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joelib.io.types
Class PDB  

java.lang.Object
  joelib.io.types.PDB

All Implemented Interfaces:

joelib.io.MoleculeFileType

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public class PDB

extends java.lang.Object

implements joelib.io.MoleculeFileType

Reader/Writer for Protein DataBank (PDB) files.

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

 

Constructor Summary

PDB()           Constructor for the Undefined 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
(package private) static boolean	parseAtomRecord(java.lang.String line, joelib.molecule.JOEMol mol, int chainNum)
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()           Description of the Method
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

Constructor Detail

PDB

public PDB()

Constructor for the Undefined object

Method Detail

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,
                    joelib.io.MoleculeIOException

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,
                    joelib.io.MoleculeIOException

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 of the Method

Specified by:

skipReaderEntry in interface joelib.io.MoleculeFileType

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write

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

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,
                     joelib.io.MoleculeIOException

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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parseAtomRecord

static boolean parseAtomRecord(java.lang.String line,
                               joelib.molecule.JOEMol mol,
                               int chainNum)

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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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