Reactor throws exception for some reactivity rules

While waiting for your response to the previous question, I went ahead and made your recommended changes and recompiled with JChem 16.2.29. A simple bromination definition worked well and gave the correct products. However, when I gave a definition that contained a reactivity rule, Reactor threw an exception, copied below. There's nothing remarkable about the reactivity rule I give here. If I delete the reactivity rule, Reactor does not throw an exception. What's going on?

(By the way, I need to include a separate reaction definition for trisubstituted alkenes because Reactor applies the wrong stereochemistry to these substrates; that is, it gives the product of syn addition to trisubstituted alkenes when the reaction defines anti addition, and vice versa. This is a longstanding bug, and I haven't asked for it to be fixed because I have a workaround in place, that is, having a separate reaction definition that applies to trisubstituted alkenes, but it would be nice if you fixed it.) 

Permutation 1 of 1: [[#6]-[#6]\[#6]=[#6](/[#6])-[#6]-[#6]]

SingleRxnSolver.calcProducts: caught ReactionException:

An error occured while evaluating reactivity rule.

Caused by:

could not convert to double: java.lang.Object@150ea69

Reaction molecule that caused exception:

<?xml version="1.0" encoding="UTF-8"?>

<cml xmlns="http://www.chemaxon.com" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.chemaxon.com/marvin/schema/mrvSchema_16_02_15.xsd" version="ChemAxon file format v16.02.15, generated by v16.2.29.0">

<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[bromination of a trisubstituted alkene]]></scalar>

        </property>

        <property dictRef="REACTIVITY" title="REACTIVITY">

          <scalar><![CDATA[hCount(ratom(1)) + hCount(ratom(2)) == 1]]></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 id="b1" atomRefs2="a1 a2" order="2"/>

            <bond id="b2" atomRefs2="a2 a3" order="1"/>

            <bond id="b3" atomRefs2="a2 a4" order="1"/>

            <bond id="b4" atomRefs2="a1 a5" order="1"/>

            <bond id="b5" 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="Br" mrvMap="8" x2="12.984649632246231" y2="6.5021996716380555"/>

            <atom id="a4" elementType="Br" mrvMap="7" x2="8.403951462668653" y2="6.441709489027713"/>

            <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 id="b1" atomRefs2="a1 a2" order="1"/>

            <bond id="b2" atomRefs2="a1 a3" order="1">

              <bondStereo>H</bondStereo>

            </bond>

            <bond id="b3" atomRefs2="a2 a4" order="1">

              <bondStereo>W</bondStereo>

            </bond>

            <bond id="b4" atomRefs2="a2 a5" order="1"/>

            <bond id="b5" atomRefs2="a2 a6" order="1"/>

            <bond id="b6" atomRefs2="a1 a7" order="1"/>

            <bond id="b7" atomRefs2="a1 a8" order="1"/>

          </bondArray>

        </molecule>

      </productList>

    </reaction>

  </MChemicalStruct>

</MDocument>

</cml>

chemaxon.reaction.ReactionException: An error occured while evaluating reactivity rule.

Caused by:

could not convert to double: java.lang.Object@150ea69

	at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:1103)

	at chemaxon.reaction.ReactionPerformer.reactOne(ReactionPerformer.java:763)

	at chemaxon.reaction.ReactionPerformer.reactOneDuplicateFiltered(ReactionPerformer.java:726)

	at chemaxon.reaction.ReactionPerformer.reactBase(ReactionPerformer.java:711)

	at chemaxon.reaction.ReactionPerformer.react(ReactionPerformer.java:651)

	at chemaxon.reaction.Reactor.react(Reactor.java:1115)

	at com.epoch.synthesis.SingleRxnSolver.submitResizedArray(SingleRxnSolver.java:423)

	at com.epoch.synthesis.SingleRxnSolver.doOneRxnLoop(SingleRxnSolver.java:352)

	at com.epoch.synthesis.SingleRxnSolver.calcProducts(SingleRxnSolver.java:175)

	at com.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:391)

	at com.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:278)

	at com.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:128)

	at org.apache.jsp.public_.ACEStructure.pasteSynthTest_jsp._jspService(pasteSynthTest_jsp.java:124)

