reaction exception due to standardizer

Hi,





I have these lines in my reaction definition:

Code:

<StandardizerConfiguration Version ="1.0"> <Actions> <Aromatize ID="aromatize" Type="general" Groups="reactant1"/> <Transformation ID="P(+)-C(-) -> P=C" Structure="[#6-][P+]>>C=P" Type="string" Groups="reactant1"/> <Aromatize ID="aromatize" Type="general" Groups="reactant2"/> <Transformation ID="P(+)-C(-) -> P=C" Structure="[#6-][P+]>>C=P" Type="string" Groups="reactant2"/> </Actions> </StandardizerConfiguration>

When I load the reaction, I get this message:

Code:

chemaxon.reaction.ReactionException: chemaxon.reaction.ReactionException: Could not read reaction: [#6-][P ]>>C=P Caused by: Could not read reaction: [#6-][P ]>>C=P         at chemaxon.reaction.Reactor.setReactionDefinedStandardizer(Reactor.java:702)         at chemaxon.reaction.Reactor.setReaction(Reactor.java:1008)         at com.prenhall.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:142)         at com.prenhall.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:53)         at org.apache.jsp.public_.pasteSynthTest_jsp._jspService(pasteSynthTest_jsp.java:72)

However, I have similar lines in a different reaction that works just fine:

Code:

<StandardizerConfiguration Version ="0.1">    <Actions> <Transformation ID="O-enolate to C-enolate" Structure="[#8-]C=C>>[#6-]C=O" Type="string" Groups="reactant1"/>   </Actions> </StandardizerConfiguration>

Is the + charge messing things up???





-- Bob

Hi,

bobgr wrote:

Hi, I have these lines in my reaction definition: Code: <StandardizerConfiguration Version ="1.0"> <Actions> <Aromatize ID="aromatize" Type="general" Groups="reactant1"/> <Transformation ID="P(+)-C(-) -> P=C" Structure="[#6-][P+]>>C=P" Type="string" Groups="reactant1"/> <Aromatize ID="aromatize" Type="general" Groups="reactant2"/> <Transformation ID="P(+)-C(-) -> P=C" Structure="[#6-][P+]>>C=P" Type="string" Groups="reactant2"/> </Actions> </StandardizerConfiguration> When I load the reaction, I get this message: Code: chemaxon.reaction.ReactionException: chemaxon.reaction.ReactionException: Could not read reaction: [#6-][P ]>>C=P Caused by: Could not read reaction: [#6-][P ]>>C=P         at chemaxon.reaction.Reactor.setReactionDefinedStandardizer(Reactor.java:702)         at chemaxon.reaction.Reactor.setReaction(Reactor.java:1008)         at com.prenhall.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:142)         at com.prenhall.epoch.synthesis.SynthSolver.getProducts(SynthSolver.java:53)         at org.apache.jsp.public_.pasteSynthTest_jsp._jspService(pasteSynthTest_jsp.java:72)

I tried to reproduce the error. I used a separate standardizer configuration XML file:

Code:

react -r reaction.mrv -S standardizer.xml reactant1.smiles reactant2.smiles

The standardizer.xml contained exactly the configuration you posted and it worked fine. If I change the "[#6-][P+]>>C=P" reaction SMARTS string to "[#6-][P ]>>C=P", then I get the same exception:

Code:

chemaxon.reaction.ReactionException: Could not read reaction: [#6-][P ]>>C=P

I think the "[#6-][P+]>>C=P" string was modified somehow, and this caused the error. Could you check it if this happened?





Zsolt

Yes, you are right. I used Javascript's escape() function to encode the reaction definition before sending it serverside, and I now learn that it does not encode the + character properly. I need to use encodeURIComponent() instead.





Sorry to bother you.