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PrevICM User's Guide
10.11 Calculate Properties
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[ Number of Atoms | Tox Score ]

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

| Video |

To calculate chemical properties for compounds within a chemical table:

  • Read in the chemical table.
  • Select Chemistry/Calculate Properties and a window as shown below will be displayed.
  • Arguments - usually the column with the chemical structure is called mol. If this is not the case click on the drop down button and select the correct column.
  • New column location - select where you would like to insert the new columns.
  • New column name - This option is usually greyed out but the column name will be the same as the property name.
  • Select the properties you wish to calculate using the 'tick' check boxes.
  • Click OK and the properties will be added as new columns in the chemical table.

Actions Button Helps with Selections

If you click on the drop down button labeled Actions you will see 3 selection options:

  • Select All properties.
  • Uncheck selected options.
  • Remove unchecked.

10.11.1 Number of Atoms


You can calculate the Number of Atoms using:

  • Chemistry/Calculate Properties
  • Choose the Function Chemical from the drop down list and then Nof_Atoms.
  • Add the SMARTS string for the atoms you are trying to count (e.g. sp3 : [*;^3] halogen : X or [F,Cl,Br,I])

Nof SP3 example:

10.11.2 ToxScore


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

The ToxScore gives a prediction for how reactive or toxic a chemical is.

How the ToxScore is Calculated

Around 1000 SMARTS strings associated with toxicity/reactivity were collected from various sources. They were assigned demerit score based on their perceived toxicity and frequency of appearance in approved drugs. The toxscore of any compound was calculated by summing up all the matching SMARTS strings. A toxscore >= 1. indicates likely toxicity based on substructure match.

How to Calculate ToxScore

  • Read into ICM an SDF file. A chemical spreadsheet will be displayed in the GUI.
  • insert a column into the chemical spreadsheet. Right click on a column header > choose insert column > choose the chemical function > select Tox Score.
  • A column containing a Tox Score and Tox Names will be displayed.


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