1		Introduction
1.1			User Interface - Dialogs
1.2			User Interface - Commands
1.3			Error Messages
1.4			Identifying Molecules and Atoms
1.5			Log Files
1.6			Command Scripts and Symbols
1.6.1				Symbols and Operators
1.6.2				Script Arguments
1.6.3				Control Commands and Relational Operators
1.6.4				Error Handling
1.6.5				Input and Output
1.6.6				Intrinsic Functions
2		Reading and Saving Molecules
2.1			Reading Molecules
2.2			Saving Molecules
2.3			Using the file explorer
3		Creating, Modifying and Deleting Atoms and Molecules
3.1			Creating Molecules
3.2			Graphical 2D editor
3.3			Modifying Molecules
3.4			Deleting Molecules
4		Visualisation
4.1			Read Molecules
4.2			View Molecules or Conformers
4.2.1				Labelling
4.2.2				Manipulation
4.3				View Diversity
4.4			View Keys
4.5			View Atom Data
4.6			View Molecular Properties
5		Conformer Generation
5.1			Read Molecule(s)
5.2			Set Search Mode
5.3			Set Bond and Ring Increments
5.4			Set Contacts Check
5.5			Generate Conformers
6		Pharmacophores
6.1			Read Molecules to be Processed
6.2			Set Pharmacophore Options
6.3			Set Conformer Options
6.4			Calculate Pharmacophores
7		Searching
7.1			Read Query Molecule
7.2			Select File to be Searched
7.3			Set Search Options
7.4			Supply Results File
7.5			Perform Search
7.6			View Search Results
8		Property Diversity
8.1			Identify File to be Processed (1)
8.2			Read Molecules to be Processed (2)
8.3			Set Calculation Options (1)
8.4			Supply Results File (1)
8.5			Select Plot Style (1,2)
8.6			Define Activity-Based Colour-Coding (2)
8.7			Calculate Diversity (1,2)
9		Data Analysis
9.1			Read Molecules
9.2			Select Activity Field
9.3			Set Activity Options
9.4			Select Data to be Analysed
9.5			Analyse Data
9.6			Apply Learn File
10		Data Clustering
10.1			Read Molecules
10.2			Set Cluster Options
10.3			Cluster Molecules
10.4			View Clusters
11		De Novo Molecule Generation
11.1			Read File Containing Initial Molecule
11.2			Set Molecule Creation Options
11.3			Run Data Analysis
11.4			Set Molecule Rejection Options
11.5			Set Annealing Options
11.6			Set Diversity Options
11.7			Identify File for Storing New Molecules
11.8			Generate Molecules
12		Combinatorial Chemistry
12.1			Read Query Molecule
12.2			Select Query Molecule
12.3			Identify Reagent File to be Searched
12.4			Set Search Options
12.5			Supply R-Group File
12.6			Perform Search
12.7			Read R-Groups
12.8			Define R-Group Files
12.9			Apply Optional Filters
12.10			Save Enumerated Molecules
Appendices
A		Structure-based Virtual Screening
A.1			Thrombin
A.1.1				Introduction
A.1.1				Creating the Query
A.1.2				Running a Search
A.1.3				Refining Search Results
A.1.4				Refining the Query
A.1.5				Further Possibilities
A.2			c-Jun N-Terminal Kinase-3 (JNK3)
A.2.1				Introduction
A.2.2				Creating a Query
A.2.3				Running a Search
A.2.3				Refining the Query