Package org.openscience.cdk.io
Class CIFReader
- java.lang.Object
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- org.openscience.cdk.io.ChemObjectIO
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- org.openscience.cdk.io.DefaultChemObjectReader
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- org.openscience.cdk.io.CIFReader
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- 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
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Nested Class Summary
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Nested classes/interfaces inherited from interface org.openscience.cdk.io.IChemObjectReader
IChemObjectReader.Mode
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Field Summary
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Fields inherited from class org.openscience.cdk.io.DefaultChemObjectReader
errorHandler, mode
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Constructor Summary
Constructors Constructor Description CIFReader()
CIFReader(InputStream input)
CIFReader(Reader input)
Create an CIF like file reader.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accepts(Class<? extends IChemObject> testClass)
Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.IResourceFormat
getFormat()
Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread(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
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Methods inherited from class org.openscience.cdk.io.ChemObjectIO
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.openscience.cdk.io.IChemObjectIO
addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
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Constructor Detail
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CIFReader
public CIFReader(Reader input)
Create an CIF like file reader.- Parameters:
input
- source of CIF data
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CIFReader
public CIFReader(InputStream input)
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CIFReader
public CIFReader()
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Method Detail
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getFormat
public IResourceFormat getFormat()
Description copied from interface:IChemObjectIO
Returns theIResourceFormat
class for this IO class.
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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
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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
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accepts
public boolean accepts(Class<? extends IChemObject> testClass)
Description copied from interface:IChemObjectIO
Returns whether the givenIChemObject
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.
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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
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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.
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