org.biojava.bio.structure.io
Class PDBFileParser

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

public class PDBFileParser
extends java.lang.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

Field Summary
static java.lang.String idCode
           
 
Constructor Summary
PDBFileParser()
           
 
Method Summary
 java.lang.Character convert_3code_1code(java.lang.String code3)
          convert three character amino acid codes into single character e.g.
protected  java.lang.String getTimeStamp()
          Returns a time stamp.
 Structure parsePDBFile(java.io.BufferedReader buf)
          parse a PDB file and return a datastructure implementing PDBStructure interface.
 Structure parsePDBFile(java.io.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
 

Field Detail

idCode

public static java.lang.String idCode
Constructor Detail

PDBFileParser

public PDBFileParser()
Method Detail

getTimeStamp

protected java.lang.String getTimeStamp()
Returns a time stamp.

Returns:
a String representing the time stamp value

convert_3code_1code

public java.lang.Character convert_3code_1code(java.lang.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(java.io.InputStream inStream)
                       throws java.io.IOException
parse a PDB file and return a datastructure implementing PDBStructure interface.

Parameters:
inStream - an InputStream object
Returns:
a Structure object
Throws:
java.io.IOException

parsePDBFile

public Structure parsePDBFile(java.io.BufferedReader buf)
                       throws java.io.IOException
parse a PDB file and return a datastructure implementing PDBStructure interface.

Parameters:
buf - a BufferedReader object
Returns:
the Structure object
Throws:
java.io.IOException - ...