Now really fixing biojava.bio.structure.* links

josemduarte · josemduarte · commit c499da89d663 · 2015-02-11T16:45:42.000+01:00
diff --git a/structure/alignment.md b/structure/alignment.md
@@ -14,7 +14,7 @@ For more info see the Wikipedia article on [protein structure alignment](http://
 BioJava comes with a number of algorithms for aligning structures. The following
 five options are displayed by default in the graphical user interface (GUI),
 although others can be accessed programmatically using the methods in
-[StructureAlignmentFactory](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/StructureAlignmentFactory.html).
+[StructureAlignmentFactory](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/StructureAlignmentFactory.html).
 
 1. Combinatorial Extension (CE)
 2. Combinatorial Extension with Circular Permutation (CE-CP)
@@ -69,10 +69,10 @@ compared are kept fixed during superposition. In some cases it may be desirable
 to break large proteins up into domains prior to aligning them (by manually
 inputing a subrange, using the [SCOP or CATH databases](externaldb.md), or by
 decomposing the protein automatically using the [Protein Domain
-Parser](http://www.biojava.org/docs/api/org/biojava/bio/structure/domain/LocalProteinDomainParser.html)
+Parser](http://www.biojava.org/docs/api/org/biojava/nbio/structure/domain/LocalProteinDomainParser.html)
 algorithm).
 
-BioJava class: [org.biojava.bio.structure.align.ce.CeMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeMain.html)
+BioJava class: [org.biojava.bio.structure.align.ce.CeMain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeMain.html)
 
 ### Combinatorial Extension with Circular Permutation (CE-CP)
 
@@ -97,7 +97,7 @@ proteins will be shown in different colors:
 
 CE-CP was developed by Spencer E. Bliven, Philip E. Bourne, and Andreas Prli&#263;.
 
-BioJava class: [org.biojava.bio.structure.align.ce.CeCPMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeCPMain.html)
+BioJava class: [org.biojava.bio.structure.align.ce.CeCPMain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeCPMain.html)
 
 ### FATCAT - rigid
 
@@ -109,7 +109,7 @@ It performs similarly to CE for most proteins. The 'rigid' flavor uses a
 rigid-body superposition and only considers alignments with matching sequence
 order.
 
-BioJava class: [org.biojava.bio.structure.align.fatcat.FatCatRigid](www.biojava.org/docs/api/org/biojava/bio/structure/align/fatcat/FatCatRigid.html)
+BioJava class: [org.biojava.bio.structure.align.fatcat.FatCatRigid](www.biojava.org/docs/api/org/biojava/nbio/structure/align/fatcat/FatCatRigid.html)
 
 ### FATCAT - flexible
 
@@ -124,7 +124,7 @@ this is that it can lead to additional false positives in unrelated structures.
 ![(Left) Rigid and (Right) flexible alignments of
 calmodulin](img/1cfd_1cll_fatcat.png)
 
-BioJava class: [org.biojava.bio.structure.align.fatcat.FatCatFlexible](www.biojava.org/docs/api/org/biojava/bio/structure/align/fatcat/FatCatFlexible.html)
+BioJava class: [org.biojava.bio.structure.align.fatcat.FatCatFlexible](www.biojava.org/docs/api/org/biojava/nbio/structure/align/fatcat/FatCatFlexible.html)
 
 ### Smith-Waterman
 
@@ -138,24 +138,24 @@ locating gaps can lead to high RMSD in the resulting superposition due to a
 small number of badly aligned residues. However, this method is faster than
 the structure-based methods.
 
-BioJava Class: [org.biojava.bio.structure.align.ce.CeCPMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeCPMain.html)
+BioJava Class: [org.biojava.bio.structure.align.ce.CeCPMain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeCPMain.html)
 
 ### Other methods
 
 The following methods are not presented in the user interface by default:
 
-* [BioJavaStructureAlignment](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/BioJavaStructureAlignment.html)
+* [BioJavaStructureAlignment](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/BioJavaStructureAlignment.html)
   A structure-based alignment method able of returning multiple alternate
   alignments. It was written by Andreas Prli&#263; and based on the PSC++ algorithm
   provided by Peter Lackner.
-* [CeSideChainMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/CeSideChainMain.html)
+* [CeSideChainMain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/CeSideChainMain.html)
   A variant of CE using CB-CB distances, which sometimes improves alignments in
   proteins with parallel sheets and helices.
-* [OptimalCECPMain](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/ce/OptimalCECPMain.html)
+* [OptimalCECPMain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/ce/OptimalCECPMain.html)
   An alternate (much slower) algorithm for finding circular permutations.
 
