org.openscience.cdk.io
Class SMILESReader

java.lang.Object
  extended by org.openscience.cdk.io.DefaultChemObjectReader
      extended by org.openscience.cdk.io.SMILESReader
All Implemented Interfaces:
IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@TestClass(value="org.openscience.cdk.io.SMILESReaderTest")
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 "SMIdbNAME" property in the Molecule.

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

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

Nested Class Summary
 
Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
 
Constructor Summary
SMILESReader()
           
SMILESReader(InputStream input)
           
SMILESReader(Reader input)
           
SMILESReader(Reader input, IChemObjectBuilder builder)
          Construct a new reader from a Reader and a specified builder object.
 
Method Summary
 boolean accepts(Class classObject)
          Returns whether the given IChemObject can be read or written.
 void close()
          Closes this IChemObjectIO's resources.
 IResourceFormat getFormat()
          Returns the IResourceFormat class for this IO class.
<T extends IChemObject>
T
read(T object)
          reads the content from a XYZ input.
 void setReader(InputStream input)
          Sets the InputStream from which this ChemObjectReader should read the contents.
 void setReader(Reader input)
          Sets the Reader from which this ChemObjectReader should read the contents.
 
Methods inherited from class org.openscience.cdk.io.DefaultChemObjectReader
addChemObjectIOListener, getIOSettings, handleError, handleError, handleError, handleError, removeChemObjectIOListener, setErrorHandler, setReaderMode
 
Methods inherited from class java.lang.Object
equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

SMILESReader

public SMILESReader(Reader input)

SMILESReader

public SMILESReader(Reader input,
                    IChemObjectBuilder builder)
Construct a new reader from a Reader and a specified builder object.

Parameters:
input - The Reader object from which to read structures
builder - the builder

SMILESReader

public SMILESReader(InputStream input)

SMILESReader

public SMILESReader()
Method Detail

getFormat

@TestMethod(value="testGetFormat")
public IResourceFormat getFormat()
Description copied from interface: IChemObjectIO
Returns the IResourceFormat class for this IO class.


setReader

@TestMethod(value="testSetReader_Reader")
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

@TestMethod(value="testSetReader_InputStream")
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

@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.

read

@TestMethod(value="testReading,testReadingSmiFile_1,testReadingSmiFile_2,testReadingSmiFile_3")
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 ChemFile

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:
IChemFile

close

@TestMethod(value="testClose")
public void close()
           throws IOException
Description copied from interface: IChemObjectIO
Closes this IChemObjectIO's resources.

Throws:
IOException