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joelib.io.types
Class POVRay  

java.lang.Object
  joelib.io.types.POVRay

All Implemented Interfaces:

joelib.io.MoleculeFileType

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public class POVRay

extends java.lang.Object

implements joelib.io.MoleculeFileType

Reader/Writer for Persitance Of Vision Raytracer (POVRay) files.

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Field Summary
private  joelib.molecule.types.AtomPropertyColoring	aPropColoring
private  java.lang.String	atomProperty2Use
private  double	atomResizeFactor
static int	BALL_AND_STICK           Description of the Field
static java.lang.String	BALL_AND_STICK_S
private  double	biggerBondRadius
static int	DEFAULT_OUTPUT_TYPE           Description of the Field
private static java.lang.String	description           Description of the Field
private  joelib.data.JOEElementTable	etab
private static java.lang.String[]	extensions
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  double	maxX
private  double	maxY
private  double	maxZ
private  double	minX
private  double	minY
private  double	minZ
private  int	moleculeCounter
private  double	mx
private  double	my
private  double	mz
private  int	outputType
private  cformat.PrintfStream	ps
private  double	smallerBondRadius
static int	SPHERE           Description of the Field
static java.lang.String	SPHERE_S
static int	STICK           Description of the Field
static java.lang.String	STICK_S
private  boolean	usePropertyColoring
private static java.lang.String	version
private  boolean	writeAromaticRings
private  boolean	writePorbitals

 

Constructor Summary

POVRay()

 

Method Summary
void	closeReader()           Description of the Method
void	closeWriter()           Description of the Method
int	getOutputType()           Gets the outputType attribute of the POVRay object
private  void	initProperties()           Description of the Method
void	initReader(java.io.InputStream is)           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
void	setOutputType(int _outputType)           Sets the outputType attribute of the POVRay object
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
private  void	write2Buffer(joelib.molecule.JOEMol mol, java.lang.StringBuffer sb)           Description of the Method
boolean	writeable()           Description of the Method
private  void	writeAtoms(joelib.molecule.JOEMol mol, java.lang.StringBuffer sb)           Description of the Method
private  void	writeBonds(joelib.molecule.JOEMol mol, java.lang.StringBuffer sb)           Description of the Method
private  void	writeRings(joelib.molecule.JOEMol mol, java.lang.StringBuffer sb)           Description of the Method

 

Methods inherited from class java.lang.Object

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

 

Field Detail

BALL_AND_STICK

public static final int BALL_AND_STICK

Description of the Field

See Also:

Constant Field Values

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BALL_AND_STICK_S

public static final java.lang.String BALL_AND_STICK_S

See Also:

Constant Field Values

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SPHERE

public static final int SPHERE

Description of the Field

See Also:

Constant Field Values

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SPHERE_S

public static final java.lang.String SPHERE_S

See Also:

Constant Field Values

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STICK

public static final int STICK

Description of the Field

See Also:

Constant Field Values

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STICK_S

public static final java.lang.String STICK_S

See Also:

Constant Field Values

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DEFAULT_OUTPUT_TYPE

public static final int DEFAULT_OUTPUT_TYPE

Description of the Field

See Also:

Constant Field Values

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logger

private static org.apache.log4j.Category logger

Obtain a suitable logger.

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version

private static final java.lang.String version

See Also:

Constant Field Values

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description

private static final java.lang.String description

Description of the Field

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extensions

private static final java.lang.String[] extensions

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aPropColoring

private joelib.molecule.types.AtomPropertyColoring aPropColoring

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etab

private joelib.data.JOEElementTable etab

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ps

private cformat.PrintfStream ps

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atomProperty2Use

private java.lang.String atomProperty2Use

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usePropertyColoring

private boolean usePropertyColoring

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writeAromaticRings

private boolean writeAromaticRings

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writePorbitals

private boolean writePorbitals

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atomResizeFactor

private double atomResizeFactor

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biggerBondRadius

private double biggerBondRadius

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maxX

private double maxX

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maxY

private double maxY

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maxZ

private double maxZ

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minX

private double minX

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minY

private double minY

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minZ

private double minZ

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mx

private double mx

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my

private double my

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mz

private double mz

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smallerBondRadius

private double smallerBondRadius

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moleculeCounter

private int moleculeCounter

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outputType

private int outputType

Constructor Detail

POVRay

public POVRay()

Method Detail

setOutputType

public void setOutputType(int _outputType)

Sets the outputType attribute of the POVRay object

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getOutputType

public int getOutputType()

Gets the outputType attribute of the POVRay object

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closeReader

public void closeReader()
                 throws java.io.IOException

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 of the Method

Specified by:

closeWriter in interface joelib.io.MoleculeFileType

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initReader

public void initReader(java.io.InputStream is)
                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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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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write2Buffer

private void write2Buffer(joelib.molecule.JOEMol mol,
                          java.lang.StringBuffer sb)

Description of the Method

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writeAtoms

private void writeAtoms(joelib.molecule.JOEMol mol,
                        java.lang.StringBuffer sb)

Description of the Method

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writeBonds

private void writeBonds(joelib.molecule.JOEMol mol,
                        java.lang.StringBuffer sb)

Description of the Method

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writeRings

private void writeRings(joelib.molecule.JOEMol mol,
                        java.lang.StringBuffer sb)

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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