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
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
ConstructorsConstructorDescriptionConstructs a new SMILESWriter that can write an list of SMILES to a given OutputStreamSMILESWriter
(OutputStream output) SMILESWriter
(Writer out) Constructs a new SMILESWriter that can write a list of SMILES 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.void
Returns theIResourceFormat
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
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
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 Details
-
SMILESWriter
Constructs a new SMILESWriter that can write a list of SMILES to a Writer- Parameters:
out
- The Writer to write to
-
SMILESWriter
-
SMILESWriter
public SMILESWriter() -
SMILESWriter
Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream- Parameters:
out
- The OutputStream to write to
-
-
Method Details
-
setFlavor
public void setFlavor(int flav) -
setWriteTitle
public void setWriteTitle(boolean val) -
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
-
setWriter
Description copied from interface:IChemObjectWriter
Sets the OutputStream from which this ChemObjectWriter should write the contents.- Throws:
CDKException
-
close
Flushes the output and closes this object.- Throws:
IOException
- when the wrapper IO class cannot be closed.
-
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.
-
write
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
Writes a list of molecules to an OutputStream.- Parameters:
som
- MoleculeSet that is written to an OutputStream
-
writeAtomContainer
Writes the content from molecule to output.- Parameters:
molecule
- Molecule of which the data is given as output.
-
customizeJob
public void customizeJob()
-