org.openscience.cdk.io
Class MDLV3000Reader

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.DefaultChemObjectReader
          org.openscience.cdk.io.MDLV3000Reader

All Implemented Interfaces:

Closeable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@TestClass(value="org.openscience.cdk.io.MDLV3000ReaderTest")
public class MDLV3000Reader
extends DefaultChemObjectReader

Class that implements the MDL mol V3000 format. This reader reads the element symbol and 2D or 3D coordinates from the ATOM block.

Author:

Egon Willighagen

Keywords:

MDL molfile V3000

Created on:

2006

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

MDLV3000Reader()

MDLV3000Reader(InputStream input)

MDLV3000Reader(InputStream input, IChemObjectReader.Mode mode)

MDLV3000Reader(Reader in)

MDLV3000Reader(Reader in, IChemObjectReader.Mode mode)

Method Summary

boolean	accepts(Class classObject) Returns whether the given IChemObject can be read or written.
void	close() Closes this IChemObjectIO's resources.
String	exhaustStringTokenizer(StringTokenizer tokenizer)
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
boolean	isReady()
<T extends IChemObject> T	read(T object) Reads an IChemObject of type "object" from input.
void	readAtomBlock(IAtomContainer readData) Reads the atoms, coordinates and charges.
void	readBondBlock(IAtomContainer readData) Reads the bond atoms, order and stereo configuration.
IAtomContainer	readConnectionTable(IChemObjectBuilder builder)
String	readHeader(IAtomContainer readData)
String	readLine()
IAtomContainer	readMolecule(IChemObjectBuilder builder)
void	readSGroup(IAtomContainer readData) Reads labels.
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

MDLV3000Reader

public MDLV3000Reader(Reader in)

MDLV3000Reader

public MDLV3000Reader(Reader in,
                      IChemObjectReader.Mode mode)

MDLV3000Reader

public MDLV3000Reader(InputStream input)

MDLV3000Reader

public MDLV3000Reader(InputStream input,
                      IChemObjectReader.Mode mode)

MDLV3000Reader

public MDLV3000Reader()

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

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

readMolecule

public IAtomContainer readMolecule(IChemObjectBuilder builder)
                            throws CDKException

Throws:

CDKException

readConnectionTable

public IAtomContainer readConnectionTable(IChemObjectBuilder builder)
                                   throws CDKException

Throws:

CDKException

readHeader

public String readHeader(IAtomContainer readData)
                  throws CDKException

Returns:

Last line read

Throws:

CDKException - when no file content is detected

readAtomBlock

public void readAtomBlock(IAtomContainer readData)
                   throws CDKException

Reads the atoms, coordinates and charges.

IMPORTANT: it does not support the atom list and its negation!

Throws:

CDKException

readBondBlock

public void readBondBlock(IAtomContainer readData)
                   throws CDKException

Reads the bond atoms, order and stereo configuration.

Throws:

CDKException

readSGroup

public void readSGroup(IAtomContainer readData)
                throws CDKException

Reads labels.

Throws:

CDKException

exhaustStringTokenizer

public String exhaustStringTokenizer(StringTokenizer tokenizer)

readLine

public String readLine()
                throws CDKException

Throws:

CDKException

isReady

public boolean isReady()
                throws CDKException

Throws:

CDKException

close

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

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException