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, IChemObjectIO, IChemObjectWriter

@TestClass(value="org.openscience.cdk.io.MDLRXNReaderTest")
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].

Keywords:

file format, MDL RXN file

Belongs to CDK module:

io

Source code:

cdk-1.4.x

Field Summary

Map

rdFields

Constructor Summary

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

boolean	accepts(Class classObject) Returns whether the given IChemObject can be read or written.
void	close() Flushes the output and closes this object.
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
void	setRdFields(Map map) Here you can set a map which will be used to build rd fields in the file.
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 RXN file formated output.

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

addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

equals, 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 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

@TestMethod(value="testGetFormat")
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

setRdFields

public void setRdFields(Map 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

@TestMethod(value="testClose")
public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException

accepts

@TestMethod(value="testAccepts")
public boolean accepts(Class 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 RXN file formated output. It can only output ChemObjects of type Reaction

Parameters:

object - class must be of type Molecule or MoleculeSet.

Throws:

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

See Also:

ChemFile