ambit2.sln.io

Class SLN2ChemObject

java.lang.Object

ambit2.sln.io.SLN2ChemObject

public class SLN2ChemObject
extends Object

Author:

nick Conversion of SLNContainer to chemical objects represented on top of CDK (AtomContainer, QueryAtomContainer)

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	SLN2ChemObject.ExpressionAtomInfo

Constructor Summary

Constructors

Constructor and Description
SLN2ChemObject()
SLN2ChemObject(SLN2ChemObjectConfig conversionConfig)

Method Summary

Modifier and Type	Method and Description
SLNContainer	atomContainerToSLNContainer(org.openscience.cdk.interfaces.IAtomContainer container)
SLNAtom	atomToSLNAtom(org.openscience.cdk.interfaces.IAtom atom)
SLNBond	bondToSLNBond(org.openscience.cdk.interfaces.IBond bond)
void	clearAllErrorsAndWarnings()
static Integer	extractFormalCharge(SLNAtomExpression slnAE)
static SLN2ChemObject.ExpressionAtomInfo	extractSimpleAtomInfoFromExprresion(SLNAtomExpression slnAE)
String	getAllErrors()
ambit2.smarts.SmartsExpressionToken	getAlternativeSmartsToken(SLNExpressionToken slnTok, int altValue)
LinearNotationType	getCompatibleNotation(SLNContainer slnContainer)
SLN2ChemObjectConfig	getConversionConfig()
List<String>	getConversionErrors()
List<String>	getConversionWarnings()
int[]	getSmartsTokenAlternativeValues(SLNExpressionToken slnTok)
boolean	hasConversionErrors()
static void	processMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
SLNContainer	QueryAtomContainerToSLNContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)
SLNAtom	queryAtomToSLNAtom(org.openscience.cdk.isomorphism.matchers.IQueryAtom queryAtom)
SLNBond	queryBondToSLNBond(org.openscience.cdk.isomorphism.matchers.IQueryBond queryBond)
org.openscience.cdk.interfaces.IAtom	slnAtomToAtom(SLNAtom slnAt)
org.openscience.cdk.isomorphism.matchers.IQueryAtom	slnAtomToQueryAtom(SLNAtom slnAt)
ambit2.smarts.SmartsAtomExpression	slnAtomToSmartsAtomExpression(SLNAtom slnAt)
org.openscience.cdk.interfaces.IBond	slnBondToBond(SLNBond slnBo)
org.openscience.cdk.isomorphism.matchers.IQueryBond	slnBondToQueryBond(SLNBond slnBo)
ambit2.smarts.SmartsBondExpression	slnBondToSmartsBondExpression(SLNBond slnBo)
org.openscience.cdk.interfaces.IAtomContainer	slnContainerToAtomContainer(SLNContainer slnContainer)
org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer	slnContainerToQueryAtomContainer(SLNContainer slnContainer)
ambit2.smarts.SMIRKSReaction	slnContainerToSMIRKSReaction(SLNContainer container)
ambit2.smarts.SmartsExpressionToken	slnExpressionTokenToSmartsExpressionToken(SLNExpressionToken slnTok)
ambit2.smarts.SmartsExpressionToken[]	slnExpressionTokenToSmartsExpressionTokenArray(SLNExpressionToken slnTok)
ambit2.smarts.SmartsExpressionToken	slnLogOperationToSmartsExpressionToken(int logOp)
SLNContainer	SMIRKSReactionToSLNContainer(ambit2.smarts.SMIRKSReaction reaction)

Methods inherited from class java.lang.Object

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

Constructor Detail

SLN2ChemObject

public SLN2ChemObject()

SLN2ChemObject

public SLN2ChemObject(SLN2ChemObjectConfig conversionConfig)

Method Detail

getConversionConfig

public SLN2ChemObjectConfig getConversionConfig()

hasConversionErrors

public boolean hasConversionErrors()

getConversionErrors

public List<String> getConversionErrors()

getConversionWarnings

public List<String> getConversionWarnings()

clearAllErrorsAndWarnings

public void clearAllErrorsAndWarnings()

getAllErrors

public String getAllErrors()

getCompatibleNotation

public LinearNotationType getCompatibleNotation(SLNContainer slnContainer)

atomContainerToSLNContainer

public SLNContainer atomContainerToSLNContainer(org.openscience.cdk.interfaces.IAtomContainer container)

slnContainerToAtomContainer

public org.openscience.cdk.interfaces.IAtomContainer slnContainerToAtomContainer(SLNContainer slnContainer)

slnContainerToQueryAtomContainer

public org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer slnContainerToQueryAtomContainer(SLNContainer slnContainer)

QueryAtomContainerToSLNContainer

public SLNContainer QueryAtomContainerToSLNContainer(org.openscience.cdk.isomorphism.matchers.IQueryAtomContainer query)

slnContainerToSMIRKSReaction

public ambit2.smarts.SMIRKSReaction slnContainerToSMIRKSReaction(SLNContainer container)

SMIRKSReactionToSLNContainer

public SLNContainer SMIRKSReactionToSLNContainer(ambit2.smarts.SMIRKSReaction reaction)

atomToSLNAtom

public SLNAtom atomToSLNAtom(org.openscience.cdk.interfaces.IAtom atom)

bondToSLNBond

public SLNBond bondToSLNBond(org.openscience.cdk.interfaces.IBond bond)

slnAtomToAtom

public org.openscience.cdk.interfaces.IAtom slnAtomToAtom(SLNAtom slnAt)

slnBondToBond

public org.openscience.cdk.interfaces.IBond slnBondToBond(SLNBond slnBo)

queryAtomToSLNAtom

public SLNAtom queryAtomToSLNAtom(org.openscience.cdk.isomorphism.matchers.IQueryAtom queryAtom)

queryBondToSLNBond

public SLNBond queryBondToSLNBond(org.openscience.cdk.isomorphism.matchers.IQueryBond queryBond)

slnAtomToQueryAtom

public org.openscience.cdk.isomorphism.matchers.IQueryAtom slnAtomToQueryAtom(SLNAtom slnAt)

slnBondToQueryBond

public org.openscience.cdk.isomorphism.matchers.IQueryBond slnBondToQueryBond(SLNBond slnBo)

slnAtomToSmartsAtomExpression

public ambit2.smarts.SmartsAtomExpression slnAtomToSmartsAtomExpression(SLNAtom slnAt)

slnBondToSmartsBondExpression

public ambit2.smarts.SmartsBondExpression slnBondToSmartsBondExpression(SLNBond slnBo)

slnLogOperationToSmartsExpressionToken

public ambit2.smarts.SmartsExpressionToken slnLogOperationToSmartsExpressionToken(int logOp)

slnExpressionTokenToSmartsExpressionTokenArray

public ambit2.smarts.SmartsExpressionToken[] slnExpressionTokenToSmartsExpressionTokenArray(SLNExpressionToken slnTok)

slnExpressionTokenToSmartsExpressionToken

public ambit2.smarts.SmartsExpressionToken slnExpressionTokenToSmartsExpressionToken(SLNExpressionToken slnTok)

getSmartsTokenAlternativeValues

public int[] getSmartsTokenAlternativeValues(SLNExpressionToken slnTok)

getAlternativeSmartsToken

public ambit2.smarts.SmartsExpressionToken getAlternativeSmartsToken(SLNExpressionToken slnTok,
                                                                     int altValue)

extractSimpleAtomInfoFromExprresion

public static SLN2ChemObject.ExpressionAtomInfo extractSimpleAtomInfoFromExprresion(SLNAtomExpression slnAE)

extractFormalCharge

public static Integer extractFormalCharge(SLNAtomExpression slnAE)

processMolecule

public static void processMolecule(org.openscience.cdk.interfaces.IAtomContainer mol)
                            throws Exception

Throws:

Exception