BioJava:CookBook:PDB:groups

Groups

The Group interface defines all methods common to a group of atoms. There are 3 types of Groups:

In order to get all amino acids that have been observed in a PDB chain, you can use the following utility method:


`           Chain chain = s.getChainByPDB("A");`  
`           List`<Group>groups = chain.getAtomGroups("amino");`  
`           for (Group group : groups) {`  
`               AminoAcid aa = (AminoAcid) group;`

`               // do something amino acid specific, e.g. print the secondary structure assignment`  
`               System.out.println(aa + " " + aa.getSecStruc());`  
`           }`

In a similar way you can access all nucleotide groups by ```java

           chain.getAtomGroups("nucleotide");


The Hetatom groups are access in a similar fashion: ```java

`           chain.getAtomGroups("hetatm");`

Since all 3 types of groups are implementing the Group interface, you can also iterate over all groups and check for the instance type:


`           List`<Group>allgroups = chain.getAtomGroups();`  
`           for (Group group : groups) {`  
`               if ( group instanceof AminoAcid) {`  
`                   AminoAcid aa = (AminoAcid) group;`  
`                   System.out.println(aa.getSecStruc());`  
`               }`  
`           }`

Next: - How to access the header information