org.openscience.cdk.io

Class RGroupQueryWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.RGroupQueryWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class RGroupQueryWriter
extends DefaultChemObjectWriter

A writer for Symyx' Rgroup files (RGFiles).
An RGfile describes a single molecular query with Rgroups. Each RGfile is a combination of Ctabs defining the root molecule and each member of each Rgroup in the query.
This class relies on the MDLV2000Writer to create CTAB data blocks.

Author:

Mark Rijnbeek

Source code:

master

Belongs to CDK module:

io

Keywords:

Rgroup, R group, R-group

Constructor Summary

Constructors

Constructor and Description
RGroupQueryWriter() Zero argument constructor.
RGroupQueryWriter(Writer out) Constructs a new writer that can write an IRGroupQuery to the Symx RGFile format.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject) Returns true for accepted input types.
void	close() Flushes the output and closes this object.
IResourceFormat	getFormat() Returns output format.
void	setWriter(OutputStream output) Sets the writer to given output stream.
void	setWriter(Writer out) Sets the writer.
void	write(IChemObject object) The actual writing of the output.

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

RGroupQueryWriter

public RGroupQueryWriter(Writer out)

Constructs a new writer that can write an IRGroupQuery to the Symx RGFile format.

Parameters:

out - The Writer to write to

RGroupQueryWriter

public RGroupQueryWriter()

Zero argument constructor.

Method Detail

accepts

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

Returns true for accepted input types.

Parameters:

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

Returns:

true, if the IChemObject can be handled.

close

public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException - when the wrapper IO class cannot be closed.

getFormat

public IResourceFormat getFormat()

Returns output format.

setWriter

public void setWriter(OutputStream output)
               throws CDKException

Sets the writer to given output stream.

Throws:

CDKException

setWriter

public void setWriter(Writer out)
               throws CDKException

Sets the writer.

Throws:

CDKException

write

public void write(IChemObject object)
           throws CDKException

The actual writing of the output.

Parameters:

object - the object of which the content is outputted

Throws:

CDKException - could not write RGroup query