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joelib.data
Class JOEPhModel  

java.lang.Object
  joelib.data.JOEGlobalDataBase
      joelib.data.JOEPhModel

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public class JOEPhModel

extends JOEGlobalDataBase

Model for the protonation/deprotonation of molecules. The definition file can be defined in the joelib.data.JOEPhModel.resourceFile property in the wsi.ra.tool.PropertyHolder. The wsi.ra.tool.ResourceLoader loads the joelib.properties file for default.

Default:
joelib.data.JOEPhModel.resourceFile=joelib/data/plain/phmodel.txt

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Field Summary
private static java.lang.String	DEFAULT_RESOURCE
private static org.apache.log4j.Category	logger           Obtain a suitable logger.
private  java.util.Vector	matchList           Match list.
private static JOEPhModel	phmodel
private  java.util.Vector	seedChargeGM           Seed charges for the Gasteiger-Marsili partial charges.
private  java.util.Vector	transformation           SMARTS based transformation patterns.

 

Fields inherited from class joelib.data.JOEGlobalDataBase

initialized, resourceFile

 

Constructor Summary
private	JOEPhModel()           Constructor for the JOEPhModel object

 

Method Summary
void	assignSeedPartialCharge(joelib.molecule.JOEMol mol)           Description of the Method
void	correctForPH(joelib.molecule.JOEMol mol)           Corrects the molecule for PH.
void	finalize()           Description of the Method
static JOEPhModel	instance()           Description of the Method
void	parseLine(java.lang.String buffer)           Description of the Method

 

Methods inherited from class joelib.data.JOEGlobalDataBase

getLineCounter, init

 

Methods inherited from class java.lang.Object

clone, equals, 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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phmodel

private static JOEPhModel phmodel

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DEFAULT_RESOURCE

private static final java.lang.String DEFAULT_RESOURCE

See Also:

Constant Field Values

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matchList

private java.util.Vector matchList

Match list. java.util.Vector of int[1]java.util.Vector

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seedChargeGM

private java.util.Vector seedChargeGM

Seed charges for the Gasteiger-Marsili partial charges. java.util.Vector of SMARTSPatternFVec

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transformation

private java.util.Vector transformation

SMARTS based transformation patterns. java.util.Vector of JOEChemTransformation

Constructor Detail

JOEPhModel

private JOEPhModel()

Constructor for the JOEPhModel object

Method Detail

finalize

public void finalize()

Description of the Method

Overrides:

finalize in class JOEGlobalDataBase

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instance

public static JOEPhModel instance()

Description of the Method

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assignSeedPartialCharge

public void assignSeedPartialCharge(joelib.molecule.JOEMol mol)

Description of the Method

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correctForPH

public void correctForPH(joelib.molecule.JOEMol mol)

Corrects the molecule for PH. Changes the state of oxygen and nitrogen atoms, if it is allowed to change the formal charges of the atoms, that means if JOEMol.automaticFormalCharge() returns true

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parseLine

public void parseLine(java.lang.String buffer)

Description of the Method

Specified by:

parseLine in class JOEGlobalDataBase

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