Package org.openscience.cdk.io.iterator

Class IteratingSMILESReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader<IAtomContainer>

org.openscience.cdk.io.iterator.IteratingSMILESReader

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator<IAtomContainer>, IChemObjectIO, IChemObjectReader, IIteratingChemObjectReader<IAtomContainer>

public class IteratingSMILESReader
extends DefaultIteratingChemObjectReader<IAtomContainer>

Iterating SMILES file reader. It allows to iterate over all molecules in the SMILES file, without being read into memory all. Suitable for very large SMILES files. These SMILES files are expected to have one molecule on each line. If a line could not be parsed and empty molecule is returned and the property BAD_SMILES_INPUT is set to the attempted input. The error is also logged.

For parsing each SMILES it still uses the normal SMILESReader.

Author:

Egon Willighagen <egonw@sci.kun.nl>

See Also:

SMILESReader

Source code:

main

Belongs to CDK module:

smiles

Keywords:

file format, SMILES

Created on:

2004-12-16

Nested Class Summary

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

IChemObjectReader.Mode

Field Summary

Fields

Modifier and Type	Field	Description
static String	BAD_SMILES_INPUT	Store the problem input as a property.

Fields inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

errorHandler, mode

Constructor Summary

Constructors

Constructor	Description
IteratingSMILESReader(InputStream in, IChemObjectBuilder builder)	Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.
IteratingSMILESReader(Reader in, IChemObjectBuilder builder)	Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

Method Summary

Modifier and Type	Method	Description
void	close()	Close the reader.
IResourceFormat	getFormat()	Get the format for this reader.
boolean	hasNext()	Checks whether there is another molecule to read.
IAtomContainer	next()	Get the next molecule from the stream.
void	remove()	File IO generally does not support removing of entries.
void	setReader(InputStream reader)	Sets the InputStream from which this ChemObjectReader should read the contents.
void	setReader(Reader reader)	Sets the Reader from which this ChemObjectReader should read the contents.

Methods inherited from class org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader

accepts, 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

Methods inherited from interface java.util.Iterator

forEachRemaining

Field Detail

BAD_SMILES_INPUT

public static final String BAD_SMILES_INPUT

Store the problem input as a property.

See Also:

Constant Field Values

Constructor Detail

IteratingSMILESReader

public IteratingSMILESReader(Reader in,
                             IChemObjectBuilder builder)

Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

Parameters:

in - The Reader to read from

builder - The builder to use

See Also:

DefaultChemObjectBuilder, SilentChemObjectBuilder

IteratingSMILESReader

public IteratingSMILESReader(InputStream in,
                             IChemObjectBuilder builder)

Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.

Parameters:

in - The input stream

builder - The builder

Method Detail

getFormat

public IResourceFormat getFormat()

Get the format for this reader.

Returns:

An instance of SMILESFormat

hasNext

public boolean hasNext()

Checks whether there is another molecule to read.

Returns:

true if there are molecules to read, false otherwise

next

public IAtomContainer next()

Get the next molecule from the stream.

Returns:

The next molecule

close

public void close()
           throws IOException

Close the reader.

Throws:

IOException - if there is an error during closing

remove

public void remove()

Description copied from class: DefaultIteratingChemObjectReader

File IO generally does not support removing of entries.

Specified by:

remove in interface Iterator<IAtomContainer>

Overrides:

remove in class DefaultIteratingChemObjectReader<IAtomContainer>

setReader

public void setReader(Reader reader)

Description copied from interface: IChemObjectReader

Sets the Reader from which this ChemObjectReader should read the contents.

setReader

public void setReader(InputStream reader)

Description copied from interface: IChemObjectReader

Sets the InputStream from which this ChemObjectReader should read the contents.