Package chemaxon.calculations

Class AlignmentPlugin

java.lang.Object

chemaxon.calculations.CalculatorPlugin

chemaxon.calculations.AlignmentPlugin

All Implemented Interfaces:

TaggedCalculator, Licensable

@PublicApi
public final class AlignmentPlugin
extends CalculatorPlugin

Calculator plugin for aligning molecule onto each other in 2D and 3D. This class provides the functionality of Alignment as a calculator plugin.

Since:

Marvin 5.2

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

Fields

Modifier and Type	Field	Description
static final int	STEP_DEFAULT

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
AlignmentPlugin()

Method Summary

Modifier and Type	Method	Description
String	getProductName()	Returns the product identifier of the plugin.
Molecule	getResultMolecule()	Returns the result molecule for display.
Object[]	getResultTypes()	Returns the result types.
double	getVolumeTanimoto()
String	getWarningMessage()	Returns the calculation warning information message.
boolean	handlesMultiFragmentMolecules()	Returns true if the plugin handles multifragment molecules, false otherwise.
boolean	run()	Runs the tool.
void	setAccuracyMode(AlignmentAccuracyMode acc)
protected void	setInputMolecule(Molecule mol)	Sets the input molecule.
void	setParameters(Properties params)	Sets the input parameters for the plugin.
void	setProgressMonitor(ProgressMonitor pmon)	Sets a progress observer to be used in run() to display progress status.
void	setRingFlexibility(int size, int rotBondCount)	If BOTH the two parameters is true for the ring then the ring is treated flexible.
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, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultAsString, getResultCount, getResultCount, getResultDomain, getResultDomain, getResultMessage, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getResultSource, getTypeString, isInputMoleculeAromatized, isLicensed, isMsCalc, isMultiThreadedRunEnabled, isNegligibleResult, isOK, isRgrouped, loadPluginClass, removeWhitespace, restoreExplicitHydrogens, setAtomIndexMap, setChemicalTermsArgument, setChemicalTermsParameters, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, 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

Field Details

STEP_DEFAULT

public static final int STEP_DEFAULT

See Also:

• Constant Field Values

Constructor Details

AlignmentPlugin

public AlignmentPlugin()

Method Details

handlesMultiFragmentMolecules

public boolean handlesMultiFragmentMolecules()

Description copied from class: CalculatorPlugin

Returns true if the plugin handles multifragment molecules, false otherwise. In the latter case the plugin takes the fragment with more atoms if a multifragment molecule is given as input. The default implementation returns false.

Overrides:

handlesMultiFragmentMolecules in class CalculatorPlugin

Returns:

true if the plugin handles multifragment molecules, false otherwise

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

getResultTypes

public Object[] getResultTypes()

Returns the result types. Possible result types: refractivity,increments,inch

Overrides:

getResultTypes in class CalculatorPlugin

Returns:

the result types

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

setProgressMonitor

public void setProgressMonitor(ProgressMonitor pmon)

Sets a progress observer to be used in run() to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.

Overrides:

setProgressMonitor in class CalculatorPlugin

Parameters:

pmon - is the progress monitor, may be null

getWarningMessage

public String getWarningMessage()

Returns the calculation warning information message.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

the calculation warning information message

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

setAccuracyMode

public void setAccuracyMode(AlignmentAccuracyMode acc)
                     throws CalculatorPluginException

Throws:

CalculatorPluginException

setRingFlexibility

public void setRingFlexibility(int size,
 int rotBondCount)

If BOTH the two parameters is true for the ring then the ring is treated flexible.

Parameters:

size - atomcount above the ring is flexible

rotBondCount - rotatable bond count in the ring above which the ring is flexible

setParameters

public void setParameters(Properties params)
                   throws CalculatorPluginException

Sets the input parameters for the plugin.

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

CalculatorPluginException - on error

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()

getVolumeTanimoto

public double getVolumeTanimoto()

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