ambit2.sln.cli

Class SLNCli

java.lang.Object

ambit2.sln.cli.SLNCli

public class SLNCli
extends Object

Field Summary

Fields

Modifier and Type	Field and Description
SLN2ChemObjectConfig.ComparisonConversion	comparisonConversion
String	comparisonConversionString
String	dictionaryFileName
Boolean	expand
Expander	expander
String	expandString
String	inputFileName
org.openscience.cdk.interfaces.IAtomContainer	inputMol
String	inputSmiles
ambit2.smarts.IsomorphismTester	isoTester
SLNSearchManager	man
ambit2.sln.cli.SLNCli._operation	operation
String	operationString
ambit2.sln.cli.SLNCli._out_format	outFormat
String	outFormatString
String	outputFileName
String	sln
SLNContainer	slnContainer
SLN2ChemObject	slnConverter
SLNHelper	slnHelper
SLNParser	slnParser
ambit2.smarts.SmartsHelper	smartsHelper
Boolean	warnings
String	warningsString

Constructor Summary

Constructors

Constructor and Description
SLNCli()

Method Summary

Modifier and Type	Method and Description
int	convert(SLNContainer container0)
int	convertToSLN(org.openscience.cdk.interfaces.IAtomContainer container)
protected static org.apache.commons.cli.Options	createOptions()
int	expandSLNContainer(SLNContainer container)
int	generateCombLibrary(SLNContainer container)
org.openscience.cdk.io.iterator.IIteratingChemObjectReader<org.openscience.cdk.interfaces.IAtomContainer>	getReader(InputStream in, String extension)
int	iterateInputFileWithSLNs()
int	iterateInputMoleculesFile()
static void	main(String[] args)
void	performTask(org.openscience.cdk.interfaces.IAtomContainer mol, String info)
void	printExtendedCT(SLNContainer container)
protected static void	printHelp(org.apache.commons.cli.Options options, String message)
int	run(String[] args)
protected int	runSLN()
void	setOption(ambit2.sln.cli.SLNCli._option option, String argument)
boolean	ssMatch(SLNContainer query, org.openscience.cdk.interfaces.IAtomContainer mol)

Methods inherited from class java.lang.Object

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

Field Detail

inputFileName

public String inputFileName

outputFileName

public String outputFileName

dictionaryFileName

public String dictionaryFileName

inputSmiles

public String inputSmiles

sln

public String sln

operationString

public String operationString

operation

public ambit2.sln.cli.SLNCli._operation operation

outFormatString

public String outFormatString

outFormat

public ambit2.sln.cli.SLNCli._out_format outFormat

comparisonConversionString

public String comparisonConversionString

comparisonConversion

public SLN2ChemObjectConfig.ComparisonConversion comparisonConversion

warningsString

public String warningsString

warnings

public Boolean warnings

expandString

public String expandString

expand

public Boolean expand

slnParser

public SLNParser slnParser

slnHelper

public SLNHelper slnHelper

slnConverter

public SLN2ChemObject slnConverter

expander

public Expander expander

isoTester

public ambit2.smarts.IsomorphismTester isoTester

smartsHelper

public ambit2.smarts.SmartsHelper smartsHelper

man

public SLNSearchManager man

slnContainer

public SLNContainer slnContainer

inputMol

public org.openscience.cdk.interfaces.IAtomContainer inputMol

Constructor Detail

SLNCli

public SLNCli()

Method Detail

main

public static void main(String[] args)

createOptions

protected static org.apache.commons.cli.Options createOptions()

printHelp

protected static void printHelp(org.apache.commons.cli.Options options,
                                String message)

setOption

public void setOption(ambit2.sln.cli.SLNCli._option option,
                      String argument)
               throws Exception

Throws:

Exception

run

public int run(String[] args)

runSLN

protected int runSLN()
              throws Exception

Throws:

Exception

convert

public int convert(SLNContainer container0)

expandSLNContainer

public int expandSLNContainer(SLNContainer container)

generateCombLibrary

public int generateCombLibrary(SLNContainer container)

convertToSLN

public int convertToSLN(org.openscience.cdk.interfaces.IAtomContainer container)

printExtendedCT

public void printExtendedCT(SLNContainer container)

iterateInputFileWithSLNs

public int iterateInputFileWithSLNs()

iterateInputMoleculesFile

public int iterateInputMoleculesFile()
                              throws Exception

Throws:

Exception

performTask

public void performTask(org.openscience.cdk.interfaces.IAtomContainer mol,
                        String info)

ssMatch

public boolean ssMatch(SLNContainer query,
                       org.openscience.cdk.interfaces.IAtomContainer mol)
                throws Exception

Throws:

Exception

getReader

public org.openscience.cdk.io.iterator.IIteratingChemObjectReader<org.openscience.cdk.interfaces.IAtomContainer> getReader(InputStream in,
                                                                                                                           String extension)
                                                                                                                    throws org.openscience.cdk.exception.CDKException,
                                                                                                                           ambit2.base.exceptions.AmbitIOException

Throws:

org.openscience.cdk.exception.CDKException

ambit2.base.exceptions.AmbitIOException