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Running update_index.py
Also fixed a minor bug in the script.
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‎bin/update_index.py‎

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@@ -44,7 +44,7 @@ def parse(self):
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filename = self.rootlink()
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with open(filename,"rw+") as file:
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with open(filename,"r+") as file:
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line = file.readline()
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had_footer=False
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‎structure/asa.md‎

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See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoAsa.java) for a fully working demo.
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[Shrake 1973]: http://www.sciencedirect.com/science/article/pii/0022283673900119
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| [Book 3: The Protein Structure modules](README.md)
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| Chapter 11 : Accessible Surface Areas
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Prev: [Chapter 10 : External Databases](externaldb.md)
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Next: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)

‎structure/contact-map.md‎

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[Emmert-Streib 2007]: http://www.biomedcentral.com/pubmed/17608939
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[Benkert 2008]: http://www.biomedcentral.com/pubmed/17932912
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[Jones 2012]: http://www.ncbi.nlm.nih.gov/pubmed/22101153
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| [Book 3: The Protein Structure modules](README.md)
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| Chapter 12 : Contacts within a chain and between chains
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Prev: [Chapter 11 : Accessible Surface Areas](asa.md)
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Next: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)

‎structure/crystal-contacts.md‎

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}
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```
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<!--automatically generated footer-->
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---
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Navigation:
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[Home](../README.md)
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| [Book 3: The Protein Structure modules](README.md)
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| Chapter 13 - Finding all interfaces in crystal: crystal contacts
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Prev: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)
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Next: [Chapter 16 : Special Cases](special.md)

‎structure/externaldb.md‎

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Prev: [Chapter 9 : Biological Assemblies](bioassembly.md)
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Next: [Chapter 13 : Special Cases](special.md)
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Next: [Chapter 11 : Accessible Surface Areas](asa.md)

‎structure/lists.md‎

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Navigation:
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[Home](../README.md)
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| [Book 3: The Protein Structure modules](README.md)
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| Chapter 14 : status information
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| Chapter 17 : status information
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Prev: [Chapter 13 : Special Cases](special.md)
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Prev: [Chapter 16 : Special Cases](special.md)

‎structure/special.md‎

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Navigation:
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[Home](../README.md)
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| [Book 3: The Protein Structure modules](README.md)
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| Chapter 13 : Special Cases
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| Chapter 16 : Special Cases
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Prev: [Chapter 10 : External Databases](externaldb.md)
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Prev: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)
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Next: [Chapter 14 : status information](lists.md)
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Next: [Chapter 17 : status information](lists.md)

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