Package org.openscience.cdk.io

Class PDBWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.PDBWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class PDBWriter
extends DefaultChemObjectWriter

Saves small molecules in a rudimentary PDB format. It does not allow writing of PDBProtein data structures.

Author:

Gilleain Torrance <gilleain.torrance@gmail.com>

Source code:

main

Belongs to CDK module:

pdb

Field Summary

Fields

Modifier and Type	Field	Description
String	ATOM_NAME_FORMAT
String	POSITION_FORMAT
String	RESIDUE_FORMAT
String	SERIAL_FORMAT

Constructor Summary

Constructors

Constructor	Description
PDBWriter()
PDBWriter(OutputStream output)
PDBWriter(Writer out)	Creates a PDB writer.

Method Summary

Modifier and Type	Method	Description
boolean	accepts(Class<? extends IChemObject> classObject)	Returns whether the given IChemObject can be read or written.
void	close()	Flushes the output and closes this object.
IResourceFormat	getFormat()	Returns the IResourceFormat class for this IO class.
void	setWriter(OutputStream output)	Sets the OutputStream from which this ChemObjectWriter should write the contents.
void	setWriter(Writer out)	Sets the Writer from which this ChemObjectWriter should write the contents.
void	write(IChemObject object)	Writes the content of "object" to output.
void	writeCrystal(ICrystal crystal)
void	writeMolecule(IAtomContainer molecule)	Writes a single frame in PDB format to the Writer.

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

Field Detail

SERIAL_FORMAT

public final String SERIAL_FORMAT

See Also:

Constant Field Values

ATOM_NAME_FORMAT

public final String ATOM_NAME_FORMAT

See Also:

Constant Field Values

POSITION_FORMAT

public final String POSITION_FORMAT

See Also:

Constant Field Values

RESIDUE_FORMAT

public final String RESIDUE_FORMAT

See Also:

Constant Field Values

Constructor Detail

PDBWriter

public PDBWriter()

PDBWriter

public PDBWriter(Writer out)

Creates a PDB writer.

Parameters:

out - the stream to write the PDB file to.

PDBWriter

public PDBWriter(OutputStream output)

Method Detail

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setWriter

public void setWriter(Writer out)
               throws CDKException

Description copied from interface: IChemObjectWriter

Sets the Writer from which this ChemObjectWriter should write the contents.

Throws:

CDKException

setWriter

public void setWriter(OutputStream output)
               throws CDKException

Description copied from interface: IChemObjectWriter

Sets the OutputStream from which this ChemObjectWriter should write the contents.

Throws:

CDKException

accepts

public boolean accepts(Class<? extends IChemObject> 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.

write

public void write(IChemObject object)
           throws CDKException

Description copied from interface: IChemObjectWriter

Writes the content of "object" to output.

Parameters:

object - the object of which the content is outputted

Throws:

CDKException - is thrown if the output does not support the data in the object

writeMolecule

public void writeMolecule(IAtomContainer molecule)
                   throws CDKException

Writes a single frame in PDB format to the Writer.

Parameters:

molecule - the Molecule to write

Throws:

CDKException

writeCrystal

public void writeCrystal(ICrystal crystal)
                  throws CDKException

Throws:

CDKException

close

public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException - when the wrapper IO class cannot be closed.