TautomerizationPlugin (Marvin API documentation (c) 1998-2019 ChemAxon Ltd.)

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

All Implemented Interfaces:: chemaxon.license.Licensable

@PublicAPI
public class TautomerizationPlugin
extends CalculatorPlugin

Plugin class for generating tautomer structures.

API usage example:

    // read input molecule
    MolImporter mi = new MolImporter("test.mol");
    Molecule mol = mi.read();

    // create plugin
    TautomerizationPlugin plugin = new TautomerizationPlugin();

    // set dominant tautomer distribution calculation
    plugin.setDominantTautomerDistributionCalculation(true);

    // set pH (consider pH effect at this pH; only has effect when dominant tautomers are generated)
    plugin.setpH(7.4);

    // set the input molecule
    plugin.setMolecule(mol);

    // run the calculation
    plugin.run();

    // get the dominant tautomers
    System.out.println("Dominant tautomer distribution");
    int count = plugin.getStructureCount();
    for (int i=0; i < count; ++i) {
        Molecule tautomer = plugin.getStructure(i);
        double distribution = plugin.getDominantTautomerDistribution(i);
        System.out.println(tautomer.toFormat("smiles") + "  " + distribution);
    }

For concurrent plugin example applications using ChemAxon's concurrent framework, refer to the Concurrent plugin examples.

Since:: Marvin 4.0
Version:: Marvin 5.12, 11/20/2012
Author:: Nora Mate, Zsolt Mohacsi

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

Field Summary

Fields
Modifier and Type Field and Description

static boolean warningMsgOn
- 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

Fields
Modifier and Type	Field and Description
`static boolean`	`warningMsgOn`

Constructor Summary

Constructors
Constructor and Description

TautomerizationPlugin()
Constructor.

