518449195 15.93828823584385 20.769236105973608 19.280654776515725 20.620936105973605 17.24892106052933 18.408570621354468"


          z3="0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 1.4967469469156063 0.9758469469156061 -0.23265305308439377 -1.3178530530843937 -0.7969530530843938 0.4115469469156062 0.4115469469156062 0.9758469469156061 0.4115469469156062 -0.23265305308439377 -0.23265305308439377 1.4967469469156063 1.4967469469156063 0.9758469469156061"


          />


      <bondArray>


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


        <bond atomRefs2="a2 a3" order="1" />


        <bond atomRefs2="a1 a4" order="1" />


        <bond atomRefs2="a4 a5" order="1" />


        <bond atomRefs2="a5 a3" order="1" />


        <bond atomRefs2="a3 a6" order="1" />


        <bond atomRefs2="a6 a7" order="1" />


        <bond atomRefs2="a7 a4" order="1" />


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


        <bond atomRefs2="a5 a9" order="1" />


        <bond atomRefs2="a6 a11" order="1" />


        <bond atomRefs2="a7 a12" order="2" />


        <bond atomRefs2="a3 a13" order="1" />


        <bond atomRefs2="a14 a15" order="1" />


        <bond atomRefs2="a14 a19" order="1" />


        <bond atomRefs2="a15 a16" order="1" />


        <bond atomRefs2="a16 a17" order="1" />


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


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


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


        <bond atomRefs2="a15 a21" order="1" />


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


        <bond atomRefs2="a20 a22" order="2" />


        <bond atomRefs2="a16 a23" order="1" />


        <bond atomRefs2="a14 a25" order="1" />


        <bond atomRefs2="a14 a26" order="1" />


        <bond atomRefs2="a15 a27" order="1" />


        <bond atomRefs2="a16 a24" order="1" />


        <bond atomRefs2="a6 a10" order="1" />


      </bondArray>


      <molecule id="sg1" role="SuperatomSgroup" title="Ph" molID="m2">


        <atomArray


            atomID="a28 a29 a30 a31 a32 a33"


            elementType="C C C C C C"


            attachmentPoint="1 0 0 0 0 0"


            x3="-14.530887853603025 -13.808997767348869 -12.394863289687544 -11.673249216462068 -12.394863289687546 -13.80899776734887"


            y3="19.8769262328723 18.665627569083224 18.663894949668915 19.876926232872304 21.089957516075692 21.088224896661384"


            z3="-3.631633523608078E-10 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


            />


        <bondArray>


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


          <bond atomRefs2="a28 a33" order="1" />


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


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


          <bond atomRefs2="a31 a32" order="1" />


          <bond atomRefs2="a32 a33" order="2" />


        </bondArray>


      </molecule>


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


        <atomArray


            atomID="a34 a35 a36 a37 a38 a39"


            elementType="C C C C C C"


            attachmentPoint="1 0 0 0 0 0"


            x3="1.254112470646243 1.976002556900399 3.3901370345617234 4.111751107787199 3.3901370345617217 1.9760025569003972"


            y3="21.753801156578355 20.54250249278928 20.54076987337497 21.75380115657836 22.966832439781747 22.96509982036744"


            z3="-3.631633523608078E-10 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


            />


        <bondArray>


          <bond atomRefs2="a34 a35" order="2" />


          <bond atomRefs2="a34 a39" order="1" />


          <bond atomRefs2="a35 a36" order="1" />


          <bond atomRefs2="a36 a37" order="2" />


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


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


        </bondArray>


      </molecule>


    </molecule>


  </MChemicalStruct>


</MDocument>





ChemUtils.ungroupRemapSGroups: clearing shortcut group Ph, no map number to set.


ChemUtils.ungroupRemapSGroups: clearing shortcut group Ph, no map number to set.


