org.openscience.cdk.io
Class INChIPlainTextReader

java.lang.Object
  org.openscience.cdk.io.ChemObjectIO
      org.openscience.cdk.io.DefaultChemObjectReader
          org.openscience.cdk.io.INChIPlainTextReader

All Implemented Interfaces:

Closeable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

@TestClass(value="org.openscience.cdk.io.INChIPlainTextReaderTest")
public class INChIPlainTextReader
extends DefaultChemObjectReader

Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document. This reader parses output generated with INChI 1.12beta like:

 
 Input_File: "E:\Program Files\INChI\inchi-samples\Figure04.mol"
 
 Structure: 1
 INChI=1.12Beta/C6H6/c1-2-4-6-5-3-1/h1-6H
 AuxInfo=1.12Beta/0/N:1,2,3,4,5,6/E:(1,2,3,4,5,6)/rA:6CCCCCC/rB:s1;d1;d2;s3;s4d5;/rC:5.6378,-4.0013,0;5.6378,-5.3313,0;4.4859,-3.3363,0;4.4859,-5.9963,0;3.3341,-4.0013,0;3.3341,-5.3313,0;
 

Author:

Egon Willighagen

See Also:

INChIReader

Keywords:

file format, INChI, chemical identifier

Created on:

2004-08-01

Requires:

java1.4+

Belongs to CDK module:

extra

Source code:

cdk-1.4.x

Nested Class Summary

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

IChemObjectReader.Mode

Constructor Summary

INChIPlainTextReader()

INChIPlainTextReader(InputStream input)

INChIPlainTextReader(Reader input)
Construct a INChI reader from a Reader object.

Method Summary

boolean	accepts(Class 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 a 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

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

INChIPlainTextReader

public INChIPlainTextReader(Reader input)

Construct a INChI reader from a Reader object.

Parameters:

input - the Reader with the content

INChIPlainTextReader

public INChIPlainTextReader(InputStream input)

INChIPlainTextReader

public INChIPlainTextReader()

Method Detail

getFormat

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

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

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

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 input)
               throws CDKException

Description copied from interface: IChemObjectReader

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

Throws:

CDKException

accepts

@TestMethod(value="testAccepts")
public boolean accepts(Class 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 a IChemObject of type object from input. Supported types are: ChemFile.

Parameters:

object - type of requested IChemObject

Returns:

the content in a ChemFile object

Throws:

CDKException - it is thrown if the type of information is not available from the input

close

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

Description copied from interface: IChemObjectIO

Closes this IChemObjectIO's resources.

Throws:

IOException