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
-
-
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
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.void
close()
Flushes the output and closes this object.IResourceFormat
getFormat()
Returns theIResourceFormat
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
-
-
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 theIResourceFormat
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 givenIChemObject
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
-
-