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joelib.io.types
Class ChemicalMarkupLanguage  

java.lang.Object
  joelib.io.types.ChemicalMarkupLanguage

All Implemented Interfaces:

joelib.io.types.cml.CMLWriterProperties, joelib.io.MoleculeFileType, joelib.io.PropertyWriter

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public class ChemicalMarkupLanguage

extends java.lang.Object

implements joelib.io.MoleculeFileType, joelib.io.PropertyWriter, joelib.io.types.cml.CMLWriterProperties

Reader/Writer for Chemical Markup Language (CML) files.

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Field Summary
private  joelib.io.types.cml.MoleculeFileCDO	cdo
static float	CML_VERSION_1
static float	CML_VERSION_2
private static float	cmlDefaultVersion
private  int	cmlOutputType
private  joelib.io.types.cml.CMLMoleculeWriter	cmlOutputWriter
static java.lang.String	DEFAULT_DELIMITER
private static java.lang.String	defaultDelimiter
private static java.lang.String	description
private  boolean	done
private  java.lang.String	dtdResourceDir
private static java.lang.String[]	extensions
private  boolean	forceFormalCharge
private  boolean	fragment
private  boolean	impliciteHydrogens
private  java.io.InputStreamReader	isr
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  boolean	moleculeReaded
static int	OUTPUT_ARRAY
static java.lang.String	OUTPUT_ARRAY_S
static int	OUTPUT_HUGE
static java.lang.String	OUTPUT_HUGE_S
static int	OUTPUT_LARGE
static java.lang.String	OUTPUT_LARGE_S
private  org.xml.sax.XMLReader	parser
private  boolean	partialCharge
private  java.io.PrintStream	ps
private  boolean	symmetryInformations

 

Constructor Summary

ChemicalMarkupLanguage()

 

Method Summary
void	closeReader()           Description of the Method
void	closeWriter()           Description of the Method
boolean	forceWriteFormalCharge()
float	getCMLversion()
static java.lang.String	getDefaultDelimiter()
private  void	initProperties()           Description of the Method
void	initReader(java.io.InputStream iStream)           Description of the Method
void	initWriter(java.io.OutputStream os)           Description of the Method
java.lang.String	inputDescription()           Description of the Method
java.lang.String[]	inputFileExtensions()           Description of the Method
java.lang.String	outputDescription()           Description of the Method
java.lang.String[]	outputFileExtensions()           Description of the Method
java.lang.String	read()           Reads an molecule entry as (unparsed) String representation.
boolean	read(joelib.molecule.JOEMol mol)           Description of the Method
boolean	read(joelib.molecule.JOEMol mol, java.lang.String title)           Loads an molecule in MDL SD-MOL format and sets the title.
boolean	readable()           Description of the Method
boolean	skipReaderEntry()           Skips an molecule or the rest of a molecule entry to grant the next read(JOEMol mol) invocation a proper starting position.
boolean	write(joelib.molecule.JOEMol mol)           Description of the Method
boolean	write(joelib.molecule.JOEMol mol, java.lang.String title)           Description of the Method
boolean	write(joelib.molecule.JOEMol mol, java.lang.String title, boolean writePairData, java.util.Vector attribs2write)           Writes a molecule with his JOEPairData .
boolean	writeable()           Description of the Method
boolean	writeImpliciteHydrogens()
boolean	writePartialCharge()
boolean	writeSymmetryInformations()

 

Methods inherited from class java.lang.Object

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

 

Field Detail

logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

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description

private static final java.lang.String description

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extensions

private static final java.lang.String[] extensions

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OUTPUT_HUGE

public static final int OUTPUT_HUGE

See Also:

Constant Field Values

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OUTPUT_LARGE

public static final int OUTPUT_LARGE

See Also:

Constant Field Values

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OUTPUT_ARRAY

public static final int OUTPUT_ARRAY

See Also:

Constant Field Values

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OUTPUT_HUGE_S

public static final java.lang.String OUTPUT_HUGE_S

See Also:

Constant Field Values

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OUTPUT_LARGE_S

public static final java.lang.String OUTPUT_LARGE_S

See Also:

Constant Field Values

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OUTPUT_ARRAY_S

public static final java.lang.String OUTPUT_ARRAY_S

See Also:

Constant Field Values

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CML_VERSION_1

public static final float CML_VERSION_1

See Also:

Constant Field Values

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CML_VERSION_2

public static final float CML_VERSION_2

See Also:

Constant Field Values

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DEFAULT_DELIMITER

public static final java.lang.String DEFAULT_DELIMITER

See Also:

