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ICM Manual
ICM Manual v.3.9
by Ruben Abagyan, Eugene Raush and Max Totrov
Copyright © 2026, Molsoft LLC
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Contents
Introduction
Reference Guide
ICM options
Editing
Graph.Controls
Alignment Editor
Constants
Subsets
Molecules
Selections
Fingerprints
Regexp
Cgi programming with icm
Xml drugbank example
Tree cluster
Arithmetics
Flow control
MolObjects
Energy Terms
Integers
Reals
Logicals
Strings
Preferences
Tables
Other
Chemical
Smiles
pipe
Chemical Functions
MolLogP
MolLogS
MolSynth
Soap
Gui programming
Commands
Functions
Icm shell functions
Macros
Files
Command Line User's Guide
References
Glossary
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ICM Language Reference
Reference Guide
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Chapter Contents
ICM command line options
Command line editing
Graphics controls
Editing pairwise sequence-structure alignments
Constants
Subsets and Index Expressions
Molecule intro
Selections
Chemical Fingerprints
Regular expressions (regexp)
CGI programming using ICM scripting language
Parsing XML example: DrugBank.
Hierarchical cluster trees
Arithmetics
Flow control
ICM molecular objects
Energy and Penalty Terms
Integer shell parameters
Real shell variables
Logical variables
String variables
Preferences
Tables
Other shell variables
Chemical arrays and tables. Operations, virtual chemistry.
SMILES and SMARTS
Pipe: ICM scripts to pipe chemical tables/SDF files
Chemical Functions
MolLogP
MolLogS
Chemical Synthetic Accessibility
SOAP services and communications
Creating your own GUI elements: Programming GUI.
Commands
Functions
ICM shell macro-like functions
Macros
Files
Prev
Scripting Tutorials
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ICM options