Now the single bond thing ... below was another problem ;-)

When I add a few reaction tags to the config file - looks a lot like your examples (see below) ;-)


I am gettin another problem. But this should be easy to solve.


I get mysterious single bonds occuring and dissappearing when normalizing ;-) This behaviour occured when I updated from JChem ver. 2.2.1 to 2.3.3 .





Example

Code:

input:: C1(=CC=C(OC)C=C1)\C=C\2NC(NC2=O)=O stdranonce1:: COc1ccc(C-C2=NC(=O)NC2=O)cc1 stdrantwice:: COc1ccc(CC2=NC(=O)NC2=O)cc1

Could you help supply a reaction rule to fix this?


My current strategy is to run standardize repetitive on my input molecules till it converges. But I don't really like this. I hope these all posts can be fixed with a slightly differnt standardize.xml.


Would be nice hearing of you -





cheers








Friedemann








PS.:


standardize.xml ::

Code:

<?xml version="1.0" encoding="UTF-8"?> <!-- Standardizer configuration file --> <StandardizerConfiguration Version ="0.1">    <Actions>       <Action ID="aromatize" Act="aromatize"/>    <Action ID="dehydrogenize" Act="dehydrogenize"/>    <ImplH ID="implh" Charged="true" Radical="true" Mapped="true" Lonely="true"/>     <Reaction ID="PlusMinus" Structure="[*+:1][*-:2]>>[*:1]=[*:2]" Type="string"/>    <Reaction ID="Enamine" Structure="[H:4][N:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[N:3]" Type="string"/>    <Reaction ID="Enol" Structure="[H:4][O:3][C:1]=[C:2]>>[H:4][C:2][C:1]=[O:3]" Type="string"/>     <!-- <Reaction ID="ClMinus" Structure="[Cl-]>>" Exact="true" Optional="true" Type="string"/> -->     <!-- <Removal ID="keepOne" Method="keepLargest" Measure="molMass"/>    <Sgroups ID="ungroup" Act="Ungroup"/>    <Clean ID="cleanIfNeeded"/> -->     </Actions> </StandardizerConfiguration>

The part which is commented out does not affect the occurance in a positive way. It rather slightly increses it ...

Unfortunately double bond stereo is not supported in the current implementation of Standardzier - the configuration XML in the documentation is an example that is not necessarily optimal for all molecules. For now, please use the attached configuration XML that I will include in the next release as a generally applicible configuration.