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Merged
sbliven merged 22 commits into from
Jul 22, 2015
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Extend structure alignment page with multiple alignments #5

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509057f
Adding basic alignmentcode page with MultipleStructureAlignment proposal
sbliven Jul 10, 2014
e60bfea
Explanation for AFPChain Data Model
lafita Jul 21, 2015
30a0202
Update references and section template
lafita Jul 21, 2015
f095f28
Explain MultipleAlignment object hierarchy
lafita Jul 21, 2015
ac15b5d
Include examples for the two data models
lafita Jul 21, 2015
fa0fae2
Change protein references to structure
lafita Jul 22, 2015
a45465c
Add figures for multiple GUI
lafita Jul 22, 2015
34a1a4d
Change multiple figures
lafita Jul 22, 2015
dd2b482
Describe the GUI for multiple alignments
lafita Jul 22, 2015
3e2f422
Update structure reference in README
lafita Jul 22, 2015
3118385
Update structure references in Structure modules
lafita Jul 22, 2015
9b6123b
Update first steps
lafita Jul 22, 2015
1990920
Update structure data model
lafita Jul 22, 2015
13b8380
Update caching
lafita Jul 22, 2015
ba593eb
Update chemcomp.md
lafita Jul 22, 2015
77fc195
Update mmCIF explanation
lafita Jul 22, 2015
bed1234
Update SEQRES
lafita Jul 22, 2015
b1b8204
Explain utility methods for MSTA manipulation
lafita Jul 22, 2015
b6b0a01
Description of the MultipleMC algorithm
lafita Jul 22, 2015
99c7cc2
Footer script compatible with python 2.6
lafita Jul 22, 2015
40b7c4d
Merge remote-tracking branch 'origin/multiplealignment' into multiple…
lafita Jul 22, 2015
bbc77f4
Update footers
lafita Jul 22, 2015
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@lafita
lafita committed Jul 22, 2015
commit bbc77f47a12b2d6728819c08cddfd3fe8d92b33b
2 changes: 1 addition & 1 deletion alignment/README.md
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Expand Up @@ -63,4 +63,4 @@ Navigation:

Prev: [Book 1: The Core module](../core/README.md)

Next: [Book 3: The Protein Structure modules](../structure/README.md)
Next: [Book 3: The Structure modules](../structure/README.md)
2 changes: 1 addition & 1 deletion genomics/README.md
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Expand Up @@ -64,4 +64,4 @@ Navigation:
[Home](../README.md)
| Book 4: The Genomics Module

Prev: [Book 3: The Protein Structure modules](../structure/README.md)
Prev: [Book 3: The Structure modules](../structure/README.md)
2 changes: 1 addition & 1 deletion structure/alignment.md
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Expand Up @@ -388,6 +388,6 @@ Navigation:
| [Book 3: The Structure modules](README.md)
| Chapter 8 : Structure Alignments

Prev: [Chapter 7 : SEQRES and ATOM records](seqres.md)
Prev: [Chapter 7 : SEQRES and ATOM Records](seqres.md)

Next: [Chapter 9 : Biological Assemblies](bioassembly.md)
4 changes: 2 additions & 2 deletions structure/asa.md
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Expand Up @@ -41,9 +41,9 @@ See [DemoAsa](https://github.com/biojava/biojava/blob/master/biojava3-structure/

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| [Book 3: The 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)
Next: [Chapter 12 : Contacts Within a Chain and between Chains](contact-map.md)
2 changes: 1 addition & 1 deletion structure/bioassembly.md
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Expand Up @@ -233,7 +233,7 @@ The RCSB PDB web site has a great [tutorial on Biological Assemblies](http://www

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| [Book 3: The Structure modules](README.md)
| Chapter 9 : Biological Assemblies

Prev: [Chapter 8 : Structure Alignments](alignment.md)
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2 changes: 1 addition & 1 deletion structure/caching.md
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Expand Up @@ -90,7 +90,7 @@ There are quite a number of external database IDs that are supported here. See t
Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| Chapter 4 : Local installations
| Chapter 4 : Local Installations

