Package 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. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32].

Source code:

main

IO options:

Name	Question	Default
WriteAgents	Output agents in the RXN file	true

Belongs to CDK module:

io

Keywords:

file format, MDL RXN file

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor	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	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.
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
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)	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, 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

OptWriteAgents

public static final String OptWriteAgents

See Also:

Constant Field Values

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()

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<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 - 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 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