ambit2.core.io
Class MDLWriter

java.lang.Object
  org.openscience.cdk.io.DefaultChemObjectWriter
      ambit2.core.io.MDLWriter

All Implemented Interfaces:

org.openscience.cdk.io.IChemObjectIO, org.openscience.cdk.io.IChemObjectWriter

public class MDLWriter
extends org.openscience.cdk.io.DefaultChemObjectWriter

Copied here from CDK source tree in order to handle the aromatic bond issue (this code writes 4 as aromatic bond code); until a proper fix is available. Writes MDL mol files and SD files.

A MDL mol file contains a single molecule, whereas a MDL SD file contains one or more molecules. This class is capable of writing both mol files and SD files. The correct format is automatically chosen:

• if write(IChemObject) is called with a MoleculeSet as an argument a SD files is written
• if one of the two writeMolecule methods (either this one or writeMolecule(org.openscience.cdk.interfaces.IMolecule) that one}) is called the first time, a mol file is written
• if one of the two writeMolecule methods is called more than once the output is a SD file

Thus, to write several molecules to a single SD file you can either use write(IChemObject) and pass a MoleculeSet or you can repeatedly call one of the two writeMolecule methods.

For writing a MDL molfile you can this code:

 MDLWriter writer = new MDLWriter(new FileWriter(new File("output.mol")));
 writer.write((IMolecule)molecule);
 writer.close();
 

See {cdk.cite DAL92}. cdk.module io cdk.svnrev $Revision: 9587 $ cdk.keyword file format, MDL molfile cdk.bug 1524466

Field Summary

java.util.Map

sdFields

Constructor Summary

MDLWriter()

MDLWriter(java.io.OutputStream output)
Contructs a new MDLWriter that can write an array of Molecules to a given OutputStream.

MDLWriter(java.io.Writer out)
Contructs a new MDLWriter that can write an array of Molecules to a Writer.

Method Summary

boolean	accepts(java.lang.Class classObject)
void	close() Flushes the output and closes this object.
void	dontWriteAromatic() Method does not do anything until now.
org.openscience.cdk.io.formats.IResourceFormat	getFormat()
void	setSdFields(java.util.Map map) Here you can set a map which will be used to build sd fields in the file.
void	setWriter(java.io.OutputStream output)
void	setWriter(java.io.Writer out)
void	write(org.openscience.cdk.interfaces.IChemObject object) Writes a IChemObject to the MDL molfile formated output.
void	writeMolecule(org.openscience.cdk.interfaces.IMolecule container) Writes a Molecule to an OutputStream in MDL sdf format.

Methods inherited from class org.openscience.cdk.io.DefaultChemObjectWriter

addChemObjectIOListener, fireIOSettingQuestion, getIOSettings, removeChemObjectIOListener

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

sdFields

public java.util.Map sdFields

Constructor Detail

MDLWriter

public MDLWriter(java.io.Writer out)

Contructs a new MDLWriter that can write an array of Molecules to a Writer.

Parameters:

out - The Writer to write to

MDLWriter

public MDLWriter(java.io.OutputStream output)

Contructs a new MDLWriter that can write an array of Molecules to a given OutputStream.

Parameters:

output - The OutputStream to write to

MDLWriter

public MDLWriter()

Method Detail

getFormat

public org.openscience.cdk.io.formats.IResourceFormat getFormat()

setWriter

public void setWriter(java.io.Writer out)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

setWriter

public void setWriter(java.io.OutputStream output)
               throws org.openscience.cdk.exception.CDKException

Throws:

org.openscience.cdk.exception.CDKException

dontWriteAromatic

public void dontWriteAromatic()

Method does not do anything until now.

setSdFields

public void setSdFields(java.util.Map map)

Here you can set a map which will be used to build sd fields in the file. The entries will be translated to sd fields like this:
> <key>
> value
empty line

Parameters:

map - The map to be used, map of String-String pairs

close

public void close()
           throws java.io.IOException

Flushes the output and closes this object.

Throws:

java.io.IOException

accepts

public boolean accepts(java.lang.Class classObject)

write

public void write(org.openscience.cdk.interfaces.IChemObject object)
           throws org.openscience.cdk.exception.CDKException

Writes a IChemObject to the MDL molfile formated output. It can only output ChemObjects of type ChemFile, Molecule and MoleculeSet.

Parameters:

object - class must be of type ChemFile, Molecule or MoleculeSet.

Throws:

org.openscience.cdk.exception.CDKException

See Also:

ChemFile

writeMolecule

public void writeMolecule(org.openscience.cdk.interfaces.IMolecule container)
                   throws java.lang.Exception

Writes a Molecule to an OutputStream in MDL sdf format.

Parameters:

container - Molecule that is written to an OutputStream

Throws:

java.lang.Exception