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 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 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 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