Package org.openscience.cdk.io

Class RGroupQueryReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.RGroupQueryReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class RGroupQueryReader
extends DefaultChemObjectReader

A reader 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.

The RGFile format is described in the manual "CTFile Formats" , Chapter 5.

Author:

Mark Rijnbeek

Source code:

main

Belongs to CDK module:

io

Keywords:

Rgroup, R group, R-group

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	Description
RGroupQueryReader()	Default constructor, input not set.
RGroupQueryReader(InputStream in)	Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.
RGroupQueryReader(Reader in)	Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.

Method Summary

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

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

RGroupQueryReader

public RGroupQueryReader()

Default constructor, input not set.

RGroupQueryReader

public RGroupQueryReader(InputStream in)

Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given InputStream.

Parameters:

in - The InputStream to read from.

RGroupQueryReader

public RGroupQueryReader(Reader in)

Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet from a given Reader.

Parameters:

in - The Reader to read from.

Method Detail

setReader

public void setReader(Reader input)
               throws CDKException

Sets the input Reader.

Parameters:

input - Reader object

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

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

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.

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.

read

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

Check input IChemObject and proceed to parse. Accepts/returns IChemObject of type RGroupQuery only.

Parameters:

object - class must be of type RGroupQuery

Returns:

IChemObject read from file

Throws:

CDKException - it is thrown if the type of information is not available from the input