ambit2.core.io

Class MDLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

ambit2.core.io.MDLReader

All Implemented Interfaces:

Closeable, AutoCloseable, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.ISimpleChemObjectReader

public class MDLReader
extends org.openscience.cdk.io.DefaultChemObjectReader

Reads a molecule from the original MDL MOL or SDF file . 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

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
MDLReader()
MDLReader(InputStream in) Constructs a new MDLReader that can read Molecule from a given InputStream.
MDLReader(InputStream in, org.openscience.cdk.io.IChemObjectReader.Mode mode)
MDLReader(Reader in) Constructs a new MDLReader that can read Molecule from a given Reader.
MDLReader(Reader in, org.openscience.cdk.io.IChemObjectReader.Mode mode)

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class classObject)
void	close()
void	customizeJob()
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
org.openscience.cdk.io.setting.IOSetting[]	getIOSettings()
org.openscience.cdk.interfaces.IChemObject	read(org.openscience.cdk.interfaces.IChemObject object) Takes an object which subclasses IChemObject, e.g.
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, 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, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Constructor Detail

MDLReader

public MDLReader()

MDLReader

public MDLReader(InputStream in)

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

Parameters:

in - The InputStream to read from

MDLReader

public MDLReader(InputStream in,
                 org.openscience.cdk.io.IChemObjectReader.Mode mode)

MDLReader

public MDLReader(Reader in)

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

Parameters:

in - The Reader to read from

MDLReader

public MDLReader(Reader in,
                 org.openscience.cdk.io.IChemObjectReader.Mode mode)

Method Detail

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

setReader

public void setReader(Reader input)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setReader

public void setReader(InputStream input)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

accepts

public boolean accepts(Class classObject)

read

public org.openscience.cdk.interfaces.IChemObject read(org.openscience.cdk.interfaces.IChemObject object)
                                                throws org.openscience.cdk.exception.CDKException

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:

org.openscience.cdk.exception.CDKException

close

public void close()
           throws IOException

Throws:

IOException

customizeJob

public void customizeJob()

getIOSettings

public org.openscience.cdk.io.setting.IOSetting[] getIOSettings()

Specified by:

getIOSettings in interface org.openscience.cdk.io.IChemObjectIO

Overrides:

getIOSettings in class org.openscience.cdk.io.ChemObjectIO