gov.nih.ncats.molwitch.cdk

Class IdAwareSdfReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

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

org.openscience.cdk.io.iterator.IteratingSDFReader

gov.nih.ncats.molwitch.cdk.IdAwareSdfReader

All Implemented Interfaces:

Closeable, AutoCloseable, Iterator<org.openscience.cdk.interfaces.IAtomContainer>, org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectReader, org.openscience.cdk.io.iterator.IIteratingChemObjectReader<org.openscience.cdk.interfaces.IAtomContainer>

public class IdAwareSdfReader
extends org.openscience.cdk.io.iterator.IteratingSDFReader

And SDF/ Mol parser file parser that uses the first line in the header record as the ID. The CDK SDF reader doesn't parse the molecule names from the header.

Author:

katzelda

Nested Class Summary

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

org.openscience.cdk.io.IChemObjectReader.Mode

Field Summary

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

errorHandler, mode

Constructor Summary

Constructors

Constructor and Description
IdAwareSdfReader(BufferedReader in, org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Summary

Modifier and Type	Method and Description
boolean	hasNext()
org.openscience.cdk.interfaces.IAtomContainer	next()

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

close, customizeJob, getFormat, remove, setReader, setReader, setSkip

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

Constructor Detail

IdAwareSdfReader

public IdAwareSdfReader(BufferedReader in,
                        org.openscience.cdk.interfaces.IChemObjectBuilder builder)

Method Detail

hasNext

public boolean hasNext()

Specified by:

hasNext in interface Iterator<org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

hasNext in class org.openscience.cdk.io.iterator.IteratingSDFReader

next

public org.openscience.cdk.interfaces.IAtomContainer next()

Specified by:

next in interface Iterator<org.openscience.cdk.interfaces.IAtomContainer>

Overrides:

next in class org.openscience.cdk.io.iterator.IteratingSDFReader