- 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
- Reference Guide
- ICM command line options
- Command line editing
- Graphics controls
- Editing pairwise sequence-structure alignments
- Constants
- Subsets and Index Expressions
- Molecule intro
- Selections
- Regular expressions (regexp)
- 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
- 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
- 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