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: <BioJava:CookBook:PDB:header> - How to access the header information