ambit2.groupcontribution

Class GroupContributionModel

java.lang.Object

ambit2.groupcontribution.GroupContributionModel

public class GroupContributionModel
extends Object

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	GroupContributionModel.GCMConfigInfo
static class	GroupContributionModel.Type

Constructor Summary

Constructors

Constructor and Description
GroupContributionModel()

Method Summary

Modifier and Type	Method and Description
void	addCorrectionFactor(ICorrectionFactor corrFactor)
void	addGroup(IGroup group)
void	addLocalDescriptor(ILocalDescriptor localDescr)
void	addToReport(String info)
String	allCorrectionFactorsToJsonString(String offset)
String	allGroupInfoToJsonString(String offset)
double	calcModelValue(DataSetObject dso, boolean missingMolDescrError)
double	calcModelValue(org.openscience.cdk.interfaces.IAtomContainer mol)
double	calcModelValue(org.openscience.cdk.interfaces.IAtomContainer mol, boolean missingMolDescrError)
void	clearCalculationErrors()
void	clearGroups()
GroupContributionModel.GCMConfigInfo	getAdditionalConfig()
String	getAtomDesignation(int[] descriptors)
String	getAtomDesignationVerbose(int[] descriptors)
List<String>	getCalculationErrors()
Double	getColStatPercentageThreshold()
List<ICorrectionFactor>	getCorrectionFactors()
String	getCorrectionFactorsAsString()
String	getCorrectionFactorsAsString(String separator)
String	getCorrectionFactorsParametersAsJsonArray(ICorrectionFactor cf)
List<List<ILocalDescriptor>>	getCustomGroupLocalDescriptors()
List<IGroup.Type>	getCustomGroups()
static String	getDescriptorDesignation(ILocalDescriptor desc, int value)
List<DescriptorInfo>	getDescriptors()
String	getDescriptorsAsString(String separator)
Map<String,IGroup>	getGroups()
String	getGroupsAsString()
List<ILocalDescriptor>	getLocalDescriptors()
String	getModelDescription()
String	getModelName()
GroupContributionModel.Type	getModelType()
String	getReport()
GCMReportConfig	getReportConfig()
String	getTargetProperty()
ValidationConfig	getValidationConfig()
boolean	isAllowGroupRegistration()
boolean	isLocalPropertyModel()
static String	makeAtomDesignation(int[] descriptors, List<ILocalDescriptor> locDescr)
void	setAdditionalConfig(GroupContributionModel.GCMConfigInfo additionalConfig)
void	setAllowGroupRegistration(boolean allowGroupRegistration)
void	setColStatPercentageThreshold(Double colStatPercentageThreshold)
void	setCorrectionFactors(List<ICorrectionFactor> correctionFactors)
void	setCustomGroupLocalDescriptors(List<List<ILocalDescriptor>> customGroupLocalDescriptors)
void	setCustomGroups(List<IGroup.Type> customGroups)
void	setDescriptors(List<DescriptorInfo> descriptors)
void	setGroups(Map<String,IGroup> groups)
void	setLocalDescriptors(List<ILocalDescriptor> localDescriptors)
void	setModelDescription(String modelDescription)
void	setModelName(String modelName)
void	setModelType(GroupContributionModel.Type modelType)
void	setReportConfig(GCMReportConfig reportConfig)
void	setTargetProperty(String targetProperty)
void	setValidationConfig(ValidationConfig validationConfig)
String	toJsonString()

Methods inherited from class java.lang.Object

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

Constructor Detail

GroupContributionModel

public GroupContributionModel()

