Updates for biojava 6.0.0 release

josemduarte · josemduarte · commit fc9f288c58ca · 2021-10-29T16:49:01.000-07:00
diff --git a/structure/firststeps.md b/structure/firststeps.md
@@ -6,14 +6,10 @@ First Steps
 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.
 
 ```java
-     public static void main(String[] args){
-        try {
-                Structure structure = StructureIO.getStructure("4HHB");
-                // and let's print out how many atoms are in this structure
-                System.out.println(StructureTools.getNrAtoms(structure));
-            } catch (Exception e){
-                e.printStackTrace();
-        }
+     public static void main(String[] args) throws Exception {
+           Structure structure = StructureIO.getStructure("4HHB");
+           // and let's print out how many atoms are in this structure
+           System.out.println(StructureTools.getNrAtoms(structure));
     }   
 ```
 
@@ -53,23 +49,17 @@ Talking about startup properties, it is also good to mention the fact that many
 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){
-        try {
-            
-            Structure struc = StructureIO.getStructure("4hhb");
-
-            StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
-
-            jmolPanel.setStructure(struc);
-
-            // send some commands to Jmol
-            jmolPanel.evalString("select * ; color chain;");            
-            jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
-            jmolPanel.evalString("select ligands; cartoon off; wireframe 0.3; spacefill 0.5; color cpk;");
-            
-        } catch (Exception e){
-            e.printStackTrace();
-        }
+    public static void main(String[] args) throws Exception {
+        Structure struc = StructureIO.getStructure("4hhb");
+
+        StructureAlignmentJmol jmolPanel = new StructureAlignmentJmol();
+
+        jmolPanel.setStructure(struc);
+
+        // send some commands to Jmol
+        jmolPanel.evalString("select * ; color chain;");            
+        jmolPanel.evalString("select *; spacefill off; wireframe off; cartoon on;  ");
+        jmolPanel.evalString("select ligands; cartoon off; wireframe 0.3; spacefill 0.5; color cpk;");         
     }
 ```
 
@@ -91,15 +81,10 @@ This will result in the following view:
 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
 
 ```java
-     public static void main(String[] args){
-
-        try {
-                Structure structure = StructureIO.getBiologicalAssembly("1GAV");
-                // and let's print out how many atoms are in this structure
-                System.out.println(StructureTools.getNrAtoms(structure));
-        } catch (Exception e){
-                e.printStackTrace();
-        }
+     public static void main(String[] args) throws Exception {
+        Structure structure = StructureIO.getBiologicalAssembly("1GAV");
+        // and let's print out how many atoms are in this structure
+        System.out.println(StructureTools.getNrAtoms(structure));
     }
 ```
 
diff --git a/structure/mmcif.md b/structure/mmcif.md
@@ -44,8 +44,8 @@ By default BioJava is using the PDB file format for parsing data. In order to sw
 
 ```java
         AtomCache cache = new AtomCache();
-            
-        cache.setUseMmCif(true);
+
+        cache.setFiletype(StructureFiletype.CIF);
             
         // if you struggled to set the PDB_DIR property correctly in the previous step, 
         // 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.
 
 ```java
         String u = "http://ftp.wwpdb.org/pub/pdb/data/biounit/mmCIF/divided/nw/4nwr-assembly1.cif.gz";
-        try {
-            Structure s = StructureIO.getStructure(u);
-
-            System.out.println(s);
-        } catch (Exception e) {
-            e.printStackTrace();
-        }
+        Structure s = StructureIO.getStructure(u);
+        System.out.println(s);
 ```
 
 ### Local URLs
@@ -86,34 +81,12 @@ BioJava can also access local files, by specifying the URL as
 
 ## Low Level Access
 
-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:
+You can load a BioJava `Structure` object using the ciftools-java parser with:
 
 ```java
         InputStream inStream =  new FileInputStream(fileName);
- 
-        MMcifParser parser = new SimpleMMcifParser();
- 
-        SimpleMMcifConsumer consumer = new SimpleMMcifConsumer();
- 
-        // The Consumer builds up the BioJava - structure object.
-        // you could also hook in your own and build up you own data model.          
-        parser.addMMcifConsumer(consumer);
- 
-        try {
-            parser.parse(new BufferedReader(new InputStreamReader(inStream)));
-        } catch (IOException e){
-            e.printStackTrace();
-        }
- 
         // now get the protein structure.
-        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/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/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);
+        Structure cifStructure = CifStructureConverter.fromInputStream(inStream);
 ```
 
 ## I Loaded a Structure Object, What Now?
