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joelib.io.types
Class ClearTextFormat  

java.lang.Object
  joelib.io.types.ClearTextFormat

All Implemented Interfaces:

joelib.io.MoleculeFileType

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public class ClearTextFormat

extends java.lang.Object

implements joelib.io.MoleculeFileType

Reader/Writer for ClearTeXt (CTX) files. For speeding up descriptor molecule files have a look at the joelib.desc.ResultFactory.

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Field Summary
static java.lang.String	ASYM_BOND_PROPERTY_INDEX           Data element for storing the access information for the asymmetric bond properties.
private static int	ATOM_PROPERTY
private static int	BOND_PROPERTY
private static java.lang.String	description
private static int	ENSEMBLE_PROPERTY
private static java.lang.String[]	extensions
private  java.io.LineNumberReader	lnr
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private static int	MOLECULE_PROPERTY
private  cformat.PrintfStream	ps

 

Constructor Summary

ClearTextFormat()

 

Method Summary
void	closeReader()           Description of the Method
void	closeWriter()           Description of the Method
private  boolean	getProperty(joelib.molecule.JOEMol mol, int propType)           Gets the property attribute of the ClearTextFormat object.
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)           Loads a ClearTextFile.
boolean	read(joelib.molecule.JOEMol mol, java.lang.String title)           Loads an molecule in ClearTextFile 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	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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ATOM_PROPERTY

private static final int ATOM_PROPERTY

See Also:

Constant Field Values

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BOND_PROPERTY

private static final int BOND_PROPERTY

See Also:

Constant Field Values

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MOLECULE_PROPERTY

private static final int MOLECULE_PROPERTY

See Also:

Constant Field Values

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ENSEMBLE_PROPERTY

private static final int ENSEMBLE_PROPERTY

See Also:

Constant Field Values

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ASYM_BOND_PROPERTY_INDEX

public static final java.lang.String ASYM_BOND_PROPERTY_INDEX

Data element for storing the access information for the asymmetric bond properties. index1=ctxID index2=idAtom1 index3=idAtom2 index4=singleEntryID The singleEntryID starts with 0. It's the internal id number which is used in JOELib.

See Also:

Constant Field Values

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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

Constructor Detail

ClearTextFormat

public ClearTextFormat()

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,
                    joelib.io.MoleculeIOException

Loads a ClearTextFile. Attention: bond properties can have the twice of the size of atoms. Use the CTX_BOND_INDEX data element to get the correct bond indices for this properties !!! This causes from circumstance, that in JOELib bonds are not stored twice !!!

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,
                    joelib.io.MoleculeIOException

Loads an molecule in ClearTextFile format and sets the title. If title is null the title line in the molecule file is used. Attention: bond properties can have the twice of the size of atoms. Use the CTX_BOND_INDEX data element to get the correct bond indices for this properties !!! This causes from circumstance, that in JOELib bonds are not stored twice !!!

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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getProperty

private boolean getProperty(joelib.molecule.JOEMol mol,
                            int propType)
                     throws java.io.IOException

Gets the property attribute of the ClearTextFormat object. Attention: bond properties can have the twice of the size of atoms. Use the CTX_BOND_INDEX data element to get the correct bond indices for this properties !!! This causes from circumstance, that in JOELib bonds are not stored twice !!!

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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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