ambit2.tautomers.tools

Class TautomerAnalysis

java.lang.Object

ambit2.tautomers.tools.TautomerAnalysis

public class TautomerAnalysis
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	TautomerAnalysis.Task

Field Summary

Fields

Modifier and Type	Field and Description
String	filePath
protected ArrayList<String>	fileRuleNames
boolean	FlagFilter
String	inputFileName
protected MoleculeFilter	molecularFilter
String	molFilterString
String	outFilePath
String	outFilePrefix
protected File[]	outFiles
String	outFileType
String	outputFileName
protected FileWriter[]	outWriters
protected int	records_error
protected int	records_processed
protected int	records_read
String	sep
TautomerAnalysis.Task	task
protected TautomerManager	tman

Constructor Summary

Constructors

Constructor and Description
TautomerAnalysis()

Method Summary

Modifier and Type	Method and Description
protected void	calcAllTautomersAndAllRanks(org.openscience.cdk.interfaces.IAtomContainer mol)
static double	calcTautomerRankCorrCoeff(double[] ranks, double[] energies)
static double	calcTautomerRankingMeasure(double[] ranks, double[] energies) This is a measure for the tautomer ranking based on a comparison with tautomers energies
static double	calcTautomerRankSpearmanCorrCoeff(double[] ranks, double[] energies, boolean isFractional)
protected void	closeWriters()
protected void	createOutWriter()
protected void	createRulePairsWriters()
protected FileWriter	createWriter(String fname)
protected void	createWriters()
protected void	doTask(org.openscience.cdk.interfaces.IAtomContainer mol)
protected void	generateRulePairs(org.openscience.cdk.interfaces.IAtomContainer mol)
protected String	getFileRuleName(String rname)
static int	getNumberOfDistinctValues(double[] values)
static double[]	getRanks(double[] values, boolean isFractionalRanking)
protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader<org.openscience.cdk.interfaces.IAtomContainer>	getReader(InputStream in, String extension)
protected void	outputTautomerPair(TautomerUtils.TautomerPair tp)
protected void	printSmiles(org.openscience.cdk.interfaces.IAtomContainer mol)
int	process()
void	setMoleculeFilter(String molFilterString)

Methods inherited from class java.lang.Object

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

Field Detail

filePath

public String filePath

outFilePath

public String outFilePath

inputFileName

public String inputFileName

outputFileName

public String outputFileName

outFilePrefix

public String outFilePrefix

outFileType

public String outFileType

molFilterString

public String molFilterString

task

public TautomerAnalysis.Task task

FlagFilter

public boolean FlagFilter

tman

protected TautomerManager tman

molecularFilter

protected MoleculeFilter molecularFilter

records_read

protected int records_read

records_processed

protected int records_processed

records_error

protected int records_error

outWriters

protected FileWriter[] outWriters

outFiles

protected File[] outFiles

fileRuleNames

protected ArrayList<String> fileRuleNames

sep

public String sep

Constructor Detail

TautomerAnalysis

public TautomerAnalysis()

Method Detail

setMoleculeFilter

public void setMoleculeFilter(String molFilterString)
                       throws Exception

Parameters:

molFilterString - expression which defines the filter e.g. "#Mol=[1,100];NA=[1,10]"

Throws:

Exception

process

public int process()
            throws Exception

Returns:

number of read structure records

Throws:

Exception

getReader

protected org.openscience.cdk.io.iterator.IIteratingChemObjectReader<org.openscience.cdk.interfaces.IAtomContainer> getReader(InputStream in,
                                                                                                                              String extension)
                                                                                                                       throws org.openscience.cdk.exception.CDKException,
                                                                                                                              AmbitIOException

Throws:

org.openscience.cdk.exception.CDKException

AmbitIOException

createWriters

protected void createWriters()
                      throws Exception

Throws:

Exception

createWriter

protected FileWriter createWriter(String fname)
                           throws Exception

Throws:

Exception

createRulePairsWriters

protected void createRulePairsWriters()
                               throws Exception

Throws:

Exception

createOutWriter

protected void createOutWriter()
                        throws Exception

Throws:

Exception

closeWriters

protected void closeWriters()

doTask

protected void doTask(org.openscience.cdk.interfaces.IAtomContainer mol)
               throws Exception

Throws:

Exception

printSmiles

protected void printSmiles(org.openscience.cdk.interfaces.IAtomContainer mol)
                    throws Exception

Throws:

Exception

generateRulePairs

protected void generateRulePairs(org.openscience.cdk.interfaces.IAtomContainer mol)
                          throws Exception

Throws:

Exception

outputTautomerPair

protected void outputTautomerPair(TautomerUtils.TautomerPair tp)

calcAllTautomersAndAllRanks

protected void calcAllTautomersAndAllRanks(org.openscience.cdk.interfaces.IAtomContainer mol)
                                    throws Exception

Throws:

Exception

getFileRuleName

protected String getFileRuleName(String rname)

calcTautomerRankingMeasure

public static double calcTautomerRankingMeasure(double[] ranks,
                                                double[] energies)

This is a measure for the tautomer ranking based on a comparison with tautomers energies

Parameters:

ranks -

energies -

Returns:

calcTautomerRankCorrCoeff

public static double calcTautomerRankCorrCoeff(double[] ranks,
                                               double[] energies)

calcTautomerRankSpearmanCorrCoeff

public static double calcTautomerRankSpearmanCorrCoeff(double[] ranks,
                                                       double[] energies,
                                                       boolean isFractional)

getRanks

public static double[] getRanks(double[] values,
                                boolean isFractionalRanking)

getNumberOfDistinctValues

public static int getNumberOfDistinctValues(double[] values)