Constructors
Constructor and Description
`TautomerizationPlugin()` Constructor.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`checkMolecule(Molecule mol)` Checks the input molecule.
`protected Molecule`	`createStandardizedMolecule(Molecule mol)` Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
`protected Molecule`	`createStandardizedMolecule(Molecule mol, boolean om)` Deprecated.
`int[]`	`getChangedAtomIndexes()` Returns the indexes of the atoms changed during tautomerization.
`double`	`getDominantTautomerDistribution(int index)` Returns the distribution of the dominant tautomer.
`java.lang.String`	`getErrorMessage()` Returns the calculation error information message or the empty string if there is no error.
`protected java.util.List<CalculatorPlugin.HydrogenData>`	`getExplicitHydrogenData(Molecule cmol, int n)`
`int[]`	`getNewOldIndexMap()`
`int[]`	`getOldNewIndexMap()`
`java.lang.String`	`getProductName()` Returns the product identifier of the plugin as given by `LicenseManager`.
`java.lang.String`	`getRemark()` Returns a warning message if there are no tautomers, `null` otherwise.
`java.lang.Object`	`getResult(java.lang.Object type, int index)` Returns the result item for the specified key and index.
`java.lang.String`	`getResultAsString(java.lang.Object type, int index, java.lang.Object result)` Returns the specified result in String format.
`int`	`getResultCount(java.lang.Object type)` Returns the number of result items for the given result key.
`int`	`getResultDomain(java.lang.Object type)` Returns the calculation domain.
`chemaxon.marvin.plugin.PluginMDocSource`	`getResultSource()` Returns the result as a document source object.
`java.lang.Object[]`	`getResultTypes()` Returns the result types.
`Molecule`	`getStructure(int index)` Returns a tautomer.
`int`	`getStructureCount()` Returns the number of different tautomers.
`Molecule[]`	`getStructures()` Deprecated. since Marvin 5.9 replaced by `getStructure(int)`
`protected java.lang.String`	`getTitle()` Returns the frame title.
`java.lang.String`	`getWarningMessage()` Returns the calculation warning information message.
`boolean`	`handlesMultiFragmentMolecules()` Returns `true` if the plugin handles multifragment molecules, `false` otherwise.
`static boolean`	`hasTautomers(Molecule mol)` Returns if a molecule has tautomers.
`boolean`	`isMultiThreadedRunEnabled()` For internal use only.
`boolean`	`run()` Calculates the tautomers.
`void`	`setCleanResultStructures(boolean clean)` Deprecated. obsolate method
`void`	`setDominantTautomerDistributionCalculation(boolean distrib)` Sets dominant tautomer distribution calculation: if `true` then dominant tautomer distribution is calculated.
`void`	`setExcludeAntiAromaticCompounds(boolean aa)` Sets whether antiaromatic compounds should be generated.
`protected void`	`setInputMolecule(Molecule mol)` Sets the input molecule.
`void`	`setInputMoleculeModified(boolean inputMoleculeModified)` Deprecated. Not used.
`void`	`setMaximumTautomerizationPathLength(int length)` Sets the maximum allowed length of the tautomerization path in chemical bonds.
`void`	`setMaxStructureCount(int max)` Sets the maximum number of structures to be generated.
`void`	`setNormalTautomerGenerationMode(boolean normal)` Generates only normal tautomers.
`void`	`setParameters(java.util.Properties params)` Sets the input parameters for the plugin.
`void`	`setpH(double pH)` Sets the pH to be considered in dominant tautomer generation.
`void`	`setProgressMonitor(MProgressMonitor pmon)` Sets a progress observer to be used in `run()` to display progress status.
`void`	`setProtectAllTetrahedralStereoCenters(boolean protect)` Sets the protection of all tetrahedral stereo centers: if `true` then all tetrahedral stereo information is preserved by the tautomer generator.
`void`	`setProtectAromaticity(boolean pa)` Sets aromaticity protection: if `true` then aromatic bonds are not modified by the tautomer generator.
`void`	`setProtectCharge(boolean pc)` Sets charge protection: if `true` then the charge of charged atoms are not modified by the tautomer generator.
`void`	`setProtectDoubleBondStereo(boolean protect)` Sets double bond stereo protection: if `true` then double bonds stereo information is preserved by the tautomer generator.
`void`	`setProtectEsterGroups(boolean protect)` Sets the protection of ester groups: if `true` then ester groups are excluded from the tautomerization.
`void`	`setProtectLabeledTetrahedralStereoCenters(boolean protect)` Sets the protection of labeled tetrahedral stereo centers: if `true` then labeled tetrahedral stereo centers are protected by the tautomer generator.
`void`	`setRationalTautomerGenerationMode(boolean rational)` Deprecated.
`void`	`setRingChainTautomerizationAllowed(boolean allowed)` Sets if ring tautomers are allowed or not. Default `true`
`void`	`setSymmetryFiltering(boolean filtering)` Sets symmetry fitlering: if `true` then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates.
`void`	`setTakeCanonicalForm(boolean canonical)` Sets whether canonical form should be generated.
`void`	`setTakeDominantTautomers(boolean dominants)` Sets whether dominant tautomers should be generated.
`void`	`setTakeGenericTautomer(boolean generic)` Sets whether generic tautomer should be generated.
`void`	`setTakeMajorTautomer(boolean major)` Sets whether major tautomer should be generated.
`void`	`setTakeMostStableTautomer(boolean mostStable)` Deprecated. Not used.
`void`	`setTakePartialNeutralization(boolean pn)` Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.
`void`	`setTakeStandardForm(boolean s)` For internal use only.
`void`	`setTimeLimit(double t)` Sets an upper time limit for the canonical tautomer generation.
`void`	`setWigglyBondVisibility(boolean vis)` Sets how wiggly bonds connected to double bonds are displayed. For internal use only.
`void`	`standardize(Molecule mol)` Standardizes the molecule.

Methods inherited from class chemaxon.marvin.plugin.CalculatorPlugin
arrangeHydrogenIncerments, canRepeat, checkLicense, checkType, containsCoordinateBond, containsMulticenterSgroup, containsPseudoAtom, containsSRUSgroup, create, createModifiedInputMolecule, dehydrogenize, format, format, format, format, getAtomCount, getAtomIndex, getAtomIndexMap, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getInputMolDim, getMainMolecule, getOriginalMolecule, getpH, getPluginResource, getQueryMoleculeErrorMessage, getResult, getResult, getResult, getResultAsRGB, getResultAsRGB, getResultAsString, getResultCount, getResultDomain, getResultMessage, getResultMolecule, getResultMolecules, getResultsAsRGB, getResultsAsRGB, getResultsAsString, getResultsAsString, getTypeString, isInputMoleculeAromatized, isLicensed, isMsCalc, 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
  - warningMsgOn
```
public static boolean warningMsgOn
```
- Constructor Detail
  - TautomerizationPlugin
```
public TautomerizationPlugin()
```
    Constructor. Creates the tautomerization object.
- Method Detail
  - getProductName
```
public java.lang.String getProductName()
```
    Returns the product identifier of the plugin as given by LicenseManager.
    
