org.biojava.bio.structure.io
Class PDBFileReader

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

All Implemented Interfaces:

StructureIO, StructureIOFile

Direct Known Subclasses:

PDBSRSReader

public class PDBFileReader

extends Object

implements StructureIOFile

A PDB file parser.

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	getId()
String	getPath()
Structure	getStructure() load a structure from local file system and return a PDBStructure object requires pdb_code to be set earlier...
Structure	getStructure(String filename) open filename (does not support compressed files!) and returns a PDBStructure object
protected String	getTimeStamp()
Structure	parsePDBFile(BufferedReader buf)
Structure	parsePDBFile(InputStream inStream) parse a PDB file and return a datastructure implementing PDBStructure interface.
void	setId(String id)
void	setPath(String p)

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

setId

public void setId(String id)

Specified by:

setId in interface StructureIO

getId

public String getId()

Specified by:

getId in interface StructureIO

setPath

public void setPath(String p)

Specified by:

setPath in interface StructureIOFile

getPath

public String getPath()

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

getTimeStamp

protected String getTimeStamp()

parsePDBFile

public Structure parsePDBFile(InputStream inStream)
                       throws IOException,
                              PDBParseException

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

Throws:

IOException

PDBParseException

parsePDBFile

public Structure parsePDBFile(BufferedReader buf)
                       throws IOException,
                              PDBParseException

Throws:

IOException

PDBParseException

getStructure

public Structure getStructure()
                       throws IOException

load a structure from local file system and return a PDBStructure object requires pdb_code to be set earlier...

Specified by:

getStructure in interface StructureIO

Throws:

IOException

getStructure

public Structure getStructure(String filename)
                       throws IOException

open filename (does not support compressed files!) and returns a PDBStructure object

Specified by:

getStructure in interface StructureIO

Throws:

IOException