org.openscience.cdk.io
Class SMILESWriter

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.DefaultChemObjectWriter
          org.openscience.cdk.io.SMILESWriter

All Implemented Interfaces:

Closeable, IChemObjectIO, IChemObjectWriter

@TestClass(value="org.openscience.cdk.io.SMILESWriterTest")
public class SMILESWriter
extends DefaultChemObjectWriter

Writes the SMILES strings to a plain text file.

Keywords:

file format, SMILES

Belongs to CDK module:

smiles

Source code:

cdk-1.4.x

Constructor Summary

SMILESWriter()

SMILESWriter(FileOutputStream out)
Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream

SMILESWriter(OutputStream output)

SMILESWriter(Writer out)
Constructs a new SMILESWriter that can write a list of SMILES 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
void	customizeJob()
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
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 the content from object to output.
void	writeAtomContainer(IAtomContainer molecule) Writes the content from molecule to output.
void	writeAtomContainerSet(IAtomContainerSet som) Writes a list of molecules to an OutputStream

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

Constructor Detail

SMILESWriter

public SMILESWriter(Writer out)

Constructs a new SMILESWriter that can write a list of SMILES to a Writer

Parameters:

out - The Writer to write to

SMILESWriter

public SMILESWriter(OutputStream output)

SMILESWriter

public SMILESWriter()

SMILESWriter

public SMILESWriter(FileOutputStream out)

Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream

Parameters:

out - The OutputStream to write to

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

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 the content from object to output.

Parameters:

object - IChemObject of which the data is outputted.

Throws:

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

writeAtomContainerSet

public void writeAtomContainerSet(IAtomContainerSet som)

Writes a list of molecules to an OutputStream

Parameters:

som - MoleculeSet that is written to an OutputStream

writeAtomContainer

public void writeAtomContainer(IAtomContainer molecule)

Writes the content from molecule to output.

Parameters:

molecule - Molecule of which the data is outputted.

customizeJob

public void customizeJob()