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Reactor throws exception for some reactivity rules
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Bob

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Link to postPosted: Fri Apr 15, 2016 5:51 pmPost subject: exception upon calculating products Reply with quote

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
Zsolt
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Link to postPosted: Mon Apr 18, 2016 2:27 pmPost subject: Reply with quote
bobgr wrote:

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

We are examining the issue.
Zsolt
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Link to postPosted: Wed Apr 20, 2016 10:50 amPost subject: Reply with quote

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

Joined: 15 Jun 2004
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Link to postPosted: Wed Apr 20, 2016 3:16 pmPost subject: Reply with quote

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.
Zsolt
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Link to postPosted: Fri Apr 22, 2016 10:13 amPost subject: Reply with quote

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

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Link to postPosted: Fri Apr 22, 2016 1:41 pmPost subject: Reply with quote

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.  
Bob

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Link to postPosted: Tue Apr 26, 2016 2:48 pmPost subject: Reply with quote
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.
Zsolt
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Link to postPosted: Mon May 02, 2016 10:47 amPost subject: Reply with quote

Thanks for the feedback. We will update the documentation.
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Reactor throws exception for some reactivity rules
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