Package org.openscience.cdk.io

Class SMILESReader

java.lang.Object
org.openscience.cdk.io.ChemObjectIO
org.openscience.cdk.io.DefaultChemObjectReader
org.openscience.cdk.io.SMILESReader
All Implemented Interfaces:
Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader
public class SMILESReader extends DefaultChemObjectReader
This Reader reads files which has one SMILES string on each line, where the format is given as below: 
 COC ethoxy ethane
Thus first the SMILES, and then after the first space (or tab) on the line a title that is stored as CDKConstants.TITLE. For legacy comparability the title is also placed in a "SMIdbNAME" property. If a line is invalid an empty molecule is inserted into the container set. The molecule with have the prop IteratingSMILESReader.BAD_SMILES_INPUT set to the input line that could not be read.

For each line a molecule is generated, and multiple Molecules are read as MoleculeSet.

See Also:
Source code:
main
Belongs to CDK module:
smiles
Keywords:
file format, SMILES

  • Constructor Details

    • SMILESReader

      public SMILESReader(Reader input)
      Construct a new reader from a Reader and a specified builder object.
      Parameters:
      input - The Reader object from which to read structures

    • SMILESReader

      public SMILESReader(InputStream input)

    • SMILESReader

      public SMILESReader()

  • Method Details

    • getFormat

      public IResourceFormat getFormat()
      Description copied from interface: IChemObjectIO
      Returns the IResourceFormat class for this IO class.

    • setReader

      public void setReader(Reader input) throws CDKException
      Description copied from interface: IChemObjectReader
      Sets the Reader from which this ChemObjectReader should read the contents.
      Throws:
      CDKException

    • setReader

      public void setReader(InputStream input) throws CDKException
      Description copied from interface: IChemObjectReader
      Sets the InputStream from which this ChemObjectReader should read the contents.
      Throws:
      CDKException

    • 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.

    • read

      public <T extends IChemObject> T read(T object) throws CDKException
      Reads the content from a XYZ input. It can only return a IChemObject of type IChemFile.
      Parameters:
      object - class must be of type ChemFile
      Returns:
      returns an object of that contains the content (or part) of the input content
      Throws:
      CDKException - it is thrown if the type of information is not available from the input
      See Also:

    • close

      public void close() throws IOException
      Description copied from interface: IChemObjectIO
      Closes this IChemObjectIO's resources.
      Throws:
      IOException - when the wrapper IO class cannot be closed.