Standardizer

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JCStandardizeStructure

Standardizer is a structure canonicalization tool in JChem for converting molecules from different sources into standard representational forms. Standardizer can automate the identification of mesomers and tautomers and can be used for counter-ion removal.

 

Notes: The function does not alter the original input molecule, it displays its standardized form in the target cell.

 

Parameters:

Molecule: The input molecule to standardize.

ActionString: The actions to perform on the input molecule.

 

http://www.chemaxon.com/jchem/doc/user/StandardizerConfiguration.html#actionstring

 

Examples:

 

 

 

Using Configuration File:

It is possible to select a configuration file in Options to specify the actions to be executed at applying the JCStandardizeStructure function for the structures. The file name of the configuration file, which is selected in Options, has to be specified as ActionString on the Function Arguments form.

 

 

OR

The file name of the configuration file has to be entered after cell address (containing the structure) as necessary parameter e.g.: =JCStandardizeStructure(A2, "Standardize.xml")

 

An example (content of a configuration file to aromatize the structures, clear the isotopes and remove the water and benzene as solvent from the structure cells):

 

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

<StandardizerConfiguration Version="0.1">

   <Actions>

       <Aromatize ID="aromatize"/>

       <Clearisotopes ID="clearisotopes"/>

       <Transformation ID="water" Structure="O>>" Exact="true"/>

       <Transformation ID="benzene" Structure="c1ccccc1>>" Exact="true"/>

   </Actions>

</StandardizerConfiguration>

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