R/S label bug - ChemAxon Forum Archive

User 870ab5b546

06-05-2005 02:00:23

The following compound doesn't show the R/S label unless the entire molecule is selected.

Code:

<?xml version="1.0" encoding="MacRoman" ?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5 a6"

elementType="C H R O C O"

sgroupRef="0 0 sg1 0 0 0"

x2="-8.633333555857341 -10.406667143503826 -8.389461846457323 -7.2681265553446 -8.633333555857341 -7.093333555857341"

y2="2.2517600874201458 3.30176003973643 4.453880189547467 2.9643678657603805 0.6534266905085244 0.6534266905085244"

/>

<bondArray>

<bond atomRefs2="a1 a5" order="1" />

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

<bondStereo>W</bondStereo>

</bond>

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

<bondStereo>W</bondStereo>

</bond>

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

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

</bondArray>

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

<atomArray

atomID="a7 a8"

elementType="C O"

attachmentPoint="1 0"

x2="-0.77 0.77"

y2="0.0 0.0"

/>

<bondArray>

<bond atomRefs2="a7 a8" order="2" />

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

</MDocument>

Strangely enough, this very similar one does:

Code:

<?xml version="1.0"?>

<MDocument>

<MChemicalStruct>

<molecule molID="m1">

<atomArray

atomID="a1 a2 a3 a4 a5"

elementType="C H C N R"

sgroupRef="0 0 0 0 sg1"

x2="-5.366666666666667 -3.8266666666666667 -5.366666666666667 -6.906666666666668 -5.366666666666667"

y2="-0.5715733333333335 0.9684266666666669 0.9684266666666669 0.9684266666666669 2.5084266666666672"

/>

<bondArray>

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

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

<bond atomRefs2="a3 a4" order="1">

<bondStereo>W</bondStereo>

</bond>

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

</bondArray>

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

<atomArray

atomID="a6 a7 a8"

elementType="C O O"

attachmentPoint="1 0 0"

x2="-5.366666666666667 -4.032933333333333 -6.700400000000001"

y2="2.5084266666666672 3.2784266666666673 3.2784266666666673"

/>

<bondArray>

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

<bond atomRefs2="a6 a8" order="2" />

</bondArray>

</molecule>

</molecule>

</MChemicalStruct>

</MDocument>

And if you convert the second structure to the first one, you can preserve the visibility of the label. But if in converting them, you make an achiral compound, the label will not come back when you make arrive at the first compound. Really, really weird.

This is with Marvin 3.5.5, but Marvin 4.0 alpha has similar behavior.