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:

IteratingSMILESReader

Source code:

master

Belongs to CDK module:

smiles

Keywords:

file format, SMILES

Nested Class Summary

Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader

IChemObjectReader.Mode

Field Summary

Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
SMILESReader()
SMILESReader(InputStream input)
SMILESReader(Reader input) Construct a new reader from a Reader and a specified builder object.

Method Summary

Modifier and Type	Method and Description
boolean	accepts(Class<? extends IChemObject> 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

fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode

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

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 Detail

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:

IChemFile

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.