org.openscience.cdk.io

Class MDLRXNWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.MDLRXNWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class MDLRXNWriter
extends DefaultChemObjectWriter

Writes a reaction to a MDL rxn or SDF file. Attention: Stoichiometric coefficients have to be natural numbers.

 MDLRXNWriter writer = new MDLRXNWriter(new FileWriter(new File("output.mol")));
 writer.write((Molecule)molecule);
 writer.close();
 

See [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].

Source code:

master

Belongs to CDK module:

io

Keywords:

file format, MDL RXN file

Field Summary

Fields

Modifier and Type	Field and Description
Map<String,Object>	rdFields

Constructor Summary

Constructors

Constructor and Description
MDLRXNWriter()
MDLRXNWriter(OutputStream output) Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.
MDLRXNWriter(Writer out) Constructs a new MDLWriter that can write an array of Molecules to a Writer.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> classObject)
void	close() Flushes the output and closes this object.
IResourceFormat	getFormat()
void	setRdFields(Map<String,Object> map) Here you can set a map which will be used to build rd fields in the file.
void	setWriter(OutputStream output)
void	setWriter(Writer out)
void	write(IChemObject object) Writes a IChemObject to the MDL RXN 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

rdFields

public Map<String,Object> rdFields

Constructor Detail

MDLRXNWriter

public MDLRXNWriter(Writer out)

Constructs a new MDLWriter that can write an array of Molecules to a Writer.

Parameters:

out - The Writer to write to

MDLRXNWriter

public MDLRXNWriter(OutputStream output)

Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.

Parameters:

output - The OutputStream to write to

MDLRXNWriter

public MDLRXNWriter()

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

setRdFields

public void setRdFields(Map<String,Object> map)

Here you can set a map which will be used to build rd fields in the file. The entries will be translated to rd fields like this:
> <key>
> value
empty line

Parameters:

map - The map to be used, map of String-String pairs

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 RXN file formated output. It can only output ChemObjects of type Reaction

Parameters:

object - class must be of type Molecule or MoleculeSet.

Throws:

CDKException

See Also:

ChemFile