org.openscience.cdk.io

Class CMLWriter

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.CMLWriter

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class CMLWriter
extends DefaultChemObjectWriter

Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code. Chemical Markup Language is an XML-based file format (Murray-Rust, P. and Rzepa, H.S.. Journal of Chemical Information and Computer Sciences. 1999. 39). Output can be redirected to other Writer objects like StringWriter and FileWriter. An example:

   StringWriter output = new StringWriter();
   boolean makeFragment = true;
   CMLWriter cmlwriter = new CMLWriter(output, makeFragment);
   cmlwriter.write(molecule);
   cmlwriter.close();
   String cmlcode = output.toString();
 

Output to a file called "molecule.cml" can done with:

   FileWriter output = new FileWriter("molecule.cml");
   CMLWriter cmlwriter = new CMLWriter(output);
   cmlwriter.write(molecule);
   cmlwriter.close();
 

For atoms it outputs: coordinates, element type and formal charge. For bonds it outputs: order, atoms (2, or more) and wedges.

Author:

Egon Willighagen

See Also:

FileWriter, StringWriter

This class is affected by these bug(s):

1565563

Source code:

master

Belongs to CDK module:

libiocml

Keywords:

file format, CML

Requires:

java1.5+

Constructor Summary

Constructors

Constructor and Description
CMLWriter()
CMLWriter(OutputStream output)
CMLWriter(Writer writer) Constructs a new CMLWriter class.

Method Summary

Modifier and Type	Method and 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	registerCustomizer(ICMLCustomizer customizer)
void	setWriter(OutputStream output) Sets the OutputStream from which this ChemObjectWriter should write the contents.
void	setWriter(Writer writer) Sets the Writer from which this ChemObjectWriter should write the contents.
void	write(IChemObject object) Serializes the IChemObject to CML and redirects it to the output 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

Constructor Detail

CMLWriter

public CMLWriter(Writer writer)

Constructs a new CMLWriter class. Output will be stored in the Writer class given as parameter. The CML code will be valid CML code with a XML header. Only one object can be stored.

Parameters:

writer - Writer to redirect the output to.

CMLWriter

public CMLWriter(OutputStream output)

CMLWriter

public CMLWriter()

Method Detail

registerCustomizer

public void registerCustomizer(ICMLCustomizer customizer)

getFormat

public IResourceFormat getFormat()

Description copied from interface: IChemObjectIO

Returns the IResourceFormat class for this IO class.

setWriter

public void setWriter(Writer writer)
               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

close

public void close()
           throws IOException

Flushes the output and closes this object.

Throws:

IOException - when the wrapper IO class cannot be closed.

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

Serializes the IChemObject to CML and redirects it to the output Writer.

Parameters:

object - A Molecule of AtomContaineSet object

Throws:

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