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.

Source code:

main

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

Belongs to CDK module:

io

Keywords:

file format, MDL SD file

Field Summary

Fields
Modifier and Type Field Description

static String OptAlwaysV3000

static String OptTruncateLongData

static String OptWriteData

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> propertiesToWrite)`	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> propertiesToWrite)`	Constructs a new SDFWriter that writes to the given `Writer`.
`SDFWriter(Set<String> propertiesToWrite)`	Writes SD-File to a String including the given properties

Method Summary

All Methods Instance Methods Concrete Methods
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 Detail
  - 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
- 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()
```
    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

Modifier and Type	Field	Description
`static String`	`OptAlwaysV3000`
`static String`	`OptTruncateLongData`
`static String`	`OptWriteData`

Class SDFWriter

Field Summary

Constructor Summary

Method Summary

Methods inherited from class org.openscience.cdk.io.ChemObjectIO

Methods inherited from class java.lang.Object

Methods inherited from interface org.openscience.cdk.io.IChemObjectIO

Field Detail

OptAlwaysV3000

OptWriteData

OptTruncateLongData

Constructor Detail

SDFWriter

SDFWriter

SDFWriter

SDFWriter

SDFWriter

SDFWriter

SDFWriter

Method Detail

getFormat

setWriter

setWriter

close

accepts

write

setAlwaysV3000

customizeJob

flush