BioJava:CookBook:PDB:header
How can I access the header information of a PDB file?
BioJava can parse the COMPND and SOURCE header files. Thanks to Jules Jacobsen (EBI) for providing the patch. The contained information is availabe via the Compound class that can be accessed from structure.getCompounds().
public static void main(String[] args) throws Exception {
String code = "1aoi";
AtomCache cache = new AtomCache();
Structure struc = cache.getStructure(code);
PDBHeader header = struc.getPDBHeader();
System.out.println(header.toString());
System.out.println("available compounds:");
List<Compound> compounds = struc.getCompounds();
for (Compound compound:compounds){
System.out.println(compound);
}
}
gives the following output:
Description: DNA BINDING PROTEIN/DNA BioAssemblies: {} NrBioAssemblies: 0 ExperimentalTechniques: [X-RAY DIFFRACTION] Classification: DNA BINDING PROTEIN/DNA DepDate: Thu Jul 03 00:00:00 CEST 1997 IdCode: 1AOI ModDate: Tue Feb 24 00:00:00 CET 2009 Title: COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT CrystallographicInfo: [P 21 21 21 - 106.04 181.78 110.12, 90.00 90.00 90.00] Resolution: 2.8 Rfree: 0.302 Authors: K.Luger,A.W.Maeder,R.K.Richmond,D.F.Sargent,T.J.Richmond
available compounds:
Compound: 1 (PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X-CHROMOSOME ALPHA SATELLITE DNA) chains: I,J
Compound: 2 (HISTONE H3) chains: A,E
Compound: 3 (HISTONE H4) chains: B,F
Compound: 4 (HISTONE H2A) chains: C,G
Compound: 5 (HISTONE H2B) chains: D,H
Next: <BioJava:CookBook:PDB:seqres> - How to deal with SEQRES and ATOM records