public class PDBReader extends DefaultChemObjectReader
A description can be found at http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html.
IChemObjectReader.Mode
errorHandler, mode
Constructor and Description |
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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.
|
Modifier and Type | Method and Description |
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boolean |
accepts(Class<? extends IChemObject> classObject)
Returns whether the given
IChemObject can be read or written. |
void |
close()
Closes this IChemObjectIO's resources.
|
void |
customizeJob() |
IResourceFormat |
getFormat()
Returns the
IResourceFormat class for this IO class. |
<T extends IChemObject> |
read(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.
|
fireFrameRead, handleError, handleError, handleError, handleError, setErrorHandler, setReaderMode
addChemObjectIOListener, addSetting, addSettings, fireIOSettingQuestion, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
addChemObjectIOListener, addSetting, addSettings, getIOSettings, getListeners, getSetting, getSetting, getSettings, hasSetting, removeChemObjectIOListener
public PDBReader(InputStream oIn)
oIn
- The InputStream to read frompublic PDBReader(Reader oIn)
oIn
- The Reader to read frompublic PDBReader()
public IResourceFormat getFormat()
IChemObjectIO
IResourceFormat
class for this IO class.public void setReader(Reader input) throws CDKException
IChemObjectReader
CDKException
public void setReader(InputStream input) throws CDKException
IChemObjectReader
CDKException
public boolean accepts(Class<? extends IChemObject> classObject)
IChemObjectIO
IChemObject
can be read or written.classObject
- IChemObject
of which is tested if it can be handled.IChemObject
can be handled.public <T extends IChemObject> T read(T oObj) throws CDKException
oObj
- The object that subclasses IChemObjectCDKException
public void close() throws IOException
IChemObjectIO
IOException
- when the wrapper IO class cannot be closed.public void customizeJob()
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