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Copy file name to clipboardExpand all lines: alignment/installation.md
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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Copy file name to clipboardExpand all lines: core/installation.md
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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Copy file name to clipboardExpand all lines: installation.md
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BioJava uses [Maven](http://maven.apache.org/) as a build and distribution system. If you are new to Maven, take a look at the [Getting Started with Maven](http://maven.apache.org/guides/getting-started/index.html) guide.
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Currently, we are providing a BioJava specific Maven repository at (http://biojava.org/download/maven/) .
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You can add the BioJava repository by adding the following XML to your project pom.xml file:
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```xml
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<repositories>
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...
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<repository>
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<id>biojava-maven-repo</id>
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<name>BioJava repository</name>
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<url>http://www.biojava.org/download/maven/</url>
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</repository>
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</repositories>
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```
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We are currently in the process of changing our distribution to Maven Central, which would not even require this configuration step.
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As of version 4, BioJava is available in maven central. This is all you would need to add a BioJava dependency to your projects:
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```xml
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<dependencies>
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<dependency>
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<groupId>org.biojava</groupId>
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<artifactId>biojava3-genomics</artifactId>
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<version>3.0.8</version>
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<artifactId>biojava-genomics</artifactId>
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<version>4.0.0</version>
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<!-- note: the genomics module depends on the BioJava-core module and will import it automatically -->
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</dependency>
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Copy file name to clipboardExpand all lines: structure/bioassembly.md
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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.
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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.
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The [StructureIO](http://www.biojava.org/docs/api/org/biojava/nbio/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.
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Let's load both representations of hemoglobin PDB ID [1HHO](http://www.rcsb.org/pdb/explore.do?structureId=1hho) and visualize it:
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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.
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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.
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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.
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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*.
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Take a look at the method getBiologicalAssembly() in [StructureIO](http://www.biojava.org/docs/api/org/biojava/nbio/structure/StructureIO.html) to see how the BioUnitDataProviders are used by the *BiologicalAssemblyBuilder*.
Copy file name to clipboardExpand all lines: structure/caching.md
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BioJava can automatically download and install most of the data files that it needs. Those downloads
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will happen only once. Future requests for the data file will re-use the local copy.
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The main class that provides this functionality is the [AtomCache](http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html).
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The main class that provides this functionality is the [AtomCache](http://www.biojava.org/docs/api/org/biojava/nbio/structure/align/util/AtomCache.html).
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It is hidden inside the StructureIO class, that we already encountered earlier.
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## File Parsing Parameters
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The AtomCache also provides access to configuring various options that are available during the
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parsing of files. The [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/bio/structure/io/FileParsingParameters.html)
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parsing of files. The [FileParsingParameters](http://www.biojava.org/docs/api/org/biojava/nbio/structure/io/FileParsingParameters.html)
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class is the main place to influence the level of detail and as a consequence the speed with which files can be loaded.
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This example turns on the use of chemical components when loading a structure. (See also the [next chapter](chemcomp.md))
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```
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There are quite a number of external database IDs that are supported here. See the
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<ahref="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.
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<ahref="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.
Copy file name to clipboardExpand all lines: structure/chemcomp.md
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1. fetch missing Chemical Component definitions on the fly (small download and parsing delays every time a new chemical compound is found), or
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2. Load all definitions at startup (slow startup, but then no further delays later on, requires more memory)
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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:
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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:
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```java
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AtomCache cache =newAtomCache();
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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)
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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)
Copy file name to clipboardExpand all lines: structure/externaldb.md
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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).
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The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDatabase.html) class.
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The SCOP classification can be accessed through the [```ScopDatabase```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDatabase.html) class.
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```java
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ScopDatabase scop =ScopFactory.getSCOP();
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You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/bio/structure/scop/ScopDomain.html) object.
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You can get lots of useful information from the [```ScopDomain```](http://www.biojava.org/docs/api/org/biojava/nbio/structure/scop/ScopDomain.html) object.
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ScopDomain domain = domains.get(0);
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String scopID = domain.getScopId(); // d4hhba_
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### Viewing the SCOP hierarchy
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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.
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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.
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