BioJava:CookbookFrench:PDB:Header

From BioJava

Comment accéder aux informations contenues dans l'en-tête d'un fichier PDB?

Avec la version 1.6 de BioJava, il est maintenant possible de lire et d'extraire les informations, souvent fort utiles , contenues dans l'en-tête d'un fichier PDB; merci à Jules Jacobsen (EBI) pour le code permettant ces opérations. Les informations sont contenues dans un objet de type Compound, accessible via la méthode getCompounds() de la classe Structure.

La recette suivante vous permet d'y accéder.

public static void main(String[] args){
		String pdbCode =  "1aoi";
 
		PDBFileReader pdbreader = new PDBFileReader();
		pdbreader.setPath("/Path/To/PDBFiles/");
		pdbreader.setParseSecStruc(true);
		pdbreader.setAlignSeqRes(true);
		pdbreader.setAutoFetch(true);
 
		try{
			Structure struc = pdbreader.getStructureById(pdbCode);
			Map<String,Object> m = struc.getHeader();
 
			Set<String> keys = m.keySet();
			for (String key: keys) {
				System.out.println(key +": " +  m.get(key));
			}
 
			System.out.println("available compounds:");
			List<Compound> compounds = struc.getCompounds();
			for (Compound compound:compounds){
				System.out.println(compound);
			}
 
 
		} catch (Exception e) {
			e.printStackTrace();
		}
	}

fournira la sortie suivante:

title: COMPLEX BETWEEN NUCLEOSOME CORE PARTICLE (H3,H4,H2A,H2B) AND 146 BP LONG DNA FRAGMENT 
technique: X-RAY DIFFRACTION 
classification: DNA BINDING PROTEIN/DNA
depDate: 03-JUL-97
modDate: 01-APR-03
idCode: 1AOI
resolution: 2.8
available compounds:
Compound: 1 HISTONE H3 Chains: ChainId: A E Engineered: YES OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG ExpressionSystem: ESCHERICHIA COLI Fragment: HISTONE H3 
Compound: 2 HISTONE H4 Chains: ChainId: B F Engineered: YES OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG ExpressionSystem: ESCHERICHIA COLI ExpressionSystemOtherDetails: SYNTHETIC GENE, OPTIMIZED CODON USAGE FOR Fragment: HISTONE H4 
Compound: 3 HISTONE H2A Chains: ChainId: C G Engineered: YES OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG ExpressionSystem: ESCHERICHIA COLI Fragment: HISTONE H2A 
Compound: 4 HISTONE H2B Chains: ChainId: D H Engineered: YES Mutation: YES OrganismScientific: XENOPUS LAEVIS OrganismCommon: AFRICAN CLAWED FROG ExpressionSystem: ESCHERICHIA COLI Fragment: HISTONE H2B 
Compound: 5 PALINDROMIC 146 BP DNA REPEAT 8/9 FROM HUMAN X- CHROMOSOME ALPHA SATELLITE DNA Chains: ChainId: I J Engineered: YES Synthetic: YES