Package org.openscience.cdk.io
Class PDBReader
- 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.PDBReader
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- All Implemented Interfaces:
Closeable
,AutoCloseable
,IChemObjectIO
,IChemObjectReader
,ISimpleChemObjectReader
public class PDBReader extends DefaultChemObjectReader
Reads the contents of a PDBFile.A description can be found at http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html.
- Author:
- Edgar Luttmann, Bradley Smith <bradley@baysmith.com>, Martin Eklund <martin.eklund@farmbio.uu.se>, Ola Spjuth <ola.spjuth@farmbio.uu.se>, Gilleain Torrance <gilleain.torrance@gmail.com>
- This class is affected by these bug(s):
- 1714141 1794439
- Source code:
- main
- Belongs to CDK module:
- pdb
- Keywords:
- file format, PDB
- Created on:
- 2001-08-06
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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 PDBReader()
PDBReader(InputStream oIn)
Constructs a new PDBReader that can read Molecules from a given InputStream.PDBReader(Reader oIn)
Constructs a new PDBReader that can read Molecules from a given Reader.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description boolean
accepts(Class<? extends IChemObject> classObject)
Returns whether the givenIChemObject
can be read or written.void
close()
Closes this IChemObjectIO's resources.void
customizeJob()
IResourceFormat
getFormat()
Returns theIResourceFormat
class for this IO class.<T extends IChemObject>
Tread(T oObj)
Takes an object which subclasses IChemObject, e.g.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
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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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PDBReader
public PDBReader(InputStream oIn)
Constructs a new PDBReader that can read Molecules from a given InputStream.- Parameters:
oIn
- The InputStream to read from
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PDBReader
public PDBReader(Reader oIn)
Constructs a new PDBReader that can read Molecules from a given Reader.- Parameters:
oIn
- The Reader to read from
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PDBReader
public PDBReader()
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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 input) 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> classObject)
Description copied from interface:IChemObjectIO
Returns whether the givenIChemObject
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.
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read
public <T extends IChemObject> T read(T oObj) throws CDKException
Takes an object which subclasses IChemObject, e.g. Molecule, and will read this (from file, database, internet etc). If the specific implementation does not support a specific IChemObject it will throw an Exception.- Parameters:
oObj
- The object that subclasses IChemObject- Returns:
- The IChemObject read
- Throws:
CDKException
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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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customizeJob
public void customizeJob()
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