Constant Field Values

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cmlDefaultVersion

private static float cmlDefaultVersion

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defaultDelimiter

private static java.lang.String defaultDelimiter

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cmlOutputWriter

private joelib.io.types.cml.CMLMoleculeWriter cmlOutputWriter

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isr

private java.io.InputStreamReader isr

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cdo

private joelib.io.types.cml.MoleculeFileCDO cdo

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ps

private java.io.PrintStream ps

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dtdResourceDir

private java.lang.String dtdResourceDir

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parser

private org.xml.sax.XMLReader parser

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done

private boolean done

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forceFormalCharge

private boolean forceFormalCharge

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fragment

private boolean fragment

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impliciteHydrogens

private boolean impliciteHydrogens

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moleculeReaded

private boolean moleculeReaded

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partialCharge

private boolean partialCharge

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symmetryInformations

private boolean symmetryInformations

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cmlOutputType

private int cmlOutputType

Constructor Detail

ChemicalMarkupLanguage

public ChemicalMarkupLanguage()

Method Detail

getCMLversion

public float getCMLversion()

Specified by:

getCMLversion in interface joelib.io.types.cml.CMLWriterProperties

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getDefaultDelimiter

public static java.lang.String getDefaultDelimiter()

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closeReader

public void closeReader()
                 throws java.io.IOException

Description copied from interface: joelib.io.MoleculeFileType

Description of the Method

Specified by:

closeReader in interface joelib.io.MoleculeFileType

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closeWriter

public void closeWriter()
                 throws java.io.IOException

Description copied from interface: joelib.io.MoleculeFileType

Description of the Method

Specified by:

closeWriter in interface joelib.io.MoleculeFileType

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forceWriteFormalCharge

public boolean forceWriteFormalCharge()

Specified by:

forceWriteFormalCharge in interface joelib.io.types.cml.CMLWriterProperties

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initReader

public void initReader(java.io.InputStream iStream)
                throws java.io.IOException

Description of the Method

Specified by:

initReader in interface joelib.io.MoleculeFileType

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initWriter

public void initWriter(java.io.OutputStream os)
                throws java.io.IOException

Description of the Method

Specified by:

initWriter in interface joelib.io.MoleculeFileType

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inputDescription

public java.lang.String inputDescription()

Description of the Method

Specified by:

inputDescription in interface joelib.io.MoleculeFileType

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inputFileExtensions

public java.lang.String[] inputFileExtensions()

Description of the Method

Specified by:

inputFileExtensions in interface joelib.io.MoleculeFileType

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outputDescription

public java.lang.String outputDescription()

Description of the Method

Specified by:

outputDescription in interface joelib.io.MoleculeFileType

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outputFileExtensions

public java.lang.String[] outputFileExtensions()

Description of the Method

Specified by:

outputFileExtensions in interface joelib.io.MoleculeFileType

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read

public java.lang.String read()
                      throws java.io.IOException

Reads an molecule entry as (unparsed) String representation.

Specified by:

read in interface joelib.io.MoleculeFileType

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read

public boolean read(joelib.molecule.JOEMol mol)
             throws java.io.IOException

Description of the Method

Specified by:

read in interface joelib.io.MoleculeFileType

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read

public boolean read(joelib.molecule.JOEMol mol,
                    java.lang.String title)
             throws java.io.IOException

Loads an molecule in MDL SD-MOL format and sets the title. If title is null the title line in the molecule file is used.

Specified by:

read in interface joelib.io.MoleculeFileType

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readable

public boolean readable()

Description of the Method

Specified by:

readable in interface joelib.io.MoleculeFileType

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skipReaderEntry

public boolean skipReaderEntry()
                        throws java.io.IOException

Description copied from interface: joelib.io.MoleculeFileType

Skips an molecule or the rest of a molecule entry to grant the next read(JOEMol mol) invocation a proper starting position. This method should always be called if you plan to throw an MoleculeIOException.

Specified by:

skipReaderEntry in interface joelib.io.MoleculeFileType

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write

public boolean write(joelib.molecule.JOEMol mol)
              throws java.io.IOException

Description of the Method

Specified by:

write in interface joelib.io.MoleculeFileType

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write

public boolean write(joelib.molecule.JOEMol mol,
                     java.lang.String title)
              throws java.io.IOException

Description of the Method

Specified by:

write in interface joelib.io.MoleculeFileType

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write

public boolean write(joelib.molecule.JOEMol mol,
                     java.lang.String title,
                     boolean writePairData,
                     java.util.Vector attribs2write)
              throws java.io.IOException

Writes a molecule with his JOEPairData .

Specified by:

write in interface joelib.io.PropertyWriter

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writeImpliciteHydrogens

public boolean writeImpliciteHydrogens()

Specified by:

writeImpliciteHydrogens in interface joelib.io.types.cml.CMLWriterProperties

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writePartialCharge

public boolean writePartialCharge()

Specified by:

writePartialCharge in interface joelib.io.types.cml.CMLWriterProperties

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writeSymmetryInformations

public boolean writeSymmetryInformations()

Specified by:

writeSymmetryInformations in interface joelib.io.types.cml.CMLWriterProperties

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writeable

public boolean writeable()

Description of the Method

Specified by:

writeable in interface joelib.io.MoleculeFileType

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initProperties

private void initProperties()

Description of the Method

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> joelib >> io >> [ types overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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