chemaxon.marvin.calculations
Class AlignmentPlugin

java.lang.Object
  chemaxon.marvin.plugin.CalculatorPlugin
      chemaxon.marvin.calculations.AlignmentPlugin

All Implemented Interfaces:

chemaxon.license.Licensable

public class AlignmentPlugin
extends CalculatorPlugin

Plugin layer for the AlignmentAPI

Since:

Marvin 5.2

Author:

Adrian Kalaszi

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin

CalculatorPlugin.HydrogenData

Field Summary

static int

STEP_DEFAULT

Fields inherited from class chemaxon.marvin.plugin.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

AlignmentPlugin()

Method Summary

java.lang.String	getProductName() Returns the product identifier of the plugin as given by LicenseManager.
Molecule	getResultMolecule() Returns the result molecule for display.
java.lang.Object[]	getResultTypes() Returns the result types.
double	getVolumeTanimoto()
java.lang.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	setMinimumCommonSize(int mcsSize) This is used only if AlignmentPreset.MCS is selected
void	setParameters(java.util.Properties params) Sets the input parameters for the plugin.
void	setProgressMonitor(chemaxon.common.util.MProgressMonitor 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.marvin.plugin.CalculatorPlugin

arrangeHydrogenIncerments, canRepeat, checkLicense, checkMolecule, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getRemark, getResult, getResult, 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, loadClass, readAttribute, removeWhitespace, restoreExplicitHydrogens, setDoublePrecision, setDoublePrecision, setDoublePrecision, setKeepHydrogens, setLicenseEnvironment, setMolecule, setMolecule, setMolecule, setMolecule, standardizeIonicGroups, standardizeNeutralGroups

Methods inherited from class java.lang.Object

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

Field Detail

STEP_DEFAULT

public static int STEP_DEFAULT

Constructor Detail

AlignmentPlugin

public AlignmentPlugin()

Method Detail

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 java.lang.String getProductName()

Description copied from class: CalculatorPlugin

Returns the product identifier of the plugin as given by LicenseManager. The name is used by the CalculatorPlugin.isLicensed() method.

Specified by:

getProductName in class CalculatorPlugin

Returns:

product identifier or a default string

getResultTypes

public java.lang.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 PluginException

Description copied from class: CalculatorPlugin

Sets the input molecule.

Specified by:

setInputMolecule in class CalculatorPlugin

Parameters:

mol - is the input molecule

Throws:

PluginException - on error

setProgressMonitor

public void setProgressMonitor(chemaxon.common.util.MProgressMonitor 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 java.lang.String getWarningMessage()

Returns the calculation warning information message.

Overrides:

getWarningMessage in class CalculatorPlugin

Returns:

the calculation warning information message

getResultMolecule

public Molecule getResultMolecule()
                           throws PluginException

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 (Molecule.getProperty(String)).

Overrides:

getResultMolecule in class CalculatorPlugin

Returns:

the result molecule

Throws:

PluginException - on error

setAccuracyMode

public void setAccuracyMode(AlignmentAccuracyMode acc)
                     throws PluginException

Throws:

PluginException

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

setMinimumCommonSize

public void setMinimumCommonSize(int mcsSize)
                          throws PluginException

This is used only if AlignmentPreset.MCS is selected

Parameters:

mcsSize -

Throws:

PluginException

setParameters

public void setParameters(java.util.Properties params)
                   throws PluginException

Sets the input parameters for the plugin.

Overrides:

setParameters in class CalculatorPlugin

Parameters:

params - is the parameter table

Throws:

PluginException - on error

run

public boolean run()
            throws PluginException

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:

PluginException - 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). TODO: replace by call to chemaxon.reaction.Standardizer

Overrides:

standardize in class CalculatorPlugin

Parameters:

mol - is the molecule to be standardized