Package org.openscience.cdk.io

Class CIFReader

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectReader

org.openscience.cdk.io.CIFReader

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectReader, ISimpleChemObjectReader

public class CIFReader
extends DefaultChemObjectReader

This is not a reader for the CIF and mmCIF crystallographic formats. It is able, however, to extract some content from such files. It's very ad hoc, not written using any dictionary. So please complain if something is not working. In addition, the things it does read are considered experimental.

The CIF example on the IUCR website has been tested, as well as Crambin (1CRN) in the PDB database.

Author:

E.L. Willighagen

Source code:

main

Belongs to CDK module:

io

Keywords:

file format, CIF, file format, mmCIF

Created on:

2003-10-12

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
CIFReader()
CIFReader(InputStream input)
CIFReader(Reader input)	Create an CIF like file reader.

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> testClass)	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)	Read a ChemFile from input.
void	setReader(InputStream input)	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.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 Detail

CIFReader

public CIFReader(Reader input)

Create an CIF like file reader.

Parameters:

input - source of CIF data

CIFReader

public CIFReader(InputStream input)

CIFReader

public CIFReader()

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setReader

public void setReader(Reader reader)
               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> testClass)

Description copied from interface: IChemObjectIO

Returns whether the given IChemObject can be read or written.

Parameters:

testClass - 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

Read a ChemFile from input.

Parameters:

object - the type of object to return

Returns:

the content in a ChemFile object

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.