	at org.apache.jasper.runtime.HttpJspBase.service(HttpJspBase.java:70)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.jasper.servlet.JspServletWrapper.service(JspServletWrapper.java:388)

	at org.apache.jasper.servlet.JspServlet.serviceJspFile(JspServlet.java:313)

	at org.apache.jasper.servlet.JspServlet.service(JspServlet.java:260)

	at javax.servlet.http.HttpServlet.service(HttpServlet.java:717)

	at org.apache.catalina.core.ApplicationFilterChain.internalDoFilter(ApplicationFilterChain.java:290)

	at org.apache.catalina.core.ApplicationFilterChain.doFilter(ApplicationFilterChain.java:206)

	at org.apache.catalina.core.StandardWrapperValve.invoke(StandardWrapperValve.java:219)

	at org.apache.catalina.core.StandardContextValve.invoke(StandardContextValve.java:191)

	at org.apache.catalina.authenticator.AuthenticatorBase.invoke(AuthenticatorBase.java:470)

	at org.apache.catalina.core.StandardHostValve.invoke(StandardHostValve.java:127)

	at org.apache.catalina.valves.ErrorReportValve.invoke(ErrorReportValve.java:102)

	at org.apache.catalina.core.StandardEngineValve.invoke(StandardEngineValve.java:109)

	at org.apache.catalina.connector.CoyoteAdapter.service(CoyoteAdapter.java:293)

	at org.apache.coyote.http11.Http11NioProcessor.process(Http11NioProcessor.java:889)

	at org.apache.coyote.http11.Http11NioProtocol$Http11ConnectionHandler.process(Http11NioProtocol.java:744)

	at org.apache.tomcat.util.net.NioEndpoint$SocketProcessor.run(NioEndpoint.java:2282)

	at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)

	at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)

	at java.lang.Thread.run(Thread.java:745)

Caused by: chemaxon.nfunk.jep.ParseException: could not convert to double: java.lang.Object@150ea69

	at chemaxon.nfunk.jep.JEP.getValue(JEP.java:470)

	at chemaxon.jep.ChemJEP.evaluate_double(ChemJEP.java:170)

	at chemaxon.jep.ChemJEP.evaluate_boolean(ChemJEP.java:227)

	at chemaxon.reaction.ReactionPerformer.reactHit(ReactionPerformer.java:1094)

	... 33 more

bobgr wrote:

OK, I understand. What about the exception thrown when a reactivity rule is present?

We are examining the issue.

The error has been fixed. The fixed version will be released next week.

Thank you. 

I don't suppose you feel any motivation to fix the longstanding bug regarding trisubstituted alkenes that I mentioned above? With this 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[bromination of an alkene]]></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="Br" mrvMap="8"

                  x2="12.984649632246231" y2="6.5021996716380555" />

            <atom id="a4" elementType="Br" mrvMap="7"

                  x2="8.403951462668653" y2="6.441709489027713" />

            <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>H</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>

C1CCC=CC1 correctly gives Br[C@H]1CCCC[C@@H]1Br.Br[C@@H]1CCCC[C@H]1Br

But CC1=CCCCC1 incorrectly gives C[C@@]1(Br)CCCC[C@@H]1Br.C[C@]1(Br)CCCC[C@H]1Br

So we need separate reaction definitions for trisubstituted alkenes versus other alkenes.

It's not about motivation, it's about priorities. Most of our users don't need this feature currently.

I understand. Still, let me just throw one more appeal to your pride as an expert programmer. Surely you don't want this ugly bug to linger in your beautiful product.  

zmohacsi wrote:

The error has been fixed. The fixed version will be released next week.

I can confirm that Reactor seems to be working properly in JChem 16.4.25. I am getting the correct stereochemical results.

I suggest that you add documentation on how to implement selective syn/anti additions to alkenes. You mention the capability on the Reactor home page:

Prochiral reaction schemes are also supported since version 5.5, allowing the user to manage syn/anti additions.

but nowhere in the documentation, at least as far as I can find, tells the user how to do it. The developer would have to search the forum to learn how to do it.

Thanks for the feedback. We will update the documentation.