org.openscience.cdk.io

Class MDLV2000Writer

java.lang.Object

org.openscience.cdk.io.ChemObjectIO

org.openscience.cdk.io.DefaultChemObjectWriter

org.openscience.cdk.io.MDLV2000Writer

All Implemented Interfaces:

Closeable, AutoCloseable, IChemObjectIO, IChemObjectWriter

public class MDLV2000Writer
extends DefaultChemObjectWriter

Writes MDL molfiles, which contains a single molecule (see [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]). For writing a MDL molfile you can this code:

 MDLV2000Writer writer = new MDLV2000Writer(
   new FileWriter(new File("output.mol"))
 );
 writer.write((IAtomContainer)molecule);
 writer.close();
 

The writer has two IO settings: one for writing 2D coordinates, even if 3D coordinates are given for the written data; the second writes aromatic bonds as bond type 4, which is, strictly speaking, a query bond type, but my many tools used to reflect aromaticity. The full IO setting API is explained in CDK News [Willighagen, E.L., Customizing file IO, CDK News, 2004, 1:2-4]. One programmatic option to set the option for writing 2D coordinates looks like:

 Properties customSettings = new Properties();
 customSettings.setProperty(
  "ForceWriteAs2DCoordinates", "true"
 );
 PropertiesListener listener =
   new PropertiesListener(customSettings);
 writer.addChemObjectIOListener(listener);
 

Source code:

master

IO options:

Name	Question	Default
WriteQueryFormatValencies	Should valencies be written in the MDL Query format? (deprecated)	false
ForceWriteAs2DCoordinates	Should coordinates always be written as 2D?	false
WriteAromaticBondTypes	Should aromatic bonds be written as bond type 4?	false

Belongs to CDK module:

io

Keywords:

file format, MDL molfile

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MDLV2000Writer.SPIN_MULTIPLICITY Enumeration of all valid radical values.

Constructor Summary

Constructors

Constructor and Description
MDLV2000Writer()
MDLV2000Writer(OutputStream output) Constructs a new MDLWriter that can write an IAtomContainer to a given OutputStream.
MDLV2000Writer(Writer out) Constructs a new MDLWriter that can write an IAtomContainer to the MDL molfile format.

Method Summary

Methods

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.
void	customizeJob()
protected static String	formatMDLFloat(float fl) Formats a float to fit into the connectiontable and changes it to a String.
protected static String	formatMDLInt(int i, int l) Formats an integer to fit into the connection table and changes it to a String.
protected static String	formatMDLString(String s, int le) Formats a String to fit into the connectiontable.
IResourceFormat	getFormat() Returns the IResourceFormat class for this IO class.
void	setWriteAromaticBondTypes(boolean val) Convenience method to set the option for writing aromatic bond types.
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 a IChemObject to the MDL molfile formated output.
void	writeMolecule(IAtomContainer container) Writes a Molecule to an OutputStream in MDL sdf format.

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

MDLV2000Writer

public MDLV2000Writer(Writer out)

Constructs a new MDLWriter that can write an IAtomContainer to the MDL molfile format.

Parameters:

out - The Writer to write to

MDLV2000Writer

public MDLV2000Writer(OutputStream output)

Constructs a new MDLWriter that can write an IAtomContainer to a given OutputStream.

Parameters:

output - The OutputStream to write to

MDLV2000Writer

public MDLV2000Writer()

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

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

Writes a IChemObject to the MDL molfile formated output. It can only output ChemObjects of type IChemFile, IChemObject and IAtomContainer.

Parameters:

object - IChemObject to write

Throws:

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

See Also:

accepts(Class)

writeMolecule

public void writeMolecule(IAtomContainer container)
                   throws Exception

Writes a Molecule to an OutputStream in MDL sdf format.

Parameters:

container - Molecule that is written to an OutputStream

Throws:

Exception

formatMDLInt

protected static String formatMDLInt(int i,
                  int l)

Formats an integer to fit into the connection table and changes it to a String.

Parameters:

i - The int to be formated

l - Length of the String

Returns:

The String to be written into the connectiontable

formatMDLFloat

protected static String formatMDLFloat(float fl)

Formats a float to fit into the connectiontable and changes it to a String.

Parameters:

fl - The float to be formated

Returns:

The String to be written into the connectiontable

formatMDLString

protected static String formatMDLString(String s,
                     int le)

Formats a String to fit into the connectiontable.

Parameters:

s - The String to be formated

le - The length of the String

Returns:

The String to be written in the connectiontable

setWriteAromaticBondTypes

public void setWriteAromaticBondTypes(boolean val)

Convenience method to set the option for writing aromatic bond types.

Parameters:

val - the value.

customizeJob

public void customizeJob()