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PrevICM User's Guide
9.12 Standardize Table

Available in the following product(s): ICM-Chemist | ICM-Chemist-Pro | ICM-VLS

NOTE: Before standardizing a chemical you may want to make a copy of the original so you do not lose any information. You can do this by right clicking on the name tab of the table and selecting clone or save as.

To remove salts, explicit hydrogens and standardize groups in a chemical table:

  • Chemistry/Standardize
  • Select the table from the drop-down list. This will also work for selections made on the table.
  • Select option - Remove Salts, Keep Salt Info in Extra Column (NOTE: option availabe in 3.7-2b and higher), Remove Explicit Hydrogens or Standardize Groups
  • Click OK.

Standardize chemical groups will apply rules from ICMHOME/CHEMNORMRULES.tab For example some chemical groups may have different representations e.g. [N+] (=O)O versus N(=O)=O

To run in batch mode:

  • Chemistry/Standardize
  • Select the Files tab
  • Enter the path and name of the sdf file you wish to standardize or use the browse button.
  • Enter the path and name of the output file or use the browse button.

To remove a salt from an individual row in a chemical table:

  • Select the row or rows.
  • Right click - Chemistry/Remove Salt (Selected Row)

Tox Score

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