org.openscience.cdk.io
Class MDLRXNV3000Reader

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.DefaultChemObjectReader
          org.openscience.cdk.io.MDLRXNV3000Reader

All Implemented Interfaces:

Closeable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@TestClass(value="org.openscience.cdk.io.MDLRXNV3000ReaderTest")
public class MDLRXNV3000Reader
extends DefaultChemObjectReader

Class that implements the new MDL mol format introduced in August 2002. The overall syntax is compatible with the old format, but I consider the format completely different, and thus implemented a separate Reader for it.

Author:

Egon Willighagen

Keywords:

MDL V3000

Created on:

2003-10-05

Requires:

java1.4+

Belongs to CDK module:

io

Source code:

cdk-1.4.x

Nested Class Summary

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

IChemObjectReader.Mode

Constructor Summary

MDLRXNV3000Reader()

MDLRXNV3000Reader(InputStream input)

MDLRXNV3000Reader(InputStream input, IChemObjectReader.Mode mode)

MDLRXNV3000Reader(Reader in)

MDLRXNV3000Reader(Reader in, IChemObjectReader.Mode mode)

Method Summary

boolean	accepts(Class classObject) Returns whether the given IChemObject can be read or written.
boolean	accepts(IChemObject object)
void	close() Closes this IChemObjectIO's resources.
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object) Reads an IChemObject of type "object" from input.
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

handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

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

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

Methods inherited from class java.lang.Object

equals, 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

MDLRXNV3000Reader

public MDLRXNV3000Reader(Reader in)

MDLRXNV3000Reader

public MDLRXNV3000Reader(Reader in,
                         IChemObjectReader.Mode mode)

MDLRXNV3000Reader

public MDLRXNV3000Reader(InputStream input)

MDLRXNV3000Reader

public MDLRXNV3000Reader(InputStream input,
                         IChemObjectReader.Mode mode)

MDLRXNV3000Reader

public MDLRXNV3000Reader()

Method Detail

getFormat

@TestMethod(value="testGetFormat")
public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

@TestMethod(value="testSetReader_Reader")
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

@TestMethod(value="testSetReader_InputStream")
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

@TestMethod(value="testAccepts")
public boolean accepts(Class 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

@TestMethod(value="testReadReactions1")
public <T extends IChemObject> T read(T object)
                           throws CDKException

Description copied from interface: ISimpleChemObjectReader

Reads an IChemObject of type "object" from input. The constructor of the actual implementation may take a Reader as input to get a very flexible reader that can read from string, files, etc.

Parameters:

object - the type of object to return

Returns:

returns an object of that contains the content (or part) of the input content

Throws:

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

accepts

@TestMethod(value="testAccepts")
public boolean accepts(IChemObject object)

close

@TestMethod(value="testClose")
public void close()
           throws IOException

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException