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Updates for biojava 6.0.0 release
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‎structure/firststeps.md

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@@ -6,14 +6,10 @@ First Steps
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The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava/nbio/structure/StructureIO.html) class.
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```java
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public static void main(String[] args){
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try {
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Structure structure = StructureIO.getStructure("4HHB");
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// and let's print out how many atoms are in this structure
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System.out.println(StructureTools.getNrAtoms(structure));
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} catch (Exception e){
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e.printStackTrace();
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}
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public static void main(String[] args) throws Exception {
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Structure structure = StructureIO.getStructure("4HHB");
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// and let's print out how many atoms are in this structure
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System.out.println(StructureTools.getNrAtoms(structure));
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}
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```
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@@ -53,23 +49,17 @@ Talking about startup properties, it is also good to mention the fact that many
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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:
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```java
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public static void main(String[] args){
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try {
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Structure struc = StructureIO.getStructure("4hhb");
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StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
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jmolPanel.setStructure(struc);
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// send some commands to Jmol
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jmolPanel.evalString("select * ; color chain;");
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jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on; ");
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jmolPanel.evalString("select ligands; cartoon off; wireframe 0.3; spacefill 0.5; color cpk;");
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} catch (Exception e){
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e.printStackTrace();
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}
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public static void main(String[] args) throws Exception {
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Structure struc = StructureIO.getStructure("4hhb");
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StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
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jmolPanel.setStructure(struc);
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// send some commands to Jmol
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jmolPanel.evalString("select * ; color chain;");
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jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on; ");
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jmolPanel.evalString("select ligands; cartoon off; wireframe 0.3; spacefill 0.5; color cpk;");
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}
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```
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@@ -91,15 +81,10 @@ This will result in the following view:
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By default many people work with the *asymmetric unit* of a protein. However for many studies the correct representation to look at is the *biological assembly* of a protein. You can request it by calling
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```java
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public static void main(String[] args){
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try {
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Structure structure = StructureIO.getBiologicalAssembly("1GAV");
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// and let's print out how many atoms are in this structure
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System.out.println(StructureTools.getNrAtoms(structure));
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} catch (Exception e){
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e.printStackTrace();
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}
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public static void main(String[] args) throws Exception {
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Structure structure = StructureIO.getBiologicalAssembly("1GAV");
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// and let's print out how many atoms are in this structure
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System.out.println(StructureTools.getNrAtoms(structure));
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}
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```
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‎structure/mmcif.md

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Original file line numberDiff line numberDiff line change
@@ -44,8 +44,8 @@ By default BioJava is using the PDB file format for parsing data. In order to sw
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```java
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AtomCache cache = new AtomCache();
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cache.setUseMmCif(true);
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cache.setFiletype(StructureFiletype.CIF);
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// if you struggled to set the PDB_DIR property correctly in the previous step,
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// you could set it manually like this:
@@ -67,13 +67,8 @@ StructureIO can also access files via URLs and fetch the data dynamically. E.g.
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```java
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String u = "http://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/divided/nw/4nwr-assembly1.cif.gz";
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try {
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Structure s = StructureIO.getStructure(u);
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System.out.println(s);
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} catch (Exception e) {
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e.printStackTrace();
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}
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Structure s = StructureIO.getStructure(u);
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System.out.println(s);
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```
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### Local URLs
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## Low Level Access
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If you want to learn how to use the BioJava mmCIF parser to populate your own data structure, let's first take a look this lower-level code:
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You can load a BioJava `Structure` object using the ciftools-java parser with:
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```java
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InputStream inStream = new FileInputStream(fileName);
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MMcifParser parser = new SimpleMMcifParser();
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SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
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// The Consumer builds up the BioJava - structure object.
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// you could also hook in your own and build up you own data model.
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parser.addMMcifConsumer(consumer);
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try {
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parser.parse(new BufferedReader(new InputStreamReader(inStream)));
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} catch (IOException e){
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e.printStackTrace();
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}
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// now get the protein structure.
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Structure cifStructure = consumer.getStructure();
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```
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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.
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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).
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```java
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parser.addMMcifConsumer(myOwnConsumerImplementation);
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Structure cifStructure = CifStructureConverter.fromInputStream(inStream);
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```
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## I Loaded a Structure Object, What Now?

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