org.biojava.bio.structure.io
Class PDBFileParser

java.lang.Object
  org.biojava.bio.structure.io.PDBFileParser

public class PDBFileParser
extends Object

A PDB file parser.

Since:

1.4

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

A:

 String filename =  "path/to/pdbfile.ent" ;

 PDBFileReader pdbreader = new PDBFileReader();

 try{
     Structure struc = pdbreader.getStructure(filename);
     System.out.println(struc);
 } catch (Exception e) {
     e.printStackTrace();
 }
 

Author:

Andreas Prlic

Constructor Summary

PDBFileParser()

Method Summary

Character	convert_3code_1code(String code3) convert three character amino acid codes into single character e.g.
protected String	getTimeStamp() Returns a time stamp.
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.

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

getTimeStamp

protected String getTimeStamp()

Returns a time stamp.

Returns:

a String representing the time stamp value

convert_3code_1code

public Character convert_3code_1code(String code3)
                              throws IllegalSymbolException

convert three character amino acid codes into single character e.g. convert CYS to C

Parameters:

code3 - a three character amino acid representation String

Returns:

a character

Throws:

IllegalSymbolException

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 - ...