Package 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:

main

IO options:

Name	Question	Default
AddStereo0d	Allow stereo created from parity value when no coordinates	true
AddStereoElements	Detect and create IStereoElements for the input.	true
InterpretHydrogenIsotopes	Should D and T be interpreted as hydrogen isotopes?	true
ForceReadAs3DCoordinates	Should coordinates always be read as 3D?	false

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	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	Description
boolean	accepts(Class<? extends IChemObject> 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(org.openscience.cdk.io.MDLV3000Reader.ReadState state)	Reads the atoms, coordinates and charges.
void	readBondBlock(IAtomContainer readData)	Reads the bond atoms, order and stereo configuration.
IAtomContainer	readConnectionTable(IChemObjectBuilder builder)
String	readHeader(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
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

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 Details

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 Details

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

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

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

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.

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(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
                  throws CDKException

Returns:

Last line read

Throws:

CDKException - when no file content is detected

readAtomBlock

public void readAtomBlock(org.openscience.cdk.io.MDLV3000Reader.ReadState state)
                   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

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.