More manual fixes

Author: josemduarte

_wikis/BioJava:CookBook:PDB:atomsCalc.md

@@ -8,23 +8,24 @@ The
 [Calc](http://www.biojava.org/docs/api/org/biojava/bio/structure/Calc.html)
 class provides a set of methods that can be used for calculations.
 
-```java public double getPhi(Group a, Group b)
+```java 
+public double getPhi(Group a, Group b)
 
-`   throws StructureException`  
-`   {`  
-`       `  
-`       if ( ! Calc.isConnected(a,b)){`  
-`           throw new StructureException("can not calc Phi - AminoAcids are not connected!") ;`  
-`       } `  
-`       `  
-`       Atom a_C  = a.getAtom("C");`  
-`       Atom b_N  = b.getAtom("N");`  
-`       Atom b_CA = b.getAtom("CA");`  
-`       Atom b_C  = b.getAtom("C");`  
-`       `  
-`       double phi = Calc.torsionAngle(a_C,b_N,b_CA,b_C);`  
-`       return phi ;`  
-`   }`
+   throws StructureException  
+   {  
+         
+       if ( ! Calc.isConnected(a,b)){  
+           throw new StructureException("can not calc Phi - AminoAcids are not connected!") ;  
+       }   
+         
+       Atom a_C  = a.getAtom("C");  
+       Atom b_N  = b.getAtom("N");  
+       Atom b_CA = b.getAtom("CA");  
+       Atom b_C  = b.getAtom("C");  
+         
+       double phi = Calc.torsionAngle(a_C,b_N,b_CA,b_C);  
+       return phi ;  
+   }
 
 ```