org.biojava.bio.structure.io
Class PDBFileReader

java.lang.Object
  extended by org.biojava.bio.structure.io.PDBFileReader
All Implemented Interfaces:
StructureIO, StructureIOFile

public class PDBFileReader
extends Object
implements StructureIOFile

A PDB file parser.

Author:
Andreas Prlic

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();
 }
 

Constructor Summary
PDBFileReader()
           
 
Method Summary
 void addExtension(String s)
          define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.
 String getPath()
          Returns the path value.
 Structure getStructure(File filename)
          opens filename, parses it and returns a Structure object
 Structure getStructure(String filename)
          opens filename, parses it and returns aStructure object .
 Structure getStructureById(String pdbId)
          load a structure from local file system and return a PDBStructure object
 void setPath(String p)
          directory where to find PDB files
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

PDBFileReader

public PDBFileReader()
Method Detail

setPath

public void setPath(String p)
directory where to find PDB files

Specified by:
setPath in interface StructureIOFile
Parameters:
p - a String specifying the path value

getPath

public String getPath()
Returns the path value.

Returns:
a String representing the path value
See Also:
setPath(java.lang.String)

addExtension

public void addExtension(String s)
define supported file extensions compressed extensions .Z,.gz do not need to be specified they are dealt with automatically.

Specified by:
addExtension in interface StructureIOFile
Parameters:
s - a String ...

getStructureById

public Structure getStructureById(String pdbId)
                           throws IOException
load a structure from local file system and return a PDBStructure object

Specified by:
getStructureById in interface StructureIO
Parameters:
pdbId - a String specifying the id value (PDB code)
Returns:
the Structure object
Throws:
IOException - ...

getStructure

public Structure getStructure(String filename)
                       throws IOException
opens filename, parses it and returns aStructure object .

Specified by:
getStructure in interface StructureIOFile
Parameters:
filename - a String
Returns:
the Structure object
Throws:
IOException - ...

getStructure

public Structure getStructure(File filename)
                       throws IOException
opens filename, parses it and returns a Structure object

Parameters:
filename - a File object
Returns:
the Structure object
Throws:
IOException - ...