BioJava:CookBook:PDB:read

From BioJava

Contents 1 How do I read a PDB file? 2 Short Example: the quickest way to read a local file 3 Example: How to work with a local installation of PDB 4 Example: How to parse a local file

How do I read a PDB file?

BioJava provides a PDB file parser, that reads the content of a PDB file into a flexible data model for managing protein structural data. It is possible to

• parse individual PDB files, or
• work with local PDB file installations.

The class providing the core functionality for this is the PDBFileReader class.

Short Example: the quickest way to read a local file

 // also works for gzip compressed files
 String filename =  "path/to/pdbfile.ent" ;
 
 PDBFileReader pdbreader = new PDBFileReader();
 
 try{
 
     Structure struc = pdbreader.getStructure(filename);
 
 } catch (Exception e){
     e.printStackTrace();
 }

Example: How to work with a local installation of PDB

		try {
			PDBFileReader reader = new PDBFileReader();
 
			// the path to the local PDB installation
			reader.setPath("/tmp");
 
			// are all files in one directory, or are the files split,
			// as on the PDB ftp servers?
			reader.setPdbDirectorySplit(true);
 
			// should a missing PDB id be fetched automatically from the FTP servers?
			reader.setAutoFetch(true);
 
			// should the ATOM and SEQRES residues be aligned when creating the internal data model?
			reader.setAlignSeqRes(false);
 
			// should secondary structure get parsed from the file
			reader.setParseSecStruc(false);
 
			Structure structure = reader.getStructureById("4hhb");
 
			System.out.println(structure);
 
		} catch (Exception e){
			e.printStackTrace();
		}

Will give this output:

Fetching ftp://ftp.wwpdb.org/pub/pdb/data/structures/all/pdb/pdb4hhb.ent.gz
writing to /tmp/hh/pdb4hhb.ent.gz
structure  4HHB Authors: G.FERMI,M.F.PERUTZ Resolution: 1.74 Technique: X-RAY DIFFRACTION  Classification: OXYGEN TRANSPORT DepDate: Wed Mar 07 00:00:00 PST 1984 IdCode: 4HHB Title: THE CRYSTAL STRUCTURE OF HUMAN DEOXYHAEMOGLOBIN AT 1.74 ANGSTROMS RESOLUTION ModDate: Tue Feb 24 00:00:00 PST 2009 
 chains:
chain 0: >A< HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
 length SEQRES: 0 length ATOM: 198 aminos: 141 hetatms: 57 nucleotides: 0
chain 1: >B< HEMOGLOBIN (DEOXY) (BETA CHAIN)
 length SEQRES: 0 length ATOM: 205 aminos: 146 hetatms: 59 nucleotides: 0
chain 2: >C< HEMOGLOBIN (DEOXY) (ALPHA CHAIN)
 length SEQRES: 0 length ATOM: 201 aminos: 141 hetatms: 60 nucleotides: 0
chain 3: >D< HEMOGLOBIN (DEOXY) (BETA CHAIN)
 length SEQRES: 0 length ATOM: 197 aminos: 146 hetatms: 51 nucleotides: 0
DBRefs: 4
DBREF  4HHB A    1   141  UNP    P69905   HBA_HUMAN        1    141
DBREF  4HHB B    1   146  UNP    P68871   HBB_HUMAN        1    146
DBREF  4HHB C    1   141  UNP    P69905   HBA_HUMAN        1    141
DBREF  4HHB D    1   146  UNP    P68871   HBB_HUMAN        1    146
Molecules: 
Compound: 1 HEMOGLOBIN (DEOXY) (ALPHA CHAIN) Chains: ChainId: A C Engineered: YES OrganismScientific: HOMO SAPIENS OrganismTaxId: 9606 OrganismCommon: HUMAN 
Compound: 2 HEMOGLOBIN (DEOXY) (BETA CHAIN) Chains: ChainId: B D Engineered: YES OrganismScientific: HOMO SAPIENS OrganismTaxId: 9606 OrganismCommon: HUMAN 

Example: How to parse a local file

This example shows how to read a PDB file from your file system, obtain a Structure object and iterate over the Groups that are contained in the file. For more examples of how to access the Atoms please go to BioJava:CookBook:PDB:atoms. For more info on how the parser deals with SEQRES and ATOM records please see BioJava:CookBook:PDB:seqres

 // also works for gzip compressed files
 String filename =  "path/to/pdbfile.ent" ;
 
 PDBFileReader pdbreader = new PDBFileReader();
 
 // the following parameters are optional: 
 
 //the parser can read the secondary structure
 // assignment from the PDB file header and add it to the amino acids
 pdbreader.setParseSecStruc(true);
 
 // align the SEQRES and ATOM records, default = true   
 // slows the parsing speed slightly down, so if speed matters turn it off.
 pdbreader.setAlignSeqRes(true);
 
 // parse the C-alpha atoms only, default = false
 pdbreader.setParseCAOnly(false);
 
 // download missing PDB files automatically from EBI ftp server, default = false
 pdbreader.setAutoFetch(false);
 
 try{
     Structure struc = pdbreader.getStructure(filename);
 
     System.out.println(struc);
 
     GroupIterator gi = new GroupIterator(struc);
 
     while (gi.hasNext()){
 
           Group g = (Group) gi.next();
 
           if ( g instanceof AminoAcid ){
               AminoAcid aa = (AminoAcid)g;
               Map sec = aa.getSecStruc();
               Chain  c = g.getParent();
               System.out.println(c.getName() + " " + g + " " + sec);
           }                
     }
 
 } catch (Exception e) {
     e.printStackTrace();
 }

To learn how to serialize a Structure object to a database see BioJava:CookBook:PDB:hibernate

Next: BioJava:CookBook:PDB:atoms - How to access atoms.