More manual fixes

Author: josemduarte

_wikis/BioJava:CookBook:PDB:seqres.md

@@ -22,7 +22,9 @@ Groups derived from SEQRES groups will be empty (i.e. they will not
 contain Atoms), unless they could be mapped to the ATOM records, in
 which case the full ATOM information can be accessed.
 
-Example: ```java import java.util.List; import
+Example: 
+```java 
+import java.util.List; import
 org.biojava.nbio.structure.Chain; import
 org.biojava.nbio.structure.Group; import
 org.biojava.nbio.structure.GroupType; import
@@ -33,39 +35,39 @@ org.biojava.nbio.structure.io.LocalPDBDirectory.FetchBehavior;
 
 public class SeqResCookBook {
 
-`   public static void main(String[] args) throws Exception {`  
-`       `  
-`       String code =  "1aoi";`  
+   public static void main(String[] args) throws Exception {  
+         
+       String code =  "1aoi";  
 
-`       PDBFileReader pdbreader = new PDBFileReader();`  
-`       FileParsingParameters params = new FileParsingParameters();`  
-`       params.setParseSecStruc(true);// parse the secondary structure information from PDB file`  
-`       params.setAlignSeqRes(true);  // align SEQRES and ATOM records`  
-`       pdbreader.setFileParsingParameters(params);`  
-`       `  
-`       pdbreader.setFetchBehavior(FetchBehavior.FETCH_FILES);   // fetch PDB files from web if they can't be found locally`
-
-`       Structure struc = pdbreader.getStructureById(code);`
-
-`       System.out.println("The SEQRES and ATOM information is available via the chains:");`
-
-`       int modelnr = 0 ; // also is 0 if structure is an XRAY structure.`
-
-`       List`<Chain>` chains = struc.getChains(modelnr);`  
-`       for (Chain cha:chains){`  
-`           List`<Group>` agr = cha.getAtomGroups(GroupType.AMINOACID);`  
-`           List`<Group>` hgr = cha.getAtomGroups(GroupType.HETATM);`  
-`           List`<Group>` ngr = cha.getAtomGroups(GroupType.NUCLEOTIDE);`
-
-`           System.out.print("chain: >"+cha.getChainID()+"<");`  
-`           System.out.print(" length SEQRES: " +cha.getSeqResLength());`  
-`           System.out.print(" length ATOM: " +cha.getAtomLength());`  
-`           System.out.print(" aminos: " +agr.size());`  
-`           System.out.print(" hetatms: "+hgr.size());`  
-`           System.out.println(" nucleotides: "+ngr.size());  `  
-`       }`
-
-`   }`
+       PDBFileReader pdbreader = new PDBFileReader();  
+       FileParsingParameters params = new FileParsingParameters();  
+       params.setParseSecStruc(true);// parse the secondary structure information from PDB file  
+       params.setAlignSeqRes(true);  // align SEQRES and ATOM records  
+       pdbreader.setFileParsingParameters(params);  
+         
+       pdbreader.setFetchBehavior(FetchBehavior.FETCH_FILES);   // fetch PDB files from web if they can't be found locally
+
+       Structure struc = pdbreader.getStructureById(code);
+
+       System.out.println("The SEQRES and ATOM information is available via the chains:");
+
+       int modelnr = 0 ; // also is 0 if structure is an XRAY structure.
+
+       List<Chain> chains = struc.getChains(modelnr);  
+       for (Chain cha:chains){  
+           List<Group> agr = cha.getAtomGroups(GroupType.AMINOACID);  
+           List<Group> hgr = cha.getAtomGroups(GroupType.HETATM);  
+           List<Group> ngr = cha.getAtomGroups(GroupType.NUCLEOTIDE);
+
+           System.out.print("chain: >"+cha.getChainID()+"<");  
+           System.out.print(" length SEQRES: " +cha.getSeqResLength());  
+           System.out.print(" length ATOM: " +cha.getAtomLength());  
+           System.out.print(" aminos: " +agr.size());  
+           System.out.print(" hetatms: "+hgr.size());  
+           System.out.println(" nucleotides: "+ngr.size());    
+       }
+
+   }
 
 }