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

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

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

PROTAC Model (protacModel.icm)

Chemical Conformational Generator

RIDGE

RIDE

Molecular Dynamics

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