Prev: [Chapter 3 : Structure Data Model](structure-data-model.md)

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2 changes: 1 addition & 1 deletion structure/chemcomp.md
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Expand Up @@ -92,6 +92,6 @@ Navigation:
| [Book 3: The Structure modules](README.md)
| Chapter 5 : Chemical Component Dictionary

Prev: [Chapter 4 : Local installations](caching.md)
Prev: [Chapter 4 : Local Installations](caching.md)

Next: [Chapter 6 : Work with mmCIF/PDBx Files](mmcif.md)
6 changes: 3 additions & 3 deletions structure/contact-map.md
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Expand Up @@ -68,9 +68,9 @@ See [DemoContacts](https://github.com/biojava/biojava/blob/master/biojava3-struc

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| Chapter 12 : Contacts within a chain and between chains
| [Book 3: The 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)
Next: [Chapter 13 - Finding all Interfaces in Crystal: Crystal Contacts](crystal-contacts.md)
6 changes: 3 additions & 3 deletions structure/crystal-contacts.md
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Expand Up @@ -65,9 +65,9 @@ One can also cluster the interfaces based on their similarity. The similarity is

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| Chapter 13 - Finding all interfaces in crystal: crystal contacts
| [Book 3: The 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)
Prev: [Chapter 12 : Contacts Within a Chain and between Chains](contact-map.md)

Next: [Chapter 16 : Special Cases](special.md)
2 changes: 1 addition & 1 deletion structure/externaldb.md
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Expand Up @@ -205,7 +205,7 @@ got 4 domains

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| [Book 3: The Structure modules](README.md)
| Chapter 10 : External Databases

Prev: [Chapter 9 : Biological Assemblies](bioassembly.md)
Expand Down
2 changes: 1 addition & 1 deletion structure/installation.md
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Expand Up @@ -43,7 +43,7 @@ If you run

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| [Book 3: The Structure modules](README.md)
| Chapter 1 : Installation

Next: [Chapter 2 : First Steps](firststeps.md)
4 changes: 2 additions & 2 deletions structure/lists.md
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Expand Up @@ -26,7 +26,7 @@ The following provides information about the status of a PDB entry

Navigation:
[Home](../README.md)
| [Book 3: The Protein Structure modules](README.md)
| Chapter 17 : status information
| [Book 3: The Structure modules](README.md)
| Chapter 17 : Status Information

Prev: [Chapter 16 : Special Cases](special.md)
2 changes: 1 addition & 1 deletion structure/mmcif.md
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Expand Up @@ -126,4 +126,4 @@ Navigation:

Prev: [Chapter 5 : Chemical Component Dictionary](chemcomp.md)

Next: [Chapter 7 : SEQRES and ATOM records](seqres.md)
Next: [Chapter 7 : SEQRES and ATOM Records](seqres.md)
4 changes: 2 additions & 2 deletions structure/seqres.md
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Expand Up @@ -104,8 +104,8 @@ This gives the following output:
Navigation:
[Home](../README.md)
| [Book 3: The Structure modules](README.md)
| Chapter 7 : SEQRES and ATOM records
| Chapter 7 : SEQRES and ATOM Records

Prev: [Chapter 6 : work with mmCIF/PDBx files](mmcif.md)
Prev: [Chapter 6 : Work with mmCIF/PDBx Files](mmcif.md)

Next: [Chapter 8 : Structure Alignments](alignment.md)
6 changes: 3 additions & 3 deletions structure/special.md
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Expand Up @@ -130,9 +130,9 @@ 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)
| [Book 3: The Structure modules](README.md)
| Chapter 16 : Special Cases

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

Next: [Chapter 17 : status information](lists.md)
Next: [Chapter 17 : Status Information](lists.md)
2 changes: 1 addition & 1 deletion structure/structure-data-model.md
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Expand Up @@ -170,4 +170,4 @@ Navigation:

Prev: [Chapter 2 : First Steps](firststeps.md)

Next: [Chapter 4 : Local installations](caching.md)
Next: [Chapter 4 : Local Installations](caching.md)