 Additional methods can be added by implementing the
-[StructureAlignment](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/StructureAlignment.html)
+[StructureAlignment](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/StructureAlignment.html)
 interface.
 
 ## PDB-wide database searches
diff --git a/structure/bioassembly.md b/structure/bioassembly.md
@@ -17,7 +17,7 @@ A crystal asymmetric unit may contain:
 
 The biological assembly (also sometimes referred to as the biological unit) is the macromolecular assembly that has either been shown to be or is believed to be the functional form of the molecule For example, the functional form of hemoglobin has four chains.
 
-The [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html) and [AtomCache](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html) classes in Biojava provide access methods to work with either asymmetric unit or biological assembly.
+The [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html) and [AtomCache](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/util/AtomCache.html) classes in Biojava provide access methods to work with either asymmetric unit or biological assembly.
 
 Let's load both representations of hemoglobin PDB ID [1HHO](http://www.rcsb.org/pdb/explore.do?structureId=1hho) and visualize it:
 
@@ -105,7 +105,7 @@ In PDB files the relevant transformations are stored in the *REMARK 350* records
 
 B) There is also a pre-computed file available that contains an assembled version of a structure. This file can be parsed directly, without having to perform rotation operations on coordinates.
 
-BioJava contains utility classes to re-create biological assemblies for both PDB and mmCIF, as well as to parse the pre-computed file. The [BioUnitDataProvider](http://www.biojava.org/docs/api/org/biojava/bio/structure/quaternary/io/BioUnitDataProvider.html) interface defines what is required to re-build an assembly. The [BioUnitDataProviderFactory](http://www.biojava.org/docs/api/org/biojava/bio/structure/quaternary/io/BioUnitDataProviderFactory.html) allows to specify which of the BioUnitDataProviders is getting used.
+BioJava contains utility classes to re-create biological assemblies for both PDB and mmCIF, as well as to parse the pre-computed file. The [BioUnitDataProvider](http://www.biojava.org/docs/api/org/biojava/nbio/structure/quaternary/io/BioUnitDataProvider.html) interface defines what is required to re-build an assembly. The [BioUnitDataProviderFactory](http://www.biojava.org/docs/api/org/biojava/nbio/structure/quaternary/io/BioUnitDataProviderFactory.html) allows to specify which of the BioUnitDataProviders is getting used.
 
 Take a look at the method getBiologicalAssembly() in [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html)  to see how the BioUnitDataProviders are used by the *BiologicalAssemblyBuilder*.
 
diff --git a/structure/caching.md b/structure/caching.md
@@ -4,7 +4,7 @@ Local PDB Installations
 BioJava can automatically download and install most of the data files that it needs. Those downloads 
 will happen only once. Future requests for the data file will re-use the local copy.
 
-The main class that provides this functionality is the [AtomCache](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html).
+The main class that provides this functionality is the [AtomCache](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/util/AtomCache.html).
 
 It is hidden inside the StructureIO class, that we already encountered earlier.
 
@@ -42,7 +42,7 @@ An alternative is to hard-code the path in this way (but setting it as a propert
 ## File Parsing Parameters
 
 The AtomCache also provides access to configuring various options that are available during the 
-parsing of files. The [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/FileParsingParameters.html)
+parsing of files. The [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/FileParsingParameters.html)
 class is the main place to influence the level of detail and as a consequence the speed with which files can be loaded.
 
