1	Introduction
2	Reading and Saving Files
2.1	SMILES
2.1.1	Key Features
2.1.2	Extensions
2.1.3	Limitations
2.2	Molfile and SDfile
2.2.1	Key Features
2.2.2	Extensions
2.2.3	Limitations
2.3	PDB Format
2.3.1	Key Features
2.3.2	Extensions
2.3.3	Molecules and Molecule Names
2.3.4	Limitations
2.4	Enumeration
2.4.1	Core-based Libraries
2.4.2	Coreless Libraries
2.4.3	Peptide Chains
2.5	Parameter Files
3	Property Calculations
3.1	2D Calculations
3.1.1	Counters
3.1.2	Volume and Surface Area
3.1.3	Partial Surface Areas
3.1.4	Flexibility
3.1.5	Lipophilicity
3.2	3D Calculations
3.2.1	CPK Contacts
3.2.2	VdW Contacts
3.3	User-Defined Properties
4	Conformer Generation
4.1	Rotational Bonds
4.2	Conformer Generation
4.3	Contacts Check
5	Data Analysis
5.1	Key Features
5.2	F-test for Properties
5.3	F-test for Functional Groups
5.4	F-test for Pharmacophores
5.5	Prediction
6	De Novo Structure Generation
6.1	Transformations
6.2	Application of Earlier Results
6.3	Rejections File
7	Pharmacophores
7.1	Centre Types
7.2	Fuzzy Pharmacophores
7.3	Pharmacophore profiles
7.4	Pharmacophore Files
8	Molecule Searching
8.1	Substructure Searching
8.2	Similarity Searching
8.3	R-group Searching
8.4	3D Searching
8.5	Site Searching
8.6	heckpoint File and Search Tracing
9	Creating Site Queries
9.1	omplementary Centres
9.2	Existing Ligand-Protein Complex
9.3	List of Active Site Residues
9.3.1	Site Records in PDB file
9.3.2	Finding Binding Sites
9.4	xtended Active Site
9.5	Centre Selection (Weighting)
9.5.1	Required Groups
9.5.2	Pharmacophore Score
9.5.3	Distance Weightings
9.5.4	Acid and Base Weighting
9.6	Reproducing Ligand-Protein Complexes
9.6.1	Visual Inspection
9.6.2	Check Site Points
9.6.3	Check Pharmacophores and Conformers
Appendix A	Parameter File Formats
A.1	Atom Types
A.2	Bond Parameters
A.3	Angle Parameters
A.4	Ring Coordinates
A.5	Ring Torsion Angles
Appendix B	Pharmacophore File Format
Appendix C	Common Variables
C.1	Counters
C.2	Constants
C.3	Flags
Appendix D	ITRACE Values