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joelib.io.types
Class XYZ  

java.lang.Object
  joelib.io.types.XYZ

All Implemented Interfaces:

joelib.io.MoleculeFileType

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public class XYZ

extends java.lang.Object

implements joelib.io.MoleculeFileType

Reader/Writer for XYZ files.

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Field Summary
private static java.lang.String	description
private static java.lang.String[]	extensions
private  long	lineCounter
private  int	linesRemaining
private  java.io.LineNumberReader	lnr
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  cformat.PrintfStream	ps

 

Constructor Summary

XYZ()           Constructor for the XYZ object

 

Method Summary
void	closeReader()           Description of the Method
void	closeWriter()           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)           Description of the Method
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	writeable()           Description of the Method

 

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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lnr

private java.io.LineNumberReader lnr

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ps

private cformat.PrintfStream ps

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linesRemaining

private int linesRemaining

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lineCounter

private long lineCounter

Constructor Detail

XYZ

public XYZ()

Constructor for the XYZ object

Method Detail

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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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

Description of the Method

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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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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