Package chemaxon.calculations

Class HLBPlugin

java.lang.Object

chemaxon.calculations.CalculatorPlugin

chemaxon.calculations.HLBPlugin

All Implemented Interfaces:

TaggedCalculator, Licensable

@PublicApi
public final class HLBPlugin
extends CalculatorPlugin

Calculates hydrophilic-lipophilic balance (HLB) of a molecule. The HLB is a measure of the degree to which molecule hydrophilic or lipophilic, determined by calculating values for the different regions of the molecule, as described by Griffin. Other methods have been suggested, notably in by Davies.

API usage example:

 // Construct the plugin class
 HLBPlugin plugin = new HLBPlugin();
 Molecule mol = ...

 // Set the input molecule and run calculation
 plugin.setMolecule(mol);
 plugin.run();

 // Get HLB values
 plugin.getDaviesHLBValue();
 plugin.getGriffinHLBValue();
 

Since:

Marvin 15.4.20

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static class	HLBPlugin.Builder	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use the constructor of HLBPlugin class directly instead.

Nested classes/interfaces inherited from class chemaxon.calculations.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

Fields inherited from class chemaxon.calculations.CalculatorPlugin

ATOM, BLUE, CALCRGB_OFF, COVALENT_HYDRATION_ERROR_REMARK, CRITICAL_ERROR_MSG, EPSILON, explicitHydrogens, INCORRECT_AROMATIC_NITROGEN_REMARK, INSTABLE_TAUTOMERIC_FORM_REMARK, KEEP_HYDROGENS, keepHydrogens, licenseEnvironment, MOLECULE, MOLECULES, NAN, PLUGIN_CLASS_KEY, PLUGIN_DIR, RED, TRUE

Constructor Summary

Constructors

Constructor	Description
HLBPlugin()

Method Summary

Modifier and Type	Method	Description
void	enableRequiredHLBValue(boolean r)	Sets whether the required HLB value (RHLB) is wanted or not.
double	getDaviesHlbValue()	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use getDaviesHLBValue() instead.
double	getDaviesHLBValue()	Returns the HLB value calculated by Davies method.
double	getGriffinHlbValue()	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use getGriffinHLBValue() instead.
double	getGriffinHLBValue()	Returns the HLB value calculated by Griffin method.
double	getHlbValue()	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use getHLBValue() instead.
double	getHLBValue()	Returns the HLB value.
String	getProductName()	Returns the product identifier of the plugin.
double	getRequiredHlbValue()	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use getRequiredHLBValue() instead.
double	getRequiredHLBValue()	Returns the Required HLB value calculated by Chemaxon method.
Object	getResult(Object type, int index)	Returns the result item for the specified type and index.
String	getResultAsString(Object type, int index, Object result)	Returns the specified result in String format.
int	getResultDomain()	Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES.
Molecule	getResultMolecule()	Returns the result molecule for display.
Object[]	getResultTypes()	Returns the result types.
boolean	run()	Runs the tool.
protected void	setInputMolecule(Molecule mol)	Sets the input molecule.
void	setParameters(Properties params)	Sets the input parameters for the plugin.
void	setRHLB(boolean r)	Deprecated, for removal: This API element is subject to removal in a future version. Deprecated, use enableRequiredHLBValue(boolean) instead.
void	standardize(Molecule mol)	Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...).

Methods inherited from class chemaxon.calculations.CalculatorPlugin

addHeavyAtomLimitChecker, addInputChecker, arrangeHydrogenIncerments, canRepeat, checkLicense, checkMolecule, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getAtomIndexMapping, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getOriginalMolecule, getpH, getPh, getQueryMoleculeErrorMessage, getRemark, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultCount, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, getWarningMessage, handlesMultiFragmentMolecules, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadPluginClass, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setChemicalTermsArgument, setChemicalTermsParameters, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, setProgressMonitor, standardizeIonicGroups

Methods inherited from class java.lang.Object

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

Methods inherited from interface chemaxon.calculations.api.TaggedCalculator

tags

Constructor Details

HLBPlugin

public HLBPlugin()

Method Details

setParameters

public void setParameters(Properties params)
                   throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Sets the input parameters for the plugin.

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

CalculatorPluginException - on error

setInputMolecule

protected void setInputMolecule(Molecule mol)
                         throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Sets the input molecule.

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

CalculatorPluginException - on error

getResultDomain

public int getResultDomain()

Description copied from class: CalculatorPlugin

Returns the calculation domain CalculatorPlugin.ATOM, CalculatorPlugin.MOLECULE or CalculatorPlugin.MOLECULES. for the first result type.

