Package org.openscience.cdk.io

Class MDLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.MDLReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@Deprecated
public class MDLReader
extends DefaultChemObjectReader

Deprecated.

This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.

Reads a molecule from the original MDL MOL or SDF file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]. An SD files is read into a IChemSequence of IChemModel's. Each ChemModel will contain one Molecule. If the MDL molfile contains a property block, the MDLV2000Reader should be used.

If all z coordinates are 0.0, then the xy coordinates are taken as 2D, otherwise the coordinates are read as 3D.

The title of the MOL file is read and can be retrieved with:

   molecule.getProperty(CDKConstants.TITLE);
 

Author:

steinbeck, Egon Willighagen

See Also:

MDLV2000Reader

Source code:

main

IO options:

Name	Question	Default
ForceReadAs3DCoordinates	Should coordinates always be read as 3D?	false

Belongs to CDK module:

io

Keywords:

file format, MDL molfile, file format, SDF

Created on:

2000-10-02

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
MDLReader()	Deprecated.
MDLReader(InputStream in)	Deprecated. Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLReader(InputStream in, IChemObjectReader.Mode mode)	Deprecated.
MDLReader(Reader in)	Deprecated. Constructs a new MDLReader that can read Molecule from a given Reader.
MDLReader(Reader in, IChemObjectReader.Mode mode)	Deprecated.

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> classObject)	Deprecated. Returns whether the given IChemObject can be read or written.
void	close()	Deprecated. Closes this IChemObjectIO's resources.
void	customizeJob()	Deprecated.
IResourceFormat	getFormat()	Deprecated. Returns the IResourceFormat class for this IO class.
<T extends IChemObject> T	read(T object)	Deprecated. Takes an object which subclasses IChemObject, e.g.
void	setReader(InputStream input)	Deprecated. Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader input)	Deprecated. 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 Detail

MDLReader

public MDLReader()

Deprecated.

MDLReader

public MDLReader(InputStream in)

Deprecated.

Constructs a new MDLReader that can read Molecule from a given InputStream.

Parameters:

in - The InputStream to read from

MDLReader

public MDLReader(InputStream in,
                 IChemObjectReader.Mode mode)

Deprecated.

MDLReader

public MDLReader(Reader in)

Deprecated.

Constructs a new MDLReader that can read Molecule from a given Reader.

Parameters:

in - The Reader to read from

MDLReader

public MDLReader(Reader in,
                 IChemObjectReader.Mode mode)

Deprecated.

Method Detail

getFormat

public IResourceFormat getFormat()

Deprecated.

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader input)
               throws CDKException

Deprecated.

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

Deprecated.

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)

Deprecated.

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

Deprecated.

Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.

Parameters:

object - The object that subclasses IChemObject

Returns:

The IChemObject read

Throws:

CDKException

close

public void close()
           throws IOException

Deprecated.

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException - when the wrapper IO class cannot be closed.

customizeJob

public void customizeJob()

Deprecated.