ChemUtils.ungroupRemapSGroups: returning:


<?xml version="1.0" ?>


<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"


          elementType="C C C C C C C C C C O O C C C C C C C C O O H C C C C C C C C C C C C C C"


          mrvMap="6 7 2 5 1 3 4 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0"


          x3="-18.774792851747844 -18.09289951841451 -16.801422317690225 -17.327192851747842 -17.196339518414508 -15.412739518414508 -15.963592851747844 -18.561560886188655 -15.832916716576339 -14.530887853603025 -14.323795075387224 -15.193592851747844 -15.712477874662941 -1.9332838018458807 -0.5363838018458802 -0.04045710773882494 -1.0825571077388245 -2.479457107738825 -2.9753838018458802 -2.1517572205416844 -0.8197471441310364 -2.793425039601066 -0.04045710773882494 1.254112470646243 -1.8878521879237615 -3.150443677040217 0.9073661409336609 -13.808997767348869 -12.394863289687544 -11.673249216462068 -12.394863289687546 -13.80899776734887 1.976002556900399 3.3901370345617234 4.111751107787199 3.3901370345617217 1.9760025569003972"


          y3="17.232299911108697 18.465233244442032 19.20935795106638 17.9608599111087 20.827686577775363 18.437046577775366 17.26963324444203 21.641589279458397 21.543702124692995 19.8769262328723 19.52599102080265 15.935954122613994 20.298302394093664 18.56772008729685 18.31232008729685 19.679236105973608 19.522536105973607 19.777936105973605 18.41102008729685 17.10521886315153 17.146549518449195 15.93828823584385 20.769236105973608 21.753801156578355 20.620936105973605 17.24892106052933 18.408570621354468 18.665627569083224 18.663894949668915 19.876926232872304 21.089957516075692 21.088224896661384 20.54250249278928 20.54076987337497 21.75380115657836 22.966832439781747 22.96509982036744"


          z3="0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 0.08944694691560619 -3.631633523608078E-10 0.08944694691560619 0.08944694691560619 0.08944694691560619 1.4967469469156063 0.9758469469156061 -0.23265305308439377 -1.3178530530843937 -0.7969530530843938 0.4115469469156062 0.4115469469156062 0.9758469469156061 0.4115469469156062 -0.23265305308439377 -3.631633523608078E-10 1.4967469469156063 1.4967469469156063 0.9758469469156061 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9 4.4656358679551396E-10 -5.25982408705269E-11 -1.351291035910818E-10 5.476814756506428E-10 -1.4627260683361136E-9"


          />


      <bondArray>


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


        <bond atomRefs2="a2 a3" order="1" />


        <bond atomRefs2="a1 a4" order="1" />


        <bond atomRefs2="a4 a5" order="1" />


        <bond atomRefs2="a5 a3" order="1" />


        <bond atomRefs2="a3 a6" order="1" />


        <bond atomRefs2="a6 a7" order="1" />


        <bond atomRefs2="a7 a4" order="1" />


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


        <bond atomRefs2="a5 a9" order="1" />


        <bond atomRefs2="a6 a11" order="1" />


        <bond atomRefs2="a7 a12" order="2" />


        <bond atomRefs2="a3 a13" order="1" />


        <bond atomRefs2="a14 a15" order="1" />


        <bond atomRefs2="a14 a19" order="1" />


        <bond atomRefs2="a15 a16" order="1" />


        <bond atomRefs2="a16 a17" order="1" />


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


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


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


        <bond atomRefs2="a15 a21" order="1" />


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


        <bond atomRefs2="a20 a22" order="2" />


        <bond atomRefs2="a16 a23" order="1" />


        <bond atomRefs2="a14 a25" order="1" />


        <bond atomRefs2="a14 a26" order="1" />


        <bond atomRefs2="a15 a27" order="1" />


        <bond atomRefs2="a16 a24" order="1" />


        <bond atomRefs2="a6 a10" order="1" />


        <bond atomRefs2="a10 a28" order="A" />


        <bond atomRefs2="a10 a32" order="A" />


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


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


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


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


        <bond atomRefs2="a24 a33" order="A" />


        <bond atomRefs2="a24 a37" order="A" />


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


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


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


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


      </bondArray>


    </molecule>


  </MChemicalStruct>


</MDocument>

ChemAxon e500b51457

15-07-2008 13:18:34

Hi Bob,





Try to add
Code:
mol.setGUIContracted(true);
to ungroupRemapSGroups in your code, that will result in a similar behavior when you ungroup the Ph in the GUI.








Regards,


Erika.