Overrides:

getResultDomain in class CalculatorPlugin

Returns:

the calculation domain

getResultTypes

public Object[] getResultTypes()

Description copied from class: CalculatorPlugin

Returns the result types. The default implementation returns null.

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

getResult

public Object getResult(Object type,
 int index)
                 throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Returns the result item for the specified type and index. The default implementation returns null.

Overrides:

getResult in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

Returns:

the result item for the specified type and index

Throws:

CalculatorPluginException - if the result cannot be returned

See Also:

• CalculatorPlugin.getResultTypes()

getResultAsString

public String getResultAsString(Object type,
 int index,
 Object result)
                         throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Returns the specified result in String format. The default implementation returns null.

Overrides:

getResultAsString in class CalculatorPlugin

Parameters:

type - is the result type

index - is the result index

result - is the result item

Returns:

the specified result in String format

Throws:

CalculatorPluginException - if an invalid result item is given

getResultMolecule

public Molecule getResultMolecule()
                           throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Returns the result molecule for display. Atomic results are stored in atom extra labels (MolAtom.getExtraLabel()). Molecular results are stored in molecule properties with keys being the result types (MPropHandler.convertToString(MPropertyContainer, String)).

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the result molecule

Throws:

CalculatorPluginException - on error

getProductName

public String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin. For internal use only!

Specified by:

getProductName in class CalculatorPlugin

standardize

public void standardize(Molecule mol)

Description copied from class: CalculatorPlugin

Standardizes the molecule by performing the transformations necessary to run the plugin (aromatize, dehydrogenize, bring nitro groups to common form, ...). This implementation performs the following transformations:

• aromatization
• nitro group transformation: [O-:1][N+:2] >> [O:1]=[N:2], [NH1+:1][O-:2] >> [H:3][O:2][N:1]
• sulphynil group transformation: [#6][S+:1]([#6])[#8-:2] >> [#6][S:1]([#6])=[O:2]

To be overridden by subclasses that require other standardization (or none at all).

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized

run

public boolean run()
            throws CalculatorPluginException

Description copied from class: CalculatorPlugin

Runs the tool.

Specified by:

run in class CalculatorPlugin

Returns:

true if the calculation was successful, false on calculation problems

Throws:

CalculatorPluginException - on error

See Also:

• CalculatorPlugin.getErrorMessage()

getHlbValue

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2027)
public double getHlbValue()

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated, use getHLBValue() instead.

Returns the HLB value. Consensus model using Davies and Griffin's models.

Returns:

the HLB value

Throws:

IllegalStateException - if run() method was not called

getHLBValue

public double getHLBValue()

Returns the HLB value. Consensus model using Davies and Griffin's models.

Returns:

the HLB value

Throws:

IllegalStateException - if run() method was not called

getDaviesHlbValue

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2027)
public double getDaviesHlbValue()

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated, use getDaviesHLBValue() instead.

Returns the HLB value calculated by Davies method.

Returns:

the Davies HLB value

Throws:

IllegalStateException - if run() method was not called

getDaviesHLBValue

public double getDaviesHLBValue()

Returns the HLB value calculated by Davies method.

Returns:

the Davies HLB value

Throws:

IllegalStateException - if run() method was not called

getGriffinHlbValue

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2027)
public double getGriffinHlbValue()

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated, use getGriffinHLBValue() instead.

Returns the HLB value calculated by Griffin method.

Returns:

the Griffin HLB value

Throws:

IllegalStateException - if run() method was not called

getGriffinHLBValue

public double getGriffinHLBValue()

Returns the HLB value calculated by Griffin method.

Returns:

the Griffin HLB value

Throws:

IllegalStateException - if run() method was not called

getRequiredHlbValue

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2027)
public double getRequiredHlbValue()

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated, use getRequiredHLBValue() instead.

Returns the Required HLB value calculated by Chemaxon method.

Returns:

the Required HLB value

Throws:

IllegalStateException - if run() method was not called or when enableRequiredHLBValue(true) was not called before running the calculation

getRequiredHLBValue

public double getRequiredHLBValue()

Returns the Required HLB value calculated by Chemaxon method.

Returns:

the Required HLB value

Throws:

IllegalStateException - if run() method was not called or when enableRequiredHLBValue(true) was not called before running the calculation

See Also:

• enableRequiredHLBValue(boolean)

setRHLB

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2027)
public void setRHLB(boolean r)

Deprecated, for removal: This API element is subject to removal in a future version.

Deprecated, use enableRequiredHLBValue(boolean) instead.

Sets whether the required HLB value (RHLB) is wanted or not. RHLB is not calculated by default.

enableRequiredHLBValue

public void enableRequiredHLBValue(boolean r)

Sets whether the required HLB value (RHLB) is wanted or not. RHLB is not calculated by default.