org.openscience.cdk.io

Class PDBReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.PDBReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class PDBReader
extends DefaultChemObjectReader

Reads the contents of a PDBFile.

A description can be found at http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html.

Author:

Edgar Luttmann, Bradley Smith <bradley@baysmith.com>, Martin Eklund <martin.eklund@farmbio.uu.se>, Ola Spjuth <ola.spjuth@farmbio.uu.se>, Gilleain Torrance <gilleain.torrance@gmail.com>

This class is affected by these bug(s):

1714141 1794439

Source code:

master

Belongs to CDK module:

pdb

Keywords:

file format, PDB

Created on:

2001-08-06

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Field Summary

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
PDBReader()
PDBReader(InputStream oIn) Constructs a new PDBReader that can read Molecules from a given InputStream.
PDBReader(Reader oIn) Constructs a new PDBReader that can read Molecules from a given Reader.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject) Returns whether the given IChemObject can be read or written.
void	close() Closes this IChemObjectIO's resources.
void	customizeJob()
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T oObj) Takes an object which subclasses IChemObject, e.g.
void	setReader(InputStream input) Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader input) Sets the Reader from which this ChemObjectReader should read the contents.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Constructor Detail

PDBReader

public PDBReader(InputStream oIn)

Constructs a new PDBReader that can read Molecules from a given InputStream.

Parameters:

oIn - The InputStream to read from

PDBReader

public PDBReader(Reader oIn)

Constructs a new PDBReader that can read Molecules from a given Reader.

Parameters:

oIn - The Reader to read from

PDBReader

public PDBReader()

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader input)
               throws CDKException

Description copied from interface: IChemObjectReader

Sets the Reader from which this ChemObjectReader should read the contents.

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

Description copied from interface: IChemObjectReader

Sets the InputStream from which this ChemObjectReader should read the contents.

Throws:

CDKException

accepts

public boolean accepts(Class<? extends IChemObject> classObject)

Description copied from interface: IChemObjectIO

Returns whether the given IChemObject can be read or written.

Parameters:

classObject - IChemObject of which is tested if it can be handled.

Returns:

true, if the IChemObject can be handled.

read

public <T extends IChemObject> T read(T oObj)
                               throws CDKException

Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.

Parameters:

oObj - The object that subclasses IChemObject

Returns:

The IChemObject read

Throws:

CDKException

close

public void close()
           throws IOException

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.

customizeJob

public void customizeJob()