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, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

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 <egonw@users.sf.net>

Source code:

master

Belongs to CDK module:

io

Keywords:

MDL molfile V3000

Created on:

2006

Requires:

java1.4+

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
MDLV3000Reader()
MDLV3000Reader(InputStream input)
MDLV3000Reader(InputStream input, IChemObjectReader.Mode mode)
MDLV3000Reader(Reader in)
MDLV3000Reader(Reader in, IChemObjectReader.Mode mode)

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject)
void	close()
String	exhaustStringTokenizer(StringTokenizer tokenizer)
IResourceFormat	getFormat()
boolean	isReady()
<T extends IChemObject> T	read(T object)
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)
void	setReader(Reader input)

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

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

public IResourceFormat getFormat()

setReader

public void setReader(Reader input)
               throws CDKException

Throws:

CDKException

setReader

public void setReader(InputStream input)
               throws CDKException

Throws:

CDKException

accepts

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

read

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

Throws:

CDKException

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

public void close()
           throws IOException

Throws:

IOException