Class 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:
NameQuestionDefault
SmilesFlavorOutput SMILES flavor, binary option12551944
WriteTitleWrite the molecule title after the SMILEStrue
UseAromaticityShould aromaticity information be stored in the SMILES?false
Belongs to CDK module:
smiles
Keywords:
file format, SMILES
  • Constructor Details

    • 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 Details

    • 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()