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. (A detailed list of action strings can be found here:

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

 

Examples:

 

 

 

Using a Rule Set File:

 

1. Define Folder for Rule Set Files

 

It is possible to select a rule set file to specify the actions to be executed at applying the JCStandardizeStructure function for the structures. The folder where the .xml file is located has to be specified in Options, the name of the file has to be given in Function Arguments dialog.

 

Form.Standardize1

 

 

In the same dialog full path of the location of the rule set file can be defined as well, in this case the folder in Options can be specified as well, but not necessary.

 

 

Form.Standardize2

 

 

2. Define the filename in the cell

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"). Or by giving the full path : =JCStandardizeStructure(A2, "D:\Documents\Standardize.xml"), in this case the folder in Options can be specified as well, but not necessary.

 

Here is an example of an .xml file containing rules 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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