org.openscience.cdk.io.iterator
Class IteratingSDFReader

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.iterator.DefaultIteratingChemObjectReader<IAtomContainer>
          org.openscience.cdk.io.iterator.IteratingSDFReader

All Implemented Interfaces:

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

@TestClass(value="org.openscience.cdk.io.iterator.IteratingSDFReaderTest")
public class IteratingSDFReader
extends DefaultIteratingChemObjectReader<IAtomContainer>

Iterating MDL SDF reader. It allows to iterate over all molecules in the SD file, without reading them into memory first. Suitable for (very) large SDF files. For parsing the molecules in the SD file, it uses the MDLV2000Reader or MDLV3000Reader reader; it does not work for SDF files with MDL formats prior to the V2000 format.

Example use:

 File sdfFile = new File("../zinc-structures/ZINC_subset3_3D_charged_wH_maxmin1000.sdf");
 IteratingMDLReader reader = new IteratingMDLReader(
   new FileInputStream(sdfFile), DefaultChemObjectBuilder.getInstance()
 );
 while (reader.hasNext()) {
   IMolecule molecule = (IMolecule)reader.next();
 }
 

Author:

Egon Willighagen

See Also:

MDLV2000Reader, MDLV3000Reader

Keywords:

file format, MDL molfile, file format, SDF

Created on:

2003-10-19

Belongs to CDK module:

io

Source code:

cdk-1.4.x

Nested Class Summary

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

IChemObjectReader.Mode

Constructor Summary

IteratingSDFReader(InputStream in, IChemObjectBuilder builder)
Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.

IteratingSDFReader(InputStream in, IChemObjectBuilder builder, boolean skip)
Constructs a new IteratingMDLReader that can read Molecule from a given a InputStream.

IteratingSDFReader(Reader in, IChemObjectBuilder builder)
Constructs a new IteratingMDLReader that can read Molecule from a given Reader.

IteratingSDFReader(Reader in, IChemObjectBuilder builder, boolean skip)
Constructs a new IteratingMDLReader that can read Molecule from a given a Reader.

Method Summary

void	close() Closes this IChemObjectIO's resources.
void	customizeJob()
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
boolean	hasNext() Returns true if another IMolecule can be read.
IAtomContainer	next() Returns the next IMolecule.
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.
void	setSkip(boolean skip) Indicate whether the reader should skip over SDF records that cause problems.

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, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener

Methods inherited from class java.lang.Object

equals, 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

IteratingSDFReader

public IteratingSDFReader(Reader in,
                          IChemObjectBuilder builder)

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

Parameters:

in - The Reader to read from

builder - The builder

IteratingSDFReader

@TestMethod(value="testReadDataItems")
public IteratingSDFReader(InputStream in,
                                          IChemObjectBuilder builder)

Constructs a new IteratingMDLReader that can read Molecule from a given InputStream.

Parameters:

in - The InputStream to read from

builder - The builder

IteratingSDFReader

public IteratingSDFReader(InputStream in,
                          IChemObjectBuilder builder,
                          boolean skip)

Constructs a new IteratingMDLReader that can read Molecule from a given a InputStream. This constructor allows specification of whether the reader will skip 'null' molecules. If skip is set to false and a broken/corrupted molecule is read the iterating reader will stop at the broken molecule. However if skip is set to true then the reader will keep trying to read more molecules until the end of the file is reached.

Parameters:

in - the InputStream to read from

builder - builder to use

skip - whether to skip null molecules

IteratingSDFReader

public IteratingSDFReader(Reader in,
                          IChemObjectBuilder builder,
                          boolean skip)

Constructs a new IteratingMDLReader that can read Molecule from a given a Reader. This constructor allows specification of whether the reader will skip 'null' molecules. If skip is set to false and a broken/corrupted molecule is read the iterating reader will stop at the broken molecule. However if skip is set to true then the reader will keep trying to read more molecules until the end of the file is reached.

Parameters:

in - the Reader to read from

builder - builder to use

skip - whether to skip null molecules

Method Detail

getFormat

@TestMethod(value="testGetFormat")
public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

hasNext

public boolean hasNext()

Returns true if another IMolecule can be read.

setSkip

public void setSkip(boolean skip)

Indicate whether the reader should skip over SDF records that cause problems. If true the reader will fetch the next molecule

Parameters:

skip - ignore error molecules continue reading

next

public IAtomContainer next()

Returns the next IMolecule.

close

@TestMethod(value="testClose")
public void close()
           throws IOException

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException

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

@TestMethod(value="testSetReader_Reader")
public void setReader(Reader reader)

Description copied from interface: IChemObjectReader

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

setReader

@TestMethod(value="testSetReader_InputStream")
public void setReader(InputStream reader)

Description copied from interface: IChemObjectReader

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

customizeJob

public void customizeJob()