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

All Implemented Interfaces:

chemaxon.license.Licensable
```
@PublicAPI
public final class AlignmentPlugin
extends CalculatorPlugin
```
Plugin layer for the AlignmentAPI

Since:

Marvin 5.2

Nested Class Summary
- Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin
  CalculatorPlugin.HydrogenData

Field Summary

Fields
Modifier and Type Field Description

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

Constructors
Constructor Description

AlignmentPlugin()

Method Summary

All Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	Description
`String`	`getProductName()`	Returns the product identifier of the plugin as given by `LicenseManager`.
`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`	`setMinimumCommonSize(int mcsSize)`	Deprecated.
`void`	`setParameters(Properties params)`	Sets the input parameters for the plugin.
`void`	`setProgressMonitor(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
addHeavyAtomLimitChecker, addInputChecker, arrangeHydrogenIncerments, canRepeat, checkLicense, checkMolecule, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, createStandardizedMolecule, createStandardizedMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getErrorMessage, getExplicitHydrogenData, getInputMolDim, getMainMolecule, getOriginalMolecule, 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, setAtomIndexMap, 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 final int STEP_DEFAULT
```
    See Also:
    
    Constant Field Values
- 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 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 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(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 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
```
@Deprecated
public void setMinimumCommonSize(int mcsSize)
                          throws PluginException
```
    Deprecated.
    
    No effect. Will be removed in later releases.
    
    Parameters:
    
    mcsSize -
    
    Throws:
    
    PluginException
  - setParameters
```
public void setParameters(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.standardizer.Standardizer
    Overrides:
    
    standardize in class CalculatorPlugin
    
    Parameters:
    
    mol - is the molecule to be standardized

Class AlignmentPlugin

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Constructor Summary

Method Summary

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin

Methods inherited from class java.lang.Object

Field Detail

STEP_DEFAULT

Constructor Detail

AlignmentPlugin

Method Detail

handlesMultiFragmentMolecules

getProductName

getResultTypes

setInputMolecule

setProgressMonitor

getWarningMessage

getResultMolecule

setAccuracyMode

setRingFlexibility

setMinimumCommonSize

setParameters

run

getVolumeTanimoto

standardize