    Specified by:
    
    getProductName in class CalculatorPlugin
    
    Returns:
    
    The identifier LicenseManager.ISOMERS_PLUGIN_GROUP
  - hasTautomers
```
public static boolean hasTautomers(Molecule mol)
```
    Returns if a molecule has tautomers.
    
    Parameters:
    
    mol - the molecule
    
    Returns:
    
    true if molecule has tautomers
    
    Since:
    
    Marvin 5.12
  - handlesMultiFragmentMolecules
```
public boolean handlesMultiFragmentMolecules()
```
    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. Returns true if parameter "single" is set to "false", false otherwise (default: false).
    
    Overrides:
    
    handlesMultiFragmentMolecules in class CalculatorPlugin
    
    Returns:
    
    true if the plugin handles multifragment molecules, false otherwise
  - 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
  - setParameters
```
public void setParameters(java.util.Properties params)
                   throws PluginException
```
    Sets the input parameters for the plugin. Tautomerization parameters and value ranges:
    - single: "true" if single fragment mode (calculation is performed separately for each fragment) (default: "false")
    - type: structure,structures,count
    - max: max structure count
    - pH: consider pH effect at this pH (default: Double.NaN - do not consider pH effect)
    - symfilter: true if filter symmetrical structures, false if allow duplicates (default: true)
    - canonical: "true" if canonical form should be taken (default: "false")
    - major: "true" if major tautomer should be taken (default: "false")
    - dominants: "true" if take dominant tautomers, "false" otherwise (default: "false")
    - distribution: "true" if calculate dominant tautomer distribution, "false" otherwise (default: "false")
    Overrides:
    
    setParameters in class CalculatorPlugin
    
    Parameters:
    
    params - is the parameter table
    
    Throws:
    
    PluginException - on error
  - setCleanResultStructures
```
@Deprecated
public void setCleanResultStructures(boolean clean)
```
    Deprecated. obsolate method
    
    Sets 2D cleaning of the result structures: if true then the changed atoms in tautomers returned by getStructure(int) are partial cleaned in 2D. Should be called before setting input molecule. Default: false.
    
    Parameters:
    
    clean - if true then result structures are cleaned in 2D
    
    Since:
    
    Marvin 5.1.2
  - getChangedAtomIndexes
```
public int[] getChangedAtomIndexes()
```
    Returns the indexes of the atoms changed during tautomerization. Should be called after run(). Returns null if none of the atoms has changed. For internal use only.
    
    Returns:
    
    the indexes of the changed atoms
    
    Since:
    
    Marvin 5.12
  - setSymmetryFiltering
```
public void setSymmetryFiltering(boolean filtering)
```
    Sets symmetry fitlering: if true then symmetrical structures are filtered out, otherwise symmetrical structures are returned as duplicates. Symmetry filtering is always performed when canonical tautomer form is taken, regardless of the actual setting of the filtering parameter. Default: true.
    
    Parameters:
    
    filtering - is true if symmetrical structures should be filtered out
    
    See Also:
    
    setTakeCanonicalForm(boolean)
  - setMaxStructureCount
```
public void setMaxStructureCount(int max)
```
    Sets the maximum number of structures to be generated. This number is the sum of unique tautomeric count and degenerated tautomeric count. Note: getStructure(int) returns only the unique tautomers, getStructureCount() returns unique tautormer count. Default: 1000.
    
    Parameters:
    
    max - is the maximum number of structures to be generated
    
    Since:
    
    Marvin 4.1
  - setpH
```
public void setpH(double pH)
```
    Sets the pH to be considered in dominant tautomer generation. By default, no pH effect considered (Double.NaN).
    
    Parameters:
    
    pH - is the pH value
    
    See Also:
    
    setTakeDominantTautomers(boolean)
  - setTimeLimit
```
public void setTimeLimit(double t)
```
    Sets an upper time limit for the canonical tautomer generation. By default, no time limit considered (Double.NaN).
    