 This example turns on the use of chemical components when loading a structure. (See also the [next chapter](chemcomp.md))
@@ -76,7 +76,7 @@ The AtomCache not only provides access to PDB, it can also fetch Structure repre
 ```
 
 There are quite a number of external database IDs that are supported here. See the 
-<a href="http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html#getStructure(java.lang.String)">AtomCache documentation</a> for more details on the supported options.
+<a href="http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/util/AtomCache.html#getStructure(java.lang.String)">AtomCache documentation</a> for more details on the supported options.
 
 
 
diff --git a/structure/chemcomp.md b/structure/chemcomp.md
@@ -56,7 +56,7 @@ By default BioJava ships with a minimal representation of standard amino acids,
 1. fetch missing Chemical Component definitions on the fly (small download and parsing delays every time a new chemical compound is found), or
 2. Load all definitions at startup (slow startup, but then no further delays later on, requires more memory)
 
-You can enable the first behaviour by doing using the [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/FileParsingParameters.html) class:
+You can enable the first behaviour by doing using the [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/FileParsingParameters.html) class:
 
 ```java
             AtomCache cache = new AtomCache();
@@ -76,7 +76,7 @@ You can enable the first behaviour by doing using the [FileParsingParameters](ht
             Structure structure = StructureIO.getStructure(...);
 ```
 
-If you want to enable the second behaviour (slow loading of all chem comps at startup, but no further small delays later on) you can use the same code but change the behaviour by switching the [ChemCompProvider](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/ChemCompProvider.html) implementation in the [ChemCompGroupFactory](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/ChemCompGroupFactory.html)
+If you want to enable the second behaviour (slow loading of all chem comps at startup, but no further small delays later on) you can use the same code but change the behaviour by switching the [ChemCompProvider](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/ChemCompProvider.html) implementation in the [ChemCompGroupFactory](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/ChemCompGroupFactory.html)
 
 ```java
      ChemCompGroupFactory.setChemCompProvider(new AllChemCompProvider());
diff --git a/structure/externaldb.md b/structure/externaldb.md
@@ -25,7 +25,7 @@ The Structural Classification of Proteins (SCOP) is a manually curated classific
 
 The structure for a known SCOP domain can be fetched via its 7-letter domain ID (eg 'd2bq6a1') via ```StructureIO.getStructure()```, as described in [Local PDB Installations](caching.md#Caching of other SCOP, CATH).
 
-The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDatabase.html) class.
+The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDatabase.html) class.
 
 ```java
     ScopDatabase scop = ScopFactory.getSCOP();
@@ -39,7 +39,7 @@ A list of domains can be retrieved for a given protein.
     List<ScopDomain> domains = scop.getDomainsForPDB("4HHB");
 ```
 
-You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDomain.html) object. 
+You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDomain.html) object. 
 
     ScopDomain domain = domains.get(0);
     String scopID = domain.getScopId(); // d4hhba_
@@ -48,7 +48,7 @@ You can get lots of useful information from the [```ScopDomain```](http://www.bi
 
 ### Viewing the SCOP hierarchy
 
-The full hierarchy is available as a tree of [```ScopNode```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopNode.html)s, which can be easily traversed using their ```getParentSunid()``` and ```getChildren()``` methods.
+The full hierarchy is available as a tree of [```ScopNode```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopNode.html)s, which can be easily traversed using their ```getParentSunid()``` and ```getChildren()``` methods.
 
 ```java
     ScopNode node = scop.getScopNode(sunId);
diff --git a/structure/firststeps.md b/structure/firststeps.md
@@ -17,7 +17,7 @@ The simplest way to load a PDB file is by using the [StructureIO](http://www.bio
     }   
 ```
 
-BioJava  automatically downloads the PDB file for hemoglobin [4HHB](http://www.rcsb.org/pdb/explore.do?structureId=4HHB) and copies it into a temporary location. Then the PDB file parser loads the data into a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) object, that provides access to the content in the file. (If you call this a second time, BioJava will automatically re-use the local file.)
+BioJava  automatically downloads the PDB file for hemoglobin [4HHB](http://www.rcsb.org/pdb/explore.do?structureId=4HHB) and copies it into a temporary location. Then the PDB file parser loads the data into a [Structure](http://www.biojava.org/docs/api/org/biojava/nbio/structure/Structure.html) object, that provides access to the content in the file. (If you call this a second time, BioJava will automatically re-use the local file.)
 
