org.openscience.cdk.io

Class SDFWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.SDFWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class SDFWriter
extends DefaultChemObjectWriter

Writes MDL SD files ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]). A MDL SD file contains one or more molecules, complemented by properties.

Source code:

master

IO options:

Name	Question	Default
ForceWriteAs2DCoordinates	Should coordinates always be written as 2D?	false
WriteAromaticBondTypes	Should aromatic bonds be written as bond type 4?	false
writeProperties	Should molecule properties be written as non-structural data	true
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated)	false
writeV3000	Write all records as V3000	false

Belongs to CDK module:

io

Keywords:

file format, MDL SD file

Constructor Summary

Constructors

Constructor and Description
SDFWriter()
SDFWriter(BufferedWriter wtr) Create an SDfile writer that will output directly to the provided buffered writer.
SDFWriter(OutputStream output) Create an SDfile writer, the provided output stream is wrapped in a UTF-8 buffered writer.
SDFWriter(OutputStream output, Set<String> propertiesToWrite) Constructs a new SdfWriter that can write to a given OutputStream.
SDFWriter(Set<String> propertiesToWrite) Writes SD-File to a String including the given properties
SDFWriter(Writer wtr) Create an SDfile writer, the provided writer is buffered if it's not an instance of BufferedWriter.
SDFWriter(Writer out, Set<String> propertiesToWrite) Constructs a new SDFWriter that writes to the given Writer.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject)
void	close() Flushes the output and closes this object.
void	customizeJob()
IResourceFormat	getFormat()
void	setAlwaysV3000(boolean val)
void	setWriter(OutputStream output)
void	setWriter(Writer out)
void	write(IChemObject object) Writes a IChemObject to the MDL SD file formated output.

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

SDFWriter

public SDFWriter(BufferedWriter wtr)

Create an SDfile writer that will output directly to the provided buffered writer.

Parameters:

wtr - writer

SDFWriter

public SDFWriter(Writer wtr)

Create an SDfile writer, the provided writer is buffered if it's not an instance of BufferedWriter. For flush control etc please create with BufferedWriter.

Parameters:

wtr - writer

SDFWriter

public SDFWriter(OutputStream output)

Create an SDfile writer, the provided output stream is wrapped in a UTF-8 buffered writer.

Parameters:

output - out stream

SDFWriter

public SDFWriter()

SDFWriter

public SDFWriter(Writer out,
                 Set<String> propertiesToWrite)

Constructs a new SDFWriter that writes to the given Writer.

Parameters:

out - The Writer to write to

SDFWriter

public SDFWriter(OutputStream output,
                 Set<String> propertiesToWrite)

Constructs a new SdfWriter that can write to a given OutputStream.

Parameters:

output - The OutputStream to write to

SDFWriter

public SDFWriter(Set<String> propertiesToWrite)

Writes SD-File to a String including the given properties

Method Detail

getFormat

public IResourceFormat getFormat()

setWriter

public void setWriter(Writer out)
               throws CDKException

Throws:

CDKException

setWriter

public void setWriter(OutputStream output)
               throws CDKException

Throws:

CDKException

close

public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException

accepts

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

write

public void write(IChemObject object)
           throws CDKException

Writes a IChemObject to the MDL SD file formated output. It can only output IChemObjects of type IChemFile, IAtomContainerSet and IAtomContainerSet.

Parameters:

object - an acceptable IChemObject

Throws:

CDKException

See Also:

accepts(Class)

setAlwaysV3000

public void setAlwaysV3000(boolean val)

customizeJob

public void customizeJob()