1	Introduction
1.1	User Interface
1.2	Error Messages
1.3	Log Files
1.4	Identifying Molecules and Atoms
1.5	Command Scripts and Symbols
1.5.1	Symbols and Operators
1.5.2	Script Arguments
1.5.3	Control Commands and Relational Operators
1.5.4	Error Handling
1.5.5	Input and Output
1.5.6	Intrinsic Functions
2	Reading and Saving Molecules
2.1	Reading Molecules
2.2	Saving Molecules
3	Creating, Modifying and Deleting Atoms
3.1	reating Molecules
3.2	diting Molecules
3.3	eleting Molecules
4	Visualisation
4.1	Input Molecules
4.2	Viewing Molecules
4.2.1	2D Display Mode
4.2.2	3D Display Mode
4.2.3	3D Manipulation
4.2.4	Annotation and Labelling
4.3	Fingerprint Keys
4.4	Molecular Properties
4.5	View Diversity
4.6	View Atom Data
5	Conformer Generation
5.1	Input 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	Input Molecules
6.2	Set Pharmacophore Options
6.3	Set Conformer Options
6.4	Calculate Pharmacophores
7	DiverseSets and FocusedSets
7.1	Molecule and Pharmacophore Inputs
7.2	Pharmacophore Options
7.3	Subset Calculation
8	Searching
8.1	Query Molecule Input
8.2	Search Options
8.3	Search Results
8.4	Perform Search
8.5	View Search Results
9	Maps
9.1	Read Molecules
9.2	Align Molecules
9.3	Calculate Map
9.4	Display Map and Molecules
9.5	Ligand Query Maps
10	Docking
10.1	Creating Site Queries
10.2	Docking Inputs
10.3	Docking Options
10.4	Search Results
10.5	View Docking Results
11	Property Diversity
11.1	Identify File to be Processed (1)
11.2	Read Molecules to be Processed (2)
11.3	Set Calculation Options (1)
11.4	Supply Results File (1)
11.5	Select Plot Style (1,2)
11.6	Define Activity-Based Colour-Coding (2)
11.7	Calculate Diversity (1,2)
12	Data Analysis
12.1	Read Molecules
12.2	Select Activity Field
12.3	Set Activity Options
12.4	Select Data to be Analysed
12.5	Analyse Data
12.6	Apply Learn File
13	Clustering
13.1	Input Molecules
13.2	Set Cluster Options
13.3	Cluster Molecules
13.4	View Clusters
14	De Novo Molecule Generation
14.1	Input Molecules
14.2	Set Molecule Creation Options
14.3	Generate Molecules
15	Combinatorial Chemistry
15.1	R-group Search Input
15.2	R-group Search Options
15.3	R-group Search Output
15.4	R-group Search
15.5	Enumeration Inputs
15.6	Enumeration Options
15.7	Enumeration Results