ambit2.groupcontribution.nmr

Class HNMRShifts

java.lang.Object

ambit2.groupcontribution.nmr.HNMRShifts

public class HNMRShifts
extends Object

Constructor Summary

Constructors

Constructor and Description
HNMRShifts()
HNMRShifts(File knowledgeBaseFile)

Method Summary

Modifier and Type	Method and Description
void	calcAlkeneHShifts(HAtomEnvironmentInstance haeInst, int atIndex)
HShift	calcHShift(HAtomEnvironmentInstance haeInst)
void	calculateHShifts()
boolean	checkSubstituentMapping(List<org.openscience.cdk.interfaces.IAtom> map, HAtomEnvironmentInstance haeInst, int substPosAtIndex, int distance)
void	findAllGroupMappings()
void	findAllSubstituents()
void	findSubstituents(HAtomEnvironmentInstance haeInst)
void	generateHShifts()
int	getBinNumber(double shiftValue)
String	getCalcLog()
List<String>	getErrors()
List<HShift>	getHShifts()
HNMRKnowledgeBase	getKnowledgeBase()
org.openscience.cdk.interfaces.IAtomContainer	getMolecule()
double	getResolutionStep()
List<String>	getWarnings()
void	handleOverlappingHAtomEnvironmentInstances()
void	registerHAtomEnvironmentInstance(HAtomEnvironmentInstance haeInst)
void	setErrors(List<String> errors)
void	setKnowledgeBase(HNMRKnowledgeBase knowledgeBase)
void	setResolutionStep(double resolutionStep)
void	setStructure(org.openscience.cdk.interfaces.IAtomContainer str)
void	setWarnings(List<String> warnings)

Methods inherited from class java.lang.Object

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

Constructor Detail

HNMRShifts

public HNMRShifts()
           throws Exception

Throws:

Exception

HNMRShifts

public HNMRShifts(File knowledgeBaseFile)
           throws Exception

Throws:

Exception

Method Detail

setStructure

public void setStructure(org.openscience.cdk.interfaces.IAtomContainer str)
                  throws Exception

Throws:

Exception

calculateHShifts

public void calculateHShifts()
                      throws EmptyMoleculeException

Throws:

EmptyMoleculeException

registerHAtomEnvironmentInstance

public void registerHAtomEnvironmentInstance(HAtomEnvironmentInstance haeInst)

handleOverlappingHAtomEnvironmentInstances

public void handleOverlappingHAtomEnvironmentInstances()

findAllSubstituents

public void findAllSubstituents()

findSubstituents

public void findSubstituents(HAtomEnvironmentInstance haeInst)

checkSubstituentMapping

public boolean checkSubstituentMapping(List<org.openscience.cdk.interfaces.IAtom> map,
                                       HAtomEnvironmentInstance haeInst,
                                       int substPosAtIndex,
                                       int distance)

findAllGroupMappings

public void findAllGroupMappings()
                          throws EmptyMoleculeException

Throws:

EmptyMoleculeException

generateHShifts

public void generateHShifts()

calcHShift

public HShift calcHShift(HAtomEnvironmentInstance haeInst)

calcAlkeneHShifts

public void calcAlkeneHShifts(HAtomEnvironmentInstance haeInst,
                              int atIndex)

getCalcLog

public String getCalcLog()

getErrors

public List<String> getErrors()

setErrors

public void setErrors(List<String> errors)

getWarnings

public List<String> getWarnings()

setWarnings

public void setWarnings(List<String> warnings)

getKnowledgeBase

public HNMRKnowledgeBase getKnowledgeBase()

setKnowledgeBase

public void setKnowledgeBase(HNMRKnowledgeBase knowledgeBase)

getHShifts

public List<HShift> getHShifts()

getBinNumber

public int getBinNumber(double shiftValue)

getResolutionStep

public double getResolutionStep()

setResolutionStep

public void setResolutionStep(double resolutionStep)

getMolecule

public org.openscience.cdk.interfaces.IAtomContainer getMolecule()