Method Detail

getModelName

public String getModelName()

setModelName

public void setModelName(String modelName)

getModelDescription

public String getModelDescription()

setModelDescription

public void setModelDescription(String modelDescription)

getLocalDescriptors

public List<ILocalDescriptor> getLocalDescriptors()

setLocalDescriptors

public void setLocalDescriptors(List<ILocalDescriptor> localDescriptors)

addLocalDescriptor

public void addLocalDescriptor(ILocalDescriptor localDescr)

getCorrectionFactors

public List<ICorrectionFactor> getCorrectionFactors()

setCorrectionFactors

public void setCorrectionFactors(List<ICorrectionFactor> correctionFactors)

addCorrectionFactor

public void addCorrectionFactor(ICorrectionFactor corrFactor)

getCustomGroups

public List<IGroup.Type> getCustomGroups()

setCustomGroups

public void setCustomGroups(List<IGroup.Type> customGroups)

getCustomGroupLocalDescriptors

public List<List<ILocalDescriptor>> getCustomGroupLocalDescriptors()

setCustomGroupLocalDescriptors

public void setCustomGroupLocalDescriptors(List<List<ILocalDescriptor>> customGroupLocalDescriptors)

getGroups

public Map<String,IGroup> getGroups()

setGroups

public void setGroups(Map<String,IGroup> groups)

clearGroups

public void clearGroups()

addGroup

public void addGroup(IGroup group)

getModelType

public GroupContributionModel.Type getModelType()

setModelType

public void setModelType(GroupContributionModel.Type modelType)

getTargetProperty

public String getTargetProperty()

setTargetProperty

public void setTargetProperty(String targetProperty)

getColStatPercentageThreshold

public Double getColStatPercentageThreshold()

setColStatPercentageThreshold

public void setColStatPercentageThreshold(Double colStatPercentageThreshold)

getReportConfig

public GCMReportConfig getReportConfig()

setReportConfig

public void setReportConfig(GCMReportConfig reportConfig)

getDescriptors

public List<DescriptorInfo> getDescriptors()

setDescriptors

public void setDescriptors(List<DescriptorInfo> descriptors)

getAdditionalConfig

public GroupContributionModel.GCMConfigInfo getAdditionalConfig()

setAdditionalConfig

public void setAdditionalConfig(GroupContributionModel.GCMConfigInfo additionalConfig)

isLocalPropertyModel

public boolean isLocalPropertyModel()

getAtomDesignation

public String getAtomDesignation(int[] descriptors)

makeAtomDesignation

public static String makeAtomDesignation(int[] descriptors,
                                         List<ILocalDescriptor> locDescr)

getDescriptorDesignation

public static String getDescriptorDesignation(ILocalDescriptor desc,
                                              int value)

getAtomDesignationVerbose

public String getAtomDesignationVerbose(int[] descriptors)

getGroupsAsString

public String getGroupsAsString()

getCorrectionFactorsAsString

public String getCorrectionFactorsAsString()

getCorrectionFactorsAsString

public String getCorrectionFactorsAsString(String separator)

getDescriptorsAsString

public String getDescriptorsAsString(String separator)

addToReport

public void addToReport(String info)

getReport

public String getReport()

getValidationConfig

public ValidationConfig getValidationConfig()

setValidationConfig

public void setValidationConfig(ValidationConfig validationConfig)

isAllowGroupRegistration

public boolean isAllowGroupRegistration()

setAllowGroupRegistration

public void setAllowGroupRegistration(boolean allowGroupRegistration)

calcModelValue

public double calcModelValue(org.openscience.cdk.interfaces.IAtomContainer mol,
                             boolean missingMolDescrError)

calcModelValue

public double calcModelValue(org.openscience.cdk.interfaces.IAtomContainer mol)

calcModelValue

public double calcModelValue(DataSetObject dso,
                             boolean missingMolDescrError)

getCalculationErrors

public List<String> getCalculationErrors()

clearCalculationErrors

public void clearCalculationErrors()

toJsonString

public String toJsonString()

allGroupInfoToJsonString

public String allGroupInfoToJsonString(String offset)

allCorrectionFactorsToJsonString

public String allCorrectionFactorsToJsonString(String offset)

getCorrectionFactorsParametersAsJsonArray

public String getCorrectionFactorsParametersAsJsonArray(ICorrectionFactor cf)