The Structure Modules of BioJava
=====================================================

A tutorial for the structure modules of [BioJava](http://www.biojava.org)

## About
<table>
    <tr>
        <td>
            <img src="img/4hhb_jmol.png"/>
        </td>
        <td>
            The <i>protein structure modules</i> of BioJava provide an API that allows to 
            <ul>
                <li>Maintain local installations of PDB</li>
                <li>Load structures and manipulate them</li>
                <li>Perform standard analysis such as sequence and structure alignments</li>
                <li>Visualize structures</li>
            </ul>
            This tutorial provides an overview of the most important functionalities.
        </td>
    </tr>
</table>   

## Index

This tutorial is split into several chapters.


Chapter 1 - Quick [Installation](installation.md)

Chapter 2 - [First Steps](firststeps.md)

Chapter 3 - The [Structure Data Model](structure-data-model.md), for the representation of macromolecular structures

Chapter 4 - [Local Installations](caching.md) of PDB

Chapter 5 - The [Chemical Component Dictionary](chemcomp.md)

Chapter 6 - How to [Work with mmCIF/PDBx Files](mmcif.md)

Chapter 7 - [SEQRES and ATOM Records](seqres.md), mapping to Uniprot (SIFTs)

Chapter 8 - [Structure Alignments](alignment.md)

Chapter 9 - [Biological Assemblies](bioassembly.md)

Chapter 10 - [External Databases](externaldb.md) like SCOP &amp; CATH

Chapter 11 - [Accessible Surface Areas](asa.md)

Chapter 12 - [Contacts Within a Chain and between Chains](contact-map.md)

Chapter 13 - Finding all Interfaces in Crystal: [Crystal Contacts](crystal-contacts.md)

Chapter 14 - [Protein Symmetry](symmetry.md)

Chapter 15 - [Protein Secondary Structure](secstruc.md)

Chapter 16 - Bonds

Chapter 17 - [Special Cases](special.md)

Chapter 18 - [Lists](lists.md) of PDB IDs and PDB [Status Information](lists.md)


## License

The content of this tutorial is available under the [CC-BY](http://creativecommons.org/licenses/by/3.0/) license, available [here](../license.md).

## Please Cite

**BioJava 5: A community driven open-source bioinformatics library**<br/>
*Aleix Lafita, Spencer Bliven, Andreas Prlić, Dmytro Guzenko, Peter W. Rose, Anthony Bradley, Paolo Pavan, Douglas Myers-Turnbull, Yana Valasatava, Michael Heuer, Matt Larson, Stephen K. Burley, & Jose M. Duarte* <br/>
[PLOS Computational Biology (2019) 15 (2):e1006791.](https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006791) <br/>
[![doi](https://img.shields.io/badge/doi-10.1371%2Fjournal.pcbi.1006791-blue.svg?style=flat)](https://doi.org/10.1371/journal.pcbi.1006791) [![pubmed](https://img.shields.io/badge/pubmed-30735498-blue.svg?style=flat)](http://www.ncbi.nlm.nih.gov/pubmed/30735498)



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