Standardizer in JChem for Excel

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. The following functions are available:

  • Hydrogen manipulations

  • Aromatic bond transformations

  • Mesomers

  • Tautomers

  • Template-based cleaning

  • Counter ion and solvent removal (by size, counter ion list)

  • Generation of 2D and 3D coordinates

  • Set or remove a chiral flag, remove stereo features

  • Enumerate stoichiometry constants

  • User-defined canonicalization rules

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

The parameters are as follows:

  • Molecule: The input molecule to standardize.

  • ActionString: The actions to perform on the input molecule. For a detailed list, see Standardizer Actions.

Use a Ruleset File

Define folder for ruleset files. The folder where the XML file is located must be specified in Options > Functions > JCStandardizeStructure. After specifying the folder, it is possible to use the XML file by entering its name into the ActionString field of the Function Arguments dialog.

images/download/attachments/1807012/JCStandardizeStructure_Function_Arguments.png
In this dialog, the full path of the location of the ruleset file can be defined as well, in this case, it is not necessary to specify the folder in Options > Functions > JCStandardizeStructure.

The XML example below contains 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>