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
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
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionMDLRXNWriter
(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 TypeMethodDescriptionboolean
accepts
(Class<? extends IChemObject> classObject) Returns whether the givenIChemObject
can be read or written.void
close()
Flushes the output and closes this object.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
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
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Field Details
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OptWriteAgents
- See Also:
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rdFields
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Constructor Details
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MDLRXNWriter
Constructs a new MDLWriter that can write an array of Molecules to a Writer.- Parameters:
out
- The Writer to write to
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MDLRXNWriter
Constructs a new MDLWriter that can write an array of Molecules to a given OutputStream.- Parameters:
output
- The OutputStream to write to
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MDLRXNWriter
public MDLRXNWriter()
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Method Details
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getFormat
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class. -
setWriter
Description copied from interface:IChemObjectWriter
Sets the Writer from which this ChemObjectWriter should write the contents.- Throws:
CDKException
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setWriter
Description copied from interface:IChemObjectWriter
Sets the OutputStream from which this ChemObjectWriter should write the contents.- Throws:
CDKException
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setRdFields
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
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close
Flushes the output and closes this object.- Throws:
IOException
- when the wrapper IO class cannot be closed.
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accepts
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.
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write
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:
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