Package 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. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]). A MDL SD file contains one or more molecules, complemented by properties.

IO options:

Name	Question	Default
WriteAromaticBondTypes	Should aromatic bonds be written as bond type 4?	false
WriteMajorIsotopes	Write atomic mass of any non-null atomic mass including major isotopes (e.g. [12]C)	true
writeProperties	Should molecule properties be written as non-structural data	true
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated)	false
TruncateLongData	Truncate long data files >200 characters	false
ProgramName	Program name to write at the top of the molfile header, should be exactly 8 characters long	CDK
ForceWriteAs2DCoordinates	Should coordinates always be written as 2D?	false
WriteDefaultProperties	Write trailing zero's on atom/bond property blocks even if they're not used.	true
writeV3000	Write all records as V3000	false

Keywords:

file format, MDL SD file

Field Summary

Fields

Modifier and Type	Field	Description
static final String	OptAlwaysV3000
static final String	OptTruncateLongData
static final String	OptWriteData
static final String	SD_RECORD_DELIM

Constructor Summary

Constructors

Constructor	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> acceptedSdTags)	Constructs a new SdfWriter that can write to a given OutputStream.
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> acceptedSdTags)	Constructs a new SDFWriter that writes to the given Writer.
SDFWriter(Set<String> acceptedSdTags)	Writes SD-File to a String including the given properties

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()	Flushes the output and closes this object.
void	customizeJob()
void	flush()
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
void	setAlwaysV3000(boolean val)
void	setWriter(OutputStream output)	Sets the OutputStream from which this ChemObjectWriter should write the contents.
void	setWriter(Writer out)	Sets the Writer from which this ChemObjectWriter should write the contents.
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

Field Details

OptAlwaysV3000

public static final String OptAlwaysV3000

See Also:

• Constant Field Values

OptWriteData

public static final String OptWriteData

See Also:

• Constant Field Values

OptTruncateLongData

public static final String OptTruncateLongData

See Also:

• Constant Field Values

SD_RECORD_DELIM

public static final String SD_RECORD_DELIM

See Also:

• Constant Field Values

Constructor Details

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> acceptedSdTags)

Constructs a new SDFWriter that writes to the given Writer.

Parameters:

out - The Writer to write to

SDFWriter

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

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

Parameters:

output - The OutputStream to write to

SDFWriter

public SDFWriter(Set<String> acceptedSdTags)

Writes SD-File to a String including the given properties

Method Details

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setWriter

public void setWriter(Writer out)
               throws CDKException

Description copied from interface: IChemObjectWriter

Sets the Writer from which this ChemObjectWriter should write the contents.

Throws:

CDKException

setWriter

public void setWriter(OutputStream output)
               throws CDKException

Description copied from interface: IChemObjectWriter

Sets the OutputStream from which this ChemObjectWriter should write the contents.

Throws:

CDKException

close

public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException - when the wrapper IO class cannot be closed.

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.

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 - is thrown if the output does not support the data in the object

See Also:

• accepts(Class)

setAlwaysV3000

public void setAlwaysV3000(boolean val)

customizeJob

public void customizeJob()

flush

public void flush()
           throws IOException

Throws:

IOException