 <table>
     <tr>
@@ -50,7 +50,7 @@ Talking about startup properties, it is also good to mention the fact that many
 
 ## A Quick 3D View
 
-If you have the *biojava-structure-gui* module installed, you can quickly visualise a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) via this:
+If you have the *biojava-structure-gui* module installed, you can quickly visualise a [Structure](http://www.biojava.org/docs/api/org/biojava/nbio/structure/Structure.html) via this:
 
 ```java
     public static void main(String[] args){
@@ -81,7 +81,7 @@ This will result in the following view:
             <img src="img/4hhb_jmol.png"/>
         </td>
         <td>
-            The <a href="http://www.biojava.org/docs/api/org/biojava/bio/structure/align/gui/jmol/StructureAlignmentJmol.html">StructureAlignmentJmol</a> class provides a wrapper for the <a href="http://jmol.sourceforge.net/">Jmol</a> viewer and provides a bridge to BioJava, so Structure objects can be sent to Jmol for visualisation.
+            The <a href="http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/gui/jmol/StructureAlignmentJmol.html">StructureAlignmentJmol</a> class provides a wrapper for the <a href="http://jmol.sourceforge.net/">Jmol</a> viewer and provides a bridge to BioJava, so Structure objects can be sent to Jmol for visualisation.
         </td>
     </tr>
 </table>   
diff --git a/structure/mmcif.md b/structure/mmcif.md
@@ -40,7 +40,7 @@ If you already have a local PDB installation, you can configure where BioJava sh
 
 ## From PDB to mmCIF
 
-By default BioJava is using the PDB file format for parsing data. In order to switch it to use mmCIF, we can take control over the underlying [AtomCache](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html) which manages your PDB ([and btw. also SCOP, CATH](externaldb.md)) installations.
+By default BioJava is using the PDB file format for parsing data. In order to switch it to use mmCIF, we can take control over the underlying [AtomCache](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/util/AtomCache.html) which manages your PDB ([and btw. also SCOP, CATH](externaldb.md)) installations.
 
 ```java
         AtomCache cache = new AtomCache();
@@ -86,9 +86,9 @@ If you want to learn how to use the BioJava mmCIF parser to populate your own da
         Structure cifStructure = consumer.getStructure();
 ```
 
-The parser operates similar to a XML parser by triggering "events". The [SimpleMMcifConsumer](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/SimpleMMcifConsumer.html) listens to new categories being read from the file and then builds up the BioJava data model.
+The parser operates similar to a XML parser by triggering "events". The [SimpleMMcifConsumer](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/SimpleMMcifConsumer.html) listens to new categories being read from the file and then builds up the BioJava data model.
 
-To re-use the parser for your own datamodel, just implement the [MMcifConsumer](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/MMcifConsumer.html) interface and add it to the [SimpleMMcifParser](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/mmcif/SimpleMMcifParser.html).
+To re-use the parser for your own datamodel, just implement the [MMcifConsumer](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/MMcifConsumer.html) interface and add it to the [SimpleMMcifParser](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.html).
 ```java
         parser.addMMcifConsumer(myOwnConsumerImplementation);
 ```
diff --git a/structure/seqres.md b/structure/seqres.md
@@ -42,7 +42,7 @@ The *mmCIF/PDBx* file format contains the information how the Seqres and atom re
 
 ## Accessing Seqres and Atom groups
 
-By default BioJava loads both the Seqres and Atom groups into the [Chain](http://www.biojava.org/docs/api/org/biojava/bio/structure/Chain.html) 
+By default BioJava loads both the Seqres and Atom groups into the [Chain](http://www.biojava.org/docs/api/org/biojava/nbio/structure/Chain.html) 
 objects.
 
 <pre>
@@ -59,7 +59,7 @@ can iterate over all Seqres groups in a chain and check, if they have observed a
 
 The mapping between PDB and UniProt changes over time, due to the dynamic nature of biological data. The [PDBe](http://www.pdbe.org) has a project that provides up-to-date mappings between the two databases, the [SIFTs](http://www.ebi.ac.uk/pdbe/docs/sifts/) project. 
 
-BioJava contains a parser for the SIFTs XML files. The [SiftsMappingProvider](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/sifts/SiftsMappingProvider.html) also acts similar to the AtomCache class, that we [discussed earlier](caching.md) and can automatically download and locally install SIFTs files.
+BioJava contains a parser for the SIFTs XML files. The [SiftsMappingProvider](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/sifts/SiftsMappingProvider.html) also acts similar to the AtomCache class, that we [discussed earlier](caching.md) and can automatically download and locally install SIFTs files.
 
 Here, how to request the mapping for one particular PDB ID.
 
diff --git a/structure/structure-data-model.md b/structure/structure-data-model.md
