now also with StructureIO example

andreasprlic · andreasprlic · commit dc4d2dacbb85 · 2016-04-09T10:59:42.000-07:00
diff --git a/_wikis/BioJava:CookBook:PDB:read3.0.md b/_wikis/BioJava:CookBook:PDB:read3.0.md
@@ -4,8 +4,8 @@ title: BioJava:CookBook:PDB:read3.0
 
 ### How do I read a PDB file?
 
-The easiest way - AtomCache
----------------------------
+The easiest way - AtomCache and StructureIO
+-------------------------------------------
 
 The easiest way is to use the AtomCache class for accessing PDB files:
 <java>
@@ -28,6 +28,18 @@ The easiest way is to use the AtomCache class for accessing PDB files:
 
 </java>
 
+As of BioJava 3.0.5 there is also a new StructureIO utility class.
+<java> import org.biojava3.structure.StructureIO;
+
+`           Structure s1 = StructureIO.getStructure("4hhb");`
+
+`           Structure bioAssembly = StructureIO.getBiologicalAssembly("1stp",1);`
+
+`           // set the PDB path in StructureIO`  
+`           StructureIO.setPdbPath("/tmp/");`
+
+</java>
+
 Getting more control
 --------------------
 
diff --git a/_wikis/BioJava:CookBook:PDB:read3.0.mediawiki b/_wikis/BioJava:CookBook:PDB:read3.0.mediawiki
@@ -1,6 +1,6 @@
 === How do I read a PDB file? ===
 
-== The easiest way - AtomCache ==
+== The easiest way - AtomCache and StructureIO ==
 
 The easiest way is to use the AtomCache class for accessing PDB files:
 <java>
@@ -21,6 +21,18 @@ The easiest way is to use the AtomCache class for accessing PDB files:
 		}
 </java>
 
+As of BioJava 3.0.5 there is also a new StructureIO utility class.
+<java>
+import org.biojava3.structure.StructureIO;
+
+			Structure s1 = StructureIO.getStructure("4hhb");
+
+			Structure bioAssembly = StructureIO.getBiologicalAssembly("1stp",1);
+
+			// set the PDB path in StructureIO
+			StructureIO.setPdbPath("/tmp/");
+</java>
+
 == Getting more control ==
 
 BioJava provides a PDB file parser, that reads the content of a PDB file into a flexible data model for managing protein structural data. It is possible to 
