ICM Manual v.3.7
by Ruben Abagyan,Eugene Raush and Max Totrov
Copyright © 2013, Molsoft LLC
Nov 26 2014

Contents
 
Introduction
Reference Guide
Command Line User's Guide
References
Glossary
 
Index

Table of contents

Introduction
Release notes
Brief history of ICM
ICM distribution and support
What can you do with ICM? (a program overview)
Notational conventions
Common abbreviations
Getting started
ICM Scripting Tutorials
Reference Guide
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
SOAP services and communications
Creating your own GUI elements: Programming GUI.
Commands
Functions
Macros
Files
Command Line User's Guide
ICM-shell
ICM graphics
Structure analysis
Sequence, searches and alignments
Molcart
Pharmacophores
Energetics and electrostatics
Manipulations with molecules
Animation
Transformations and symmetry
Maps and factors
How to plot
How-to: Docking and Virtual Ligand Screening
Example scripts
Chemical Superposition using APF - Ligand Based Screening
Chemical Conformational Generator
References
General literature references
The main description of the ICM method
ICM algorithms
ICM applications
Credits
Glossary
A
B
C
D
E-H
I-N
O-R
S
T
U-Z

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