allene enantiomers

As of JChem 5.9, allene enantiomers do not match to one another when ENANTIOMER mode is specified.

Target:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="C"

              x2="-3.128124952316284" y2="0.7699999809265137" />

        <atom id="a2" elementType="C"

              x2="-1.5881249523162841" y2="0.7699999809265137" />

        <atom id="a3" elementType="C"

              x2="-0.04812495231628411" y2="0.7699999809265137" />

        <atom id="a4" elementType="C"

              x2="1.1068751573562625" y2="2.1518041909694237" />

        <atom id="a5" elementType="C"

              x2="-4.61565072480145" y2="0.3714186514686313" />

      </atomArray>

      <bondArray>

        <bond atomRefs2="a1 a2" order="2" />

        <bond atomRefs2="a2 a3" order="2" />

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

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

          <bondStereo>H</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Query:

<?xml version="1.0" ?>

<cml>

<MDocument>

  <MChemicalStruct>

    <molecule molID="m1">

      <atomArray>

        <atom id="a1" elementType="C"

              x2="-3.128124952316284" y2="0.7699999809265137" />

        <atom id="a2" elementType="C"

              x2="-1.5881249523162841" y2="0.7699999809265137" />

        <atom id="a3" elementType="C"

              x2="-0.04812495231628411" y2="0.7699999809265137" />

        <atom id="a4" elementType="C"

              x2="0.7218750476837161" y2="2.1036791027545494" />

        <atom id="a5" elementType="C"

              x2="-4.61565072480145" y2="0.3714186514686313" />

      </atomArray>

      <bondArray>

        <bond atomRefs2="a1 a2" order="2" />

        <bond atomRefs2="a2 a3" order="2" />

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

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

          <bondStereo>W</bondStereo>

        </bond>

      </bondArray>

    </molecule>

  </MChemicalStruct>

</MDocument>

</cml>

Search options:

JChemCompare.jsp: searchType = FULL

JChemCompare.jsp: setStereoSearch = STEREO_ENANTIOMER

JChemCompare.jsp: considerDoubleBondStereoMatching = false

JChemCompare.jsp: considerOddCumuleneStereoMatching = true

JChemCompare.jsp: considerAxialStereoMatching = true

JChemCompare.jsp: considerSynAntiStereoMatching = true

JChemCompare.jsp: stereoMatchingModel = STEREO_MODEL_LOCAL

JChemCompare.jsp: chargeType = 1

JChemCompare.jsp: radicalType = 1

JChemCompare.jsp: isotopeType = 1

JChemCompare.jsp: valenceType = true

I wrote in a workaround -- see if there's a stereogenic allene in the structure, and if so, get the allene enantiomer and redo the search -- but it would be much nicer if you would have MolSearch account for allene enantiomers as well, even if you have to work in the workaround.

Hi Bob,

We have put this issue on our list of feature requests and will report you when it's ready.

Bye,

Robert