CONTENTS
========

1 How to Use HBPLUS - Quick Instructions

2 How to Use HBPLUS - Full Instructions

2.1 Installation
2.2 Glossary of terms used in this guide, and in the program
2.3 The Command-Line Options
2.4 Input Files
2.5 Output File(s) Format
2.6 Adding New Residue Types

3 The Science

3.1 Introduction to Hydrogen Bonds
3.2 The Algorithm
     3.2.1 Calculation of the Hydrogen Positions
          3.2.1.1 Hydrogens Bound to sp2 Hybridised (Trigonal Planar) Donors
	  3.2.1.2 Hydrogens Bound to sp3 Hybridised (Tetrahedral) Donors
3.3 Selecting Potential Hydrogen Bonds
3.4 Orienting ASN, GLN and HIS side-chains
     3.4.1 Introduction	
     3.4.2 The Algorithm	
4 References