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`‎bin/update_index.py‎`

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+1-1Lines changed: 1 addition & 1 deletion

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`@@ -44,7 +44,7 @@ def parse(self):`
`44`	`44`
`45`	`45`	`filename = self.rootlink()`
`46`	`46`
`47`		`- with open(filename,"rw+") as file:`
	`47`	`+ with open(filename,"r+") as file:`
`48`	`48`	`line = file.readline()`
`49`	`49`	`had_footer=False`
`50`	`50`

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`‎structure/asa.md‎`

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`@@ -34,3 +34,16 @@ This code will do the ASA calculation and output the values per residue and the`
`34`	`34`	`See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/src/main/java/demo/DemoAsa.java) for a fully working demo.`
`35`	`35`
`36`	`36`	`[Shrake 1973]: http://www.sciencedirect.com/science/article/pii/0022283673900119`
	`37`	`+`
	`38`	`+<!--automatically generated footer-->`
	`39`	`+`
	`40`	`+---`
	`41`	`+`
	`42`	`+Navigation:`
	`43`	`+[Home](../README.md)`
	`44`	`+\| [Book 3: The Protein Structure modules](README.md)`
	`45`	`+\| Chapter 11 : Accessible Surface Areas`
	`46`	`+`
	`47`	`+Prev: [Chapter 10 : External Databases](externaldb.md)`
	`48`	`+`
	`49`	`+Next: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)`

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`‎structure/contact-map.md‎`

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`@@ -61,3 +61,16 @@ See [DemoContacts](https://github.com/biojava/biojava/blob/master/biojava3-struc`
`61`	`61`	`[Emmert-Streib 2007]: http://www.biomedcentral.com/pubmed/17608939`
`62`	`62`	`[Benkert 2008]: http://www.biomedcentral.com/pubmed/17932912`
`63`	`63`	`[Jones 2012]: http://www.ncbi.nlm.nih.gov/pubmed/22101153`
	`64`	`+`
	`65`	`+<!--automatically generated footer-->`
	`66`	`+`
	`67`	`+---`
	`68`	`+`
	`69`	`+Navigation:`
	`70`	`+[Home](../README.md)`
	`71`	`+\| [Book 3: The Protein Structure modules](README.md)`
	`72`	`+\| Chapter 12 : Contacts within a chain and between chains`
	`73`	`+`
	`74`	`+Prev: [Chapter 11 : Accessible Surface Areas](asa.md)`
	`75`	`+`
	`76`	`+Next: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)`

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`‎structure/crystal-contacts.md‎`

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`@@ -58,3 +58,16 @@ One can also cluster the interfaces based on their similarity. The similarity is`
`58`	`58`	`}`
`59`	`59`	```
`60`	`60`
	`61`	`+`
	`62`	`+<!--automatically generated footer-->`
	`63`	`+`
	`64`	`+---`
	`65`	`+`
	`66`	`+Navigation:`
	`67`	`+[Home](../README.md)`
	`68`	`+\| [Book 3: The Protein Structure modules](README.md)`
	`69`	`+\| Chapter 13 - Finding all interfaces in crystal: crystal contacts`
	`70`	`+`
	`71`	`+Prev: [Chapter 12 : Contacts within a chain and between chains](contact-map.md)`
	`72`	`+`
	`73`	`+Next: [Chapter 16 : Special Cases](special.md)`

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`‎structure/externaldb.md‎`

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`@@ -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)`

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`‎structure/lists.md‎`

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`@@ -27,6 +27,6 @@ The following provides information about the status of a PDB entry`
`27`	`27`	`Navigation:`
`28`	`28`	`[Home](../README.md)`
`29`	`29`	`\| [Book 3: The Protein Structure modules](README.md)`
`30`		`-\| Chapter 14 : status information`
	`30`	`+\| Chapter 17 : status information`
`31`	`31`
`32`		`-Prev: [Chapter 13 : Special Cases](special.md)`
	`32`	`+Prev: [Chapter 16 : Special Cases](special.md)`

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`‎structure/special.md‎`

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`@@ -131,8 +131,8 @@ DYG is an unusual group - it has 3 characters as a result of .getOne_letter_code`
`131`	`131`	`Navigation:`
`132`	`132`	`[Home](../README.md)`
`133`	`133`	`\| [Book 3: The Protein Structure modules](README.md)`
`134`		`-\| Chapter 13 : Special Cases`
	`134`	`+\| Chapter 16 : Special Cases`
`135`	`135`
`136`		`-Prev: [Chapter 10 : External Databases](externaldb.md)`
	`136`	`+Prev: [Chapter 13 - Finding all interfaces in crystal: crystal contacts](crystal-contacts.md)`
`137`	`137`
`138`		`-Next: [Chapter 14 : status information](lists.md)`
	`138`	`+Next: [Chapter 17 : status information](lists.md)`

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