Package 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, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class SMILESWriter
extends DefaultChemObjectWriter

Writes the SMILES strings to a plain text file.

Source code:

main

IO options:

Name	Question	Default
SmilesFlavor	Output SMILES flavor, binary option	12551944
WriteTitle	Write the molecule title after the SMILES	true
UseAromaticity	Should aromaticity information be stored in the SMILES?	false

Belongs to CDK module:

smiles

Keywords:

file format, SMILES

Constructor Summary

Constructors

Constructor	Description
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

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.
void	customizeJob()
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
void	setFlavor(int flav)
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	setWriteTitle(boolean val)
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, 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

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

setFlavor

public void setFlavor(int flav)

setWriteTitle

public void setWriteTitle(boolean val)

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

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 the content from object to output.

Parameters:

object - IChemObject of which the data is given as output.

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 given as output.

customizeJob

public void customizeJob()