User 870ab5b546
17-04-2013 18:53:28
The molecule:
<?xml version="1.0"?>
<cml version="ChemAxon file format v5.10.0, generated by v5.11.5">
<MDocument>
<MChemicalStruct>
<molecule molID="m1">
<atomArray>
<atom id="a1" elementType="Pd" formalCharge="1" x2="-7.409023443106326" y2="3.177521889459070">
<scalar id="a1.prop1" title="paired electrons" convention="atomprop" dataType="xsd:integer">6</scalar>
</atom>
<atom id="a2" elementType="Cl" x2="-8.497967886133610" y2="4.266466332486353">
<scalar id="a2.prop1" title="paired electrons" convention="atomprop" dataType="xsd:integer">6</scalar>
</atom>
<atom id="a3" elementType="Cl" x2="-8.497967886133610" y2="2.088577446431787">
<scalar id="a3.prop1" title="paired electrons" convention="atomprop" dataType="xsd:integer">6</scalar>
</atom>
<atom id="a4" elementType="C" sgroupRef="sg1" x2="-4.186874866485596" y2="4.716249942779541"/>
<atom id="a5" elementType="C" sgroupRef="sg1" x2="-3.4168748664855952" y2="3.3825708209515053"/>
<atom id="a6" elementType="C" x2="-4.186874866485595" y2="2.0488916991234696"/>
<atom id="a7" elementType="Cl" formalCharge="-1" x2="-3.097930423458312" y2="0.9599472560961864">
<scalar id="a7.prop1" title="paired electrons" convention="atomprop" dataType="xsd:integer">8</scalar>
</atom>
<atom id="a8" elementType="X" x2="-3.8018748664855955" y2="4.049410381865523">
<scalar id="a8.prop1" title="paired electrons" convention="atomprop" dataType="xsd:integer">-2</scalar>
</atom>
</atomArray>
<bondArray>
<bond atomRefs2="a1 a2" order="1"/>
<bond atomRefs2="a1 a3" order="1"/>
<bond atomRefs2="a4 a5" order="2"/>
<bond atomRefs2="a6 a5" order="1"/>
<bond atomRefs2="a6 a1" order="1"/>
<bond atomRefs2="a8 a1" convention="cxn:coord"/>
</bondArray>
<molecule id="sg1" role="MulticenterSgroup" molID="m2" atomRefs="a4 a5" center="a8"/>
</molecule>
</MChemicalStruct>
</MDocument>
</cml>
The standardizer configuration:
<?xml version="1.0" encoding="UTF-8"?>
<!-- Standardizer configuration file -->
<StandardizerConfiguration Version ="0.1">
<Actions>
<Transformation ID="h1,h2_to_h3" Structure="*[!#1!#2!#5!#6!#7!#8!#9!#10!#14!#15!#16!#17!#18!#33!#34!#35!#36!#52!#53!#54!#85!#86]CC=C>>[!#1!#2!#5!#6!#7!#8!#9!#10!#14!#15!#16!#17!#18!#33!#34!#35!#36!#52!#53!#54!#85!#86]*.c:c:c |$;M_p;;;;M_p;;;;$,m:0:4.3,6:7.8.9,C:0.0,6.4|"/>
</Actions>
</StandardizerConfiguration>
The error message:
java.lang.ArrayIndexOutOfBoundsException: 4
at chemaxon.marvin.modules.MCS.visit(MCS.java:1427)
at chemaxon.marvin.modules.MCS.createSpannigTree(MCS.java:1406)
at chemaxon.marvin.modules.MCS.findFirst(MCS.java:533)
at chemaxon.marvin.modules.MCS.search(MCS.java:516)
at chemaxon.marvin.modules.AutoMapper.calculatePairWiseMCS(AutoMapper.java:2205)
at chemaxon.marvin.modules.AutoMapper.perceiveMCSMaps(AutoMapper.java:2170)
at chemaxon.marvin.modules.AutoMapper.init(AutoMapper.java:1972)
at chemaxon.marvin.modules.AutoMapper.map(AutoMapper.java:844)
at chemaxon.marvin.modules.AutoMapper.setReaction(AutoMapper.java:778)
at chemaxon.marvin.modules.AutoMapper.map(AutoMapper.java:1116)
at chemaxon.reaction.Reaction.setReaction(Reaction.java:958)
at chemaxon.reaction.Reaction.setReaction(Reaction.java:916)
at chemaxon.reaction.Reaction.setReaction(Reaction.java:900)
at chemaxon.standardizer.advancedactions.TransformAction.initialize(TransformAction.java:259)
at chemaxon.standardizer.advancedactions.TransformAction.standardize1(TransformAction.java:183)
at chemaxon.standardizer.AbstractStandardizerAction.standardize(AbstractStandardizerAction.java:136)
at chemaxon.standardizer.runner.BasicStandardizerRunner$1.standardize(BasicStandardizerRunner.java:121)
at chemaxon.standardizer.runner.BasicStandardizerRunner$1.run(BasicStandardizerRunner.java:86)
at chemaxon.standardizer.runner.BasicStandardizerRunner.standardizeAndWait(BasicStandardizerRunner.java:253)
at chemaxon.standardizer.Standardizer.standardize(Standardizer.java:343)
at com.epoch.mechanisms.MechSolver.makeEtaOdd(MechSolver.java:952)
at com.epoch.mechanisms.MechSolver.getProducts(MechSolver.java:143)
at org.apache.jsp.public_.mechmarvin_jsp._jspService(mechmarvin_jsp.java:112)
Same result with this configuration:
<?xml version="1.0" encoding="UTF-8"?>
<!-- Standardizer configuration file -->
<StandardizerConfiguration Version ="0.1">
<Actions>
<Transformation ID="h1,h2_to_h3" Structure="**-[#6]-[#6]=[#6]>>**.c:c:c |m:0:4.3,6:7.8.9,C:1.0,5.4|"/>
<Transformation ID="h1,h4_to_h5" Structure="**-[#6]-[#6]=[#6]-[#6]=[#6]>>**.c:c:c:c:c |m:0:3.4.5.6,8:11.10.9.12.13,C:1.0,7.6|"/>
</Actions>
</StandardizerConfiguration>
???