Package org.openscience.cdk.io

Class PCSubstanceXMLReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.PCSubstanceXMLReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class PCSubstanceXMLReader
extends DefaultChemObjectReader

Reads an object from ASN formated input for PubChem Compound entries. The following bits are supported: atoms.aid, atoms.element, bonds.aid1, bonds.aid2. Additionally, it extracts the InChI and canonical SMILES properties.

Source code:

main

Belongs to CDK module:

io

Keywords:

file format, PubChem Compound ASN

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	Description
PCSubstanceXMLReader()
PCSubstanceXMLReader(InputStream input)
PCSubstanceXMLReader(Reader input)	Construct a new reader from a Reader type object.

Method Summary

Modifier and Type	Method	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 an IChemObject of type "object" from 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 Details

PCSubstanceXMLReader

public PCSubstanceXMLReader(Reader input)
                     throws Exception

Construct a new reader from a Reader type object.

Parameters:

input - reader from which input is read

Throws:

Exception

PCSubstanceXMLReader

public PCSubstanceXMLReader(InputStream input)
                     throws Exception

Throws:

Exception

PCSubstanceXMLReader

public PCSubstanceXMLReader()
                     throws Exception

Throws:

Exception

Method Details

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

Description copied from interface: ISimpleChemObjectReader

Reads an IChemObject of type "object" from input. The constructor of the actual implementation may take a Reader as input to get a very flexible reader that can read from string, files, etc.

Parameters:

object - the type of object to return

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

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.