org.biojava.bio.structure.io
Class PDBFileReader

java.lang.Object
  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 - ...