ICM Manual v.3.8
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2019, Molsoft LLC
Jun 9 2022

 Scripting Tutorials
Reference Guide
Command Line User's Guide
PrevICM Language Reference
ICM Scripting Tutorials

If you are interested in learning more about the ICM command line language please download the Scripting Tutorials (the instructions are below). The tutorials contain a comprehensive guide to ICM scripting including a guide to the language, best practices, and worked examples. The interactive hyperlinked text in the icb files help you learn ICM scripting efficiently. Tutorials were prepared by Eugene Raush (Principal Software Developer, MolSoft LLC).


  • Please download (right click and Save Link As) the turorials.
  • Unzip the file.
  • Save the unzipped folder to a directory.
  • Open the ICM graphical user interface and set the working directory to the location where you saved the files. To do this go to Tools menu and choose the option "Change Working Directory" and then browse for the directory.
  • Go to File/Open and open one of the .icb files listed below and follow the links.
  • Follow the html text in the icb files and click on the interactive links.
  • Expand the size of the command line window so you can see the commands and the output.

Guide to the Tutorials


ICM Scripting Language Basics - Topics include:
  • ICM Command Line
  • Basic Data Types
  • Control Structures
  • Commands and Functions


Molecular Objects - Topics include:
  • Selections
  • Internal Variable Selections
  • Sequences
  • Alignments
  • Grobs


ICM Scripts - Topics include:
  • Command line arguments
  • Working with large SD files and piping
  • SQL interface to relational databases
  • Macros


Working with Tables and Chemical Spreadsheets - Topics include:
  • Tables introduction
  • Table creation
  • Collection(hash table)
  • Deletion of columns and rows
  • Filtering
  • Columns with formulas
  • Assigning custom actions to the table cells
  • Grouping
  • Plotting
  • Chemical structures in tables
  • Substructure and Similarity Search
  • Annotate by matching fragments
  • Find/Replace chemical groups
  • Perform standardisation
  • Clustering Trees
  • Chemical objects vs 3D molecular objects


Regular Expressions for Text Processing - Topics include:
  • Simple expressions
  • Repetitions and back-references
  • Useful shortcuts
  • Common tasks in the text processing
  • Practical example: Conversion of DrugBank text format to SDF


Creating your own GUI elements - Topics include:
  • Dialog definition syntax
  • Layout
  • Referencing to the input values from the ICM command
  • Ways to add a dialog to the interface
  • Adding a link in the html page
  • New top menu item
  • Adding a button
  • Askg() function


ActiveICM enables you to display fully interactive 3D objects in PowerPoint and Web. - Topics include:
  • Client side
  • GET and POST methods
  • Server side


Copyright© 1989-2019, Molsoft,LLC - All Rights Reserved. Copyright© 1989-2019, Molsoft,LLC - All Rights Reserved. This document contains proprietary and confidential information of Molsoft, LLC. The content of this document may not be disclosed to third parties, copied or duplicated in any form, in whole or in part, without the prior written permission from Molsoft, LLC.