Running update_index.py

sbliven · sbliven · commit bfc881ad99ff · 2014-12-09T14:14:43.000+01:00
Also fixed a minor bug in the script.
diff --git a/bin/update_index.py b/bin/update_index.py
@@ -44,7 +44,7 @@ def parse(self):
 
         filename = self.rootlink()
 
-        with open(filename,"rw+") as file:
+        with open(filename,"r+") as file:
             line = file.readline()
             had_footer=False
 
diff --git a/structure/asa.md b/structure/asa.md
@@ -34,3 +34,16 @@ This code will do the ASA calculation and output the values per residue and the
 See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoAsa.java) for a fully working demo.
 
 [Shrake 1973]: http://www.sciencedirect.com/science/article/pii/0022283673900119
+
+<!--automatically generated footer-->
+
+---
+
+Navigation:
+[Home](../README.md)
+| [Book 3: The Protein Structure modules](README.md)
+| Chapter 11 : Accessible Surface Areas
+
+Prev: [Chapter 10 : External Databases](externaldb.md)
+
+Next: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)
diff --git a/structure/contact-map.md b/structure/contact-map.md
@@ -61,3 +61,16 @@ See [DemoContacts](https://github.com/biojava/biojava/blob/master/biojava3-struc
 [Emmert-Streib 2007]: http://www.biomedcentral.com/pubmed/17608939
 [Benkert 2008]: http://www.biomedcentral.com/pubmed/17932912
 [Jones 2012]: http://www.ncbi.nlm.nih.gov/pubmed/22101153
+
+<!--automatically generated footer-->
+
+---
+
+Navigation:
+[Home](../README.md)
+| [Book 3: The Protein Structure modules](README.md)
+| Chapter 12 : Contacts within a chain and between chains
+
+Prev: [Chapter 11 : Accessible Surface Areas](asa.md)
+
+Next: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)
diff --git a/structure/crystal-contacts.md b/structure/crystal-contacts.md
@@ -58,3 +58,16 @@ One can also cluster the interfaces based on their similarity. The similarity is
 		}
 ```
 
+
+<!--automatically generated footer-->
+
+---
+
+Navigation:
+[Home](../README.md)
+| [Book 3: The Protein Structure modules](README.md)
+| Chapter 13 - Finding all interfaces in crystal: crystal contacts
+
+Prev: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)
+
+Next: [Chapter 16 : Special Cases](special.md)
diff --git a/structure/externaldb.md b/structure/externaldb.md
@@ -210,4 +210,4 @@ Navigation:
 
 Prev: [Chapter 9 : Biological Assemblies](bioassembly.md)
 
-Next: [Chapter 13 : Special Cases](special.md)
+Next: [Chapter 11 : Accessible Surface Areas](asa.md)
diff --git a/structure/lists.md b/structure/lists.md
@@ -27,6 +27,6 @@ The following provides information about the status of a PDB entry
 Navigation:
 [Home](../README.md)
 | [Book 3: The Protein Structure modules](README.md)
-| Chapter 14 : status information
+| Chapter 17 : status information
 
-Prev: [Chapter 13 : Special Cases](special.md)
+Prev: [Chapter 16 : Special Cases](special.md)
diff --git a/structure/special.md b/structure/special.md
@@ -131,8 +131,8 @@ DYG is an unusual group - it has 3 characters as a result of .getOne_letter_code
 Navigation:
 [Home](../README.md)
 | [Book 3: The Protein Structure modules](README.md)
-| Chapter 13 : Special Cases
+| Chapter 16 : Special Cases
 
-Prev: [Chapter 10 : External Databases](externaldb.md)
+Prev: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)
 
-Next: [Chapter 14 : status information](lists.md)
+Next: [Chapter 17 : status information](lists.md)

Original file line number	Diff line number	Diff line change
`@@ -210,4 +210,4 @@ Navigation:`
`210`	`210`
`211`	`211`	`Prev: [Chapter 9 : Biological Assemblies](bioassembly.md)`
`212`	`212`
`213`		`-Next: [Chapter 13 : Special Cases](special.md)`
	`213`	`+Next: [Chapter 11 : Accessible Surface Areas](asa.md)`