stereochemistry problem

The reaction definition:

<?xml version="1.0" ?>
<cml>
<MDocument>
  <MChemicalStruct>
    <reaction>
      <arrow type="DEFAULT" x1="1.9145117558843503" y1="6.634543318508632" x2="6.349019568100871" y2="6.543534057100593" />
      <propertyList>
        <property dictRef="NAME" title="NAME">
          <scalar><![CDATA[syn dihydroxylation of an alkene]]></scalar>
        </property>
        <property dictRef="SELECTIVITY" title="SELECTIVITY">
          <scalar><![CDATA[charge(ratom(1), "total") + charge(ratom(2), "total")]]></scalar>
        </property>
        <property dictRef="EXPLAIN_SELECTIVITY" title="EXPLAIN_SELECTIVITY">
          <scalar><![CDATA[The more electron-rich alkene reacts fastest.]]></scalar>
        </property>
        <property dictRef="Stop after one reaction" title="Stop after one reaction">
          <scalar>true</scalar>
        </property>
      </propertyList>
      <reactantList>
        <molecule molID="m1">
          <atomArray>
            <atom id="a1" elementType="C" mrvMap="1"
                  x2="-0.30241796163212165" y2="6.695844328841227" />
            <atom id="a2" elementType="C" mrvMap="2"
                  x2="-1.8424518427502026" y2="6.695844328841227" />
            <atom id="a3" elementType="R" mrvMap="3" rgroupRef="1"
                  x2="-2.612451842750202" y2="8.029523450669263"
                  ligandOrder="a2" />
            <atom id="a4" elementType="R" mrvMap="4" rgroupRef="2"
                  x2="-2.612451842750202" y2="5.3621652070131915"
                  ligandOrder="a2" />
            <atom id="a5" elementType="R" mrvMap="5" rgroupRef="3"
                  x2="0.4675820383678786" y2="5.3621652070131915"
                  ligandOrder="a1" />
            <atom id="a6" elementType="R" mrvMap="6" rgroupRef="4"
                  x2="0.4675820383678786" y2="8.029523450669263"
                  ligandOrder="a1" />
          </atomArray>
          <bondArray>
            <bond atomRefs2="a1 a2" order="2" />
            <bond atomRefs2="a2 a3" order="1" />
            <bond atomRefs2="a2 a4" order="1" />
            <bond atomRefs2="a1 a5" order="1" />
            <bond atomRefs2="a1 a6" order="1" />
          </bondArray>
        </molecule>
      </reactantList>
      <productList>
        <molecule molID="m2">
          <atomArray>
            <atom id="a1" elementType="C" mrvMap="1"
                  x2="11.378104480231892" y2="6.440502322157878" />
            <atom id="a2" elementType="C" mrvMap="2"
                  x2="9.838070599113811" y2="6.440502322157878" />
            <atom id="a3" elementType="O" mrvMap="8"
                  x2="12.964899990827774" y2="6.474656126868768" />
            <atom id="a4" elementType="O" mrvMap="7"
                  x2="8.284056004447217" y2="6.416397542158816" />
            <atom id="a5" elementType="R" mrvMap="3" rgroupRef="1"
                  x2="9.068070599113812" y2="7.774181443985913"
                  ligandOrder="a2" />
            <atom id="a6" elementType="R" mrvMap="4" rgroupRef="2"
                  x2="9.068070599113812" y2="5.106823200329842"
                  ligandOrder="a2" />
            <atom id="a7" elementType="R" mrvMap="5" rgroupRef="3"
                  x2="12.148104480231892" y2="5.106823200329842"
                  ligandOrder="a1" />
            <atom id="a8" elementType="R" mrvMap="6" rgroupRef="4"
                  x2="12.148104480231892" y2="7.774181443985913"
                  ligandOrder="a1" />
          </atomArray>
          <bondArray>
            <bond atomRefs2="a1 a2" order="1" />
            <bond atomRefs2="a1 a3" order="1">
              <bondStereo>W</bondStereo>
            </bond>
            <bond atomRefs2="a2 a4" order="1">
              <bondStereo>W</bondStereo>
            </bond>
            <bond atomRefs2="a2 a5" order="1" />
            <bond atomRefs2="a2 a6" order="1" />
            <bond atomRefs2="a1 a7" order="1" />
            <bond atomRefs2="a1 a8" order="1" />
          </bondArray>
        </molecule>
      </productList>
    </reaction>
  </MChemicalStruct>
</MDocument>
</cml>

Submitting C1CCC=CC1, Reactor correctly returns [H][C@]1(O)CCCC[C@@]1([H])O.

Submitting [#6]C1=C([#6])CCCC1, Reactor correctly returns [#6][C@@]1(O)CCCC[C@]1([#6])O.

But submitting [#6]C1=CCCCC1, Reactor incorrectly returns [H][C@@]1(O)CCCC[C@@]1([#6])O.

The problem occurs for trisubstituted alkenes regardless of whether they are cyclic.  It also occurs for a bromination reaction defined to give anti addition: di- and tetra-substituted alkenes give anti addition, but trisubstituted alkenes give syn addition.

???

P.S.  Marvin renders [H:3][C@:2]1([O:7])[C:4]CC[C:5][C@@:1]1([H:6])[O:8] by making C4 and C5 into divalent radicals and the two O atoms into monovalent radicals.  When the atom maps are removed, this problem goes away.   

We can reproduce the error. Unfortunatelly it will not be fixed in JChem 5.5.

Zsolt

OK, I have devised a workaround (one reaction definition for trisubstituted alkenes, a second one for other alkenes), so I can wait.

This bug has still not been fixed as of JChem 5.9.  ??!

No, it hasn't. There is a workaround for this bug, so it has lower priority.

Zsolt

I'm sorry I told you there was a workaround.  There might be other cases where the workaround can't be applied, and the workaround adds to the calculational load -- we need to do two different calculations for the same reaction, depending on whether a substrate is trisubstituted or not.  A year seems like no priority, not low priority.  Please fix the problem.  

We increased the priority of this bugfix.

Zsolt

Has this bug been fixed?

No, it hasn't been fixed yet.

Do you expect to fix it in 5.12?

No, it won't be fixed before 6.1. Sorry for the delay.