org.biojava.nbio.structure.io

Class PDBFileParser

java.lang.Object

org.biojava.nbio.structure.io.PDBFileParser

public class PDBFileParser
extends Object

This class implements the actual PDB file parsing. Do not access it directly, but via the PDBFileReader class.

Parsing

During the PDBfile parsing several Flags can be set. See the setFileParsingParameters(FileParsingParameters) methods.

To provide excessive memory usage for large PDB files, there is the ATOM_CA_THRESHOLD. If more Atoms than this threshold are being parsed in a PDB file, the parser will automatically switch to a C-alpha only representation.

The result of the parsing of the PDB file is a new Structure object.

For more documentation on how to work with the Structure API please see http://biojava.org/wiki/BioJava:CookBook#Protein_Structure

Example

Q: How can I get a Structure object from a PDB file?

A:

 public Structure loadStructure(String pathToPDBFile){
        // The PDBFileParser is wrapped by the PDBFileReader
        PDBFileReader pdbreader = new PDBFileReader();

        Structure structure = null;
        try{
                structure = pdbreader.getStructure(pathToPDBFile);
                System.out.println(structure);
        } catch (IOException e) {
                e.printStackTrace();
        }
        return structure;
 }
 

Since:

1.4

Author:

Andreas Prlic, Jules Jacobsen, Jose Duarte

Constructor Summary

Constructors

Constructor and Description
PDBFileParser()

Method Summary

Modifier and Type	Method and Description
FileParsingParameters	getFileParsingParameters()
void	linkChains2Compound(Structure s) After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.
Structure	parsePDBFile(BufferedReader buf) Parse a PDB file and return a datastructure implementing PDBStructure interface.
Structure	parsePDBFile(InputStream inStream) Parse a PDB file and return a datastructure implementing PDBStructure interface.
void	setFileParsingParameters(FileParsingParameters params)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

PDBFileParser

public PDBFileParser()

Method Detail

parsePDBFile

public Structure parsePDBFile(InputStream inStream)
                       throws IOException

Parse a PDB file and return a datastructure implementing PDBStructure interface.

Parameters:

inStream - an InputStream object

Returns:

a Structure object

Throws:

IOException

parsePDBFile

public Structure parsePDBFile(BufferedReader buf)
                       throws IOException

Parse a PDB file and return a datastructure implementing PDBStructure interface.

Parameters:

buf - a BufferedReader object

Returns:

the Structure object

Throws:

IOException - ...

linkChains2Compound

public void linkChains2Compound(Structure s)

After the parsing of a PDB file the Chain and Compound objects need to be linked to each other.

Parameters:

s - the structure

setFileParsingParameters

public void setFileParsingParameters(FileParsingParameters params)

getFileParsingParameters

public FileParsingParameters getFileParsingParameters()