    Parameters:
    
    t - is the maximum allowed calculation time/molecule. It should be given in second.
    
    See Also:
    
    setTakeCanonicalForm(boolean)
  - setMaximumTautomerizationPathLength
```
public void setMaximumTautomerizationPathLength(int length)
```
    Sets the maximum allowed length of the tautomerization path in chemical bonds. If length = 0 is set then no limit is applied. Default: 4.
    
    Parameters:
    
    length - is the maximum allowed tautomerization path length
    
    Since:
    
    Marvin 4.1.11
  - setProtectAromaticity
```
public void setProtectAromaticity(boolean pa)
```
    Sets aromaticity protection: if true then aromatic bonds are not modified by the tautomer generator. Has no effect in case of generic tautomer. Default: true.
    
    Parameters:
    
    pa - is true if aromaticity should be protected
    
    Since:
    
    Marvin 5.0.2
  - setProtectCharge
```
public void setProtectCharge(boolean pc)
```
    Sets charge protection: if true then the charge of charged atoms are not modified by the tautomer generator. Has no effect in case of generic tautomer. Default: true.
    
    Parameters:
    
    pc - is true if charges should be protected
    
    Since:
    
    Marvin 5.0.1
  - setExcludeAntiAromaticCompounds
```
public void setExcludeAntiAromaticCompounds(boolean aa)
```
    Sets whether antiaromatic compounds should be generated. If true then antiaromatic compounds are not generated. Has no effect in case of generic tautomer. Default: true.
    
    Parameters:
    
    aa - is true if antiaromatic compounds should not be generated
    
    Since:
    
    Marvin 5.0.1
  - setProtectDoubleBondStereo
```
public void setProtectDoubleBondStereo(boolean protect)
```
    Sets double bond stereo protection: if true then double bonds stereo information is preserved by the tautomer generator. Has no effect in case of generic tautomer. Default: false.
    
    Parameters:
    
    protect - is true if double bond stereo information should be protected by the tautomer generator
    
    Since:
    
    Marvin 5.1
  - setProtectAllTetrahedralStereoCenters
```
public void setProtectAllTetrahedralStereoCenters(boolean protect)
```
    Sets the protection of all tetrahedral stereo centers: if true then all tetrahedral stereo information is preserved by the tautomer generator. Default: false.
    
    Parameters:
    
    protect - is true if all tetrahedral stereo information should be preserved by the tautomer generator
    
    Since:
    
    Marvin 5.1
  - setProtectLabeledTetrahedralStereoCenters
```
public void setProtectLabeledTetrahedralStereoCenters(boolean protect)
```
    Sets the protection of labeled tetrahedral stereo centers: if true then labeled tetrahedral stereo centers are protected by the tautomer generator. Has no effect in case of generic tautomer. Default: false.
    
    Parameters:
    
    protect - is true if labeled tetrahedral stereo centers should be protected by the tautomer generator
    
    Since:
    
    Marvin 5.1
  - setProtectEsterGroups
```
public void setProtectEsterGroups(boolean protect)
```
    Sets the protection of ester groups: if true then ester groups are excluded from the tautomerization. Default: true. Has no effect in case of generic tautomer.
    
    Parameters:
    
    protect - is true if ester groups should be excluded from the tautomerization
    
    Since:
    
    Marvin 5.3
  - setRingChainTautomerizationAllowed
```
public void setRingChainTautomerizationAllowed(boolean allowed)
```
    Sets if ring tautomers are allowed or not.
    Default true
    
    Parameters:
    
    allowed -
    
    Since:
    
    Marvin 5.8
  - setInputMoleculeModified
```
@Deprecated
public void setInputMoleculeModified(boolean inputMoleculeModified)
```
    Deprecated. Not used.
    
    Sets whether the input molecule should be modified and returned as calculation result. Default: false.
    
    Parameters:
    
    inputMoleculeModified - is true if input molecule should be modified, false if it should be preserved
    
    Since:
    
    Marvin 4.1
  - checkMolecule
```
public void checkMolecule(Molecule mol)
                   throws PluginException
```
    Checks the input molecule. Throws exception if the molecule contains R-groups.
    
    Overrides:
    
    checkMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - with error message for the user if the molecule is refused
  - createStandardizedMolecule
```
@Deprecated
protected Molecule createStandardizedMolecule(Molecule mol,
                                                          boolean om)
                                                   throws PluginException
```
    Deprecated.
    
    Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
    
    Overrides:
    
    createStandardizedMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    om - is true if original input molecule is to be used for atom indexing false if modified molecule is to be used for atom indexing
    
    Returns:
    
    the standardized molecule
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    #see #is InputMoleculeModified()
  - createStandardizedMolecule
```
protected Molecule createStandardizedMolecule(Molecule mol)
                                       throws PluginException
```
    Creates standardized molecule, the original input molecule is cloned only if the original molecule should not be modified.
    
    Overrides:
    
    createStandardizedMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    Returns:
    
    the standardized molecule
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    #see #is InputMoleculeModified()
  - getExplicitHydrogenData
```
protected java.util.List<CalculatorPlugin.HydrogenData> getExplicitHydrogenData(Molecule cmol,
                                                                                int n)
```
    Overrides:
    
    getExplicitHydrogenData in class CalculatorPlugin
  - setInputMolecule
```
protected void setInputMolecule(Molecule mol)
                         throws PluginException
```
    Sets the input molecule.
    
    Specified by:
    
    setInputMolecule in class CalculatorPlugin
    
    Parameters:
    
    mol - is the input molecule
    
    Throws:
    
    PluginException - on error
  - setTakePartialNeutralization
```
public void setTakePartialNeutralization(boolean pn)
```
    Sets if partial neutralization prior to canonical tauotmer generation is allowed or not.
    
    Parameters:
    
    pn - if true then partial neutralization is allowed
    
    Since:
    
    Marvin 5.5
  - setWigglyBondVisibility
```
public void setWigglyBondVisibility(boolean vis)
```
    Sets how wiggly bonds connected to double bonds are displayed.
    For internal use only.
    
    Parameters:
    
    vis - if true then wiggly bonds connected to double bonds are show as wiggly bonds, if false then wiggly bonds connected to double bonds are show as single bonds
    
    Since:
    
    Marvin 5.5
  - setTakeCanonicalForm
```
public void setTakeCanonicalForm(boolean canonical)
```
    Sets whether canonical form should be generated. Default: false.
    
    Parameters:
    
    canonical - is true if canonical form should be generated
    
    Since:
    
    Marvin 4.1
    
    See Also:
    
    getStructure(int), getStructures(), getStructureCount(), setSymmetryFiltering(boolean)
  - setTakeStandardForm
```
public void setTakeStandardForm(boolean s)
```
    For internal use only.
    
    Since:
    
    Marvin 5.5
  - setNormalTautomerGenerationMode
```
public void setNormalTautomerGenerationMode(boolean normal)
```
    Generates only normal tautomers.
    
    Parameters:
    
    normal -
    
    Since:
    
    Marvin 14.4.13
  - setRationalTautomerGenerationMode
```
@Deprecated
public void setRationalTautomerGenerationMode(boolean rational)
```
    Deprecated.
    
    Generates only rational tautomers. Use setNormalTautomerGenerationMode(boolean) instead
  - setTakeGenericTautomer
```
public void setTakeGenericTautomer(boolean generic)
```
    Sets whether generic tautomer should be generated. If generic tautomer is generated then all protect options except "protect all tetrahedral stereo centers" are ignored. Default: false.
    
    Parameters:
    
    generic - is true if generic tautomer should be generated
    
    Since:
    
    Marvin 5.1
    
    See Also:
    
    getStructure(int), getStructures(), getStructureCount(), setProtectAllTetrahedralStereoCenters(boolean)
  - setTakeMostStableTautomer
```
@Deprecated
public void setTakeMostStableTautomer(boolean mostStable)
```
    Deprecated. Not used.
    
    Sets whether most stable tautomer should be generated. Default: false.
    
    Parameters:
    
    mostStable - is true if most stable tautomer should be generated
    
    Since:
    
    Marvin 5.1
    
    See Also:
    
    getStructure(int), getStructures(), getStructureCount(), setpH(double)
  - setTakeMajorTautomer
```
public void setTakeMajorTautomer(boolean major)
```
    Sets whether major tautomer should be generated. Default: false.
    
    Parameters:
    
    major - is true if major tautomer should be generated
    
    Since:
    
    Marvin 5.2.2
    
    See Also:
    
    getStructure(int), getStructures(), getStructureCount(), setpH(double)
  - setTakeDominantTautomers
```
public void setTakeDominantTautomers(boolean dominants)
```
    Sets whether dominant tautomers should be generated. Default: false.
    
    Parameters:
    
    dominants - is true if dominant structures should be generated
    
    See Also:
    
    getStructure(int), getStructures(), getStructureCount(), setpH(double)
  - setDominantTautomerDistributionCalculation
```
public void setDominantTautomerDistributionCalculation(boolean distrib)
```
    Sets dominant tautomer distribution calculation: if true then dominant tautomer distribution is calculated. Use getStructure(int) to get the dominant tautomer structure and getDominantTautomerDistribution(int) to get its distribution.
    
    Parameters:
    
    distrib - if true then dominant tautomer distribution calculation is performed
    
    Since:
    
    Marvin 4.1.11
    
    See Also:
    
    getDominantTautomerDistribution(int), getStructure(int), getStructures(), getStructureCount(), setpH(double)
  - run
```
public boolean run()
            throws PluginException
```
    Calculates the tautomers.
    
    Specified by:
    
    run in class CalculatorPlugin
    
    Returns:
    
    true if the calculation was successful, false if the number of ionizable atoms exceeds the specified limit
    
    Throws:
    
    PluginException - on error
    
    See Also:
    
    CalculatorPlugin.getErrorMessage()
  - getDominantTautomerDistribution
```
public double getDominantTautomerDistribution(int index)
```
    Returns the distribution of the dominant tautomer. Dominant tautomers are ordered by distribution: first (index = 0) is the major tautomer with largest distribution, followed by other dominant tautomers in descending distribution order. Use getStructure(int) to get the dominant tautomer structure.
    
    Parameters:
    
    index - is the dominant tautomer index
    
    Returns:
    
    the distribution of the dominant tautomer
    
    Since:
    
    Marvin 4.1.11
    
    See Also:
    
    setDominantTautomerDistributionCalculation(boolean), getStructure(int)
  - getNewOldIndexMap
```
public int[] getNewOldIndexMap()
```
    Returns:
    
    the index mapping relations between the implicit-explicit molecule forms new -> old mapping , atom indexing starts form "0" e.g. if the "2" is the new index in the implicitized form then the "map[2]" will be the old index in the explicit form
  - getOldNewIndexMap
```
public int[] getOldNewIndexMap()
```
    Returns:
    
    the index mapping relations between the explicit- implicit molecule forms old -> new mapping , atom indexing starts form "0" e.g. if the "2" is the old index in the explicit form then the "map[2]" will be the new index in the implicitized form
  - getResultSource
```
public chemaxon.marvin.plugin.PluginMDocSource getResultSource()
                                                        throws PluginException
```
    Returns the result as a document source object. This is useful for displaying the molecules in a viewer dynamically as they become available instead of collecting all results before display.
    
    Overrides:
    
    getResultSource in class CalculatorPlugin
    
    Returns:
    
    the document source interface
    
    Throws:
    
    PluginException - on error
    
    Since:
    
    Marvin 5.0
  - getStructureCount
```
public int getStructureCount()
```
    Returns the number of different tautomers.
    
    Returns:
    
    the number of different structures
    
    See Also:
    
    setTakeCanonicalForm(boolean), setTakeDominantTautomers(boolean)
  - getStructure
```
public Molecule getStructure(int index)
```
    Returns a tautomer.
    
    Parameters:
    
    index - is the structure index
    
    Returns:
    
    the structure
    
    See Also:
    
    setTakeCanonicalForm(boolean), setTakeGenericTautomer(boolean), setTakeMajorTautomer(boolean), setTakeDominantTautomers(boolean), setDominantTautomerDistributionCalculation(boolean)
  - getStructures
```
@Deprecated
public Molecule[] getStructures()
```
    Deprecated. since Marvin 5.9 replaced by getStructure(int)
    
    Returns tautomers in Molecule[] array..
    
    Returns:
    
    tautomers
    
    See Also:
    
    setTakeCanonicalForm(boolean), setTakeDominantTautomers(boolean)
  - getResultTypes
```
public java.lang.Object[] getResultTypes()
```
    Returns the result types.
    
    Overrides:
    
    getResultTypes in class CalculatorPlugin
    
    Returns:
    
    the result types
  - getResultDomain
```
public int getResultDomain(java.lang.Object type)
```
    Returns the calculation domain.
    
    Overrides:
    
    getResultDomain in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the calculation domain
    
    See Also:
    
    getResultTypes()
  - getResultCount
```
public int getResultCount(java.lang.Object type)
```
    Returns the number of result items for the given result key.
    
    Overrides:
    
    getResultCount in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    Returns:
    
    the number of result items
    
    See Also:
    
    getResultTypes()
  - getResult
```
public java.lang.Object getResult(java.lang.Object type,
                                  int index)
                           throws PluginException
```
    Returns the result item for the specified key and index.
    
    Overrides:
    
    getResult in class CalculatorPlugin
    
    Parameters:
    
    type - is the result type
    
    index - is the result index
    
    Returns:
    
    the result item for the specified key and index
    
    Throws:
    
    PluginException - if the result cannot be returned
    
    See Also:
    
    CalculatorPlugin.getResultTypes()
  - getResultAsString
```
public java.lang.String getResultAsString(java.lang.Object type,
                                          int index,
                                          java.lang.Object result)
                                   throws PluginException
```
    Returns the specified result in String format.
    
    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:
    
    PluginException - if an invalid result item is given
  - getRemark
```
public java.lang.String getRemark()
```
    Returns a warning message if there are no tautomers, null otherwise.
    
    Overrides:
    
    getRemark in class CalculatorPlugin
    
    Returns:
    
    a warning message if there are no tautomers
  - getErrorMessage
```
public java.lang.String getErrorMessage()
```
    Returns the calculation error information message or the empty string if there is no error.
    
    Overrides:
    
    getErrorMessage in class CalculatorPlugin
    
    Returns:
    
    the calculation error information message
  - getTitle
```
protected java.lang.String getTitle()
```
    Returns the frame title.
    
    Returns:
    
    the frame title
    
    Since:
    
    Marvin 5.2
  - standardize
```
public void standardize(Molecule mol)
```
    Standardizes the molecule. This is the same as the default standardization, but performs daylight aromatization.
    
    Overrides:
    
    standardize in class CalculatorPlugin
    
    Parameters:
    
    mol - is the molecule to be standardized
  - isMultiThreadedRunEnabled
```
public boolean isMultiThreadedRunEnabled()
```
    For internal use only.
    
    Overrides:
    
    isMultiThreadedRunEnabled in class CalculatorPlugin
    
    Returns:
    
    true if multi-threaded run is enabled
  - getWarningMessage
```
public java.lang.String getWarningMessage()
```
    Description copied from class: CalculatorPlugin
    
    Returns the calculation warning information message. The default implementation returns the empty string.
    
    Overrides:
    
    getWarningMessage in class CalculatorPlugin
    
    Returns:
    
    the calculation warning information message

Class TautomerizationPlugin

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

warningMsgOn

Constructor Detail

TautomerizationPlugin

Method Detail

getProductName

hasTautomers

handlesMultiFragmentMolecules

setProgressMonitor

setParameters

setCleanResultStructures

getChangedAtomIndexes

setSymmetryFiltering

setMaxStructureCount

setpH

setTimeLimit

setMaximumTautomerizationPathLength

setProtectAromaticity

setProtectCharge

setExcludeAntiAromaticCompounds

setProtectDoubleBondStereo

setProtectAllTetrahedralStereoCenters

setProtectLabeledTetrahedralStereoCenters

setProtectEsterGroups

setRingChainTautomerizationAllowed

setInputMoleculeModified

checkMolecule

createStandardizedMolecule

createStandardizedMolecule

getExplicitHydrogenData

setInputMolecule

setTakePartialNeutralization

setWigglyBondVisibility

setTakeCanonicalForm

setTakeStandardForm

setNormalTautomerGenerationMode

setRationalTautomerGenerationMode

setTakeGenericTautomer

setTakeMostStableTautomer

setTakeMajorTautomer

setTakeDominantTautomers

setDominantTautomerDistributionCalculation

run

getDominantTautomerDistribution

getNewOldIndexMap

getOldNewIndexMap

getResultSource

getStructureCount

getStructure

getStructures

getResultTypes

getResultDomain

getResultCount

getResult

getResultAsString

getRemark

getErrorMessage

getTitle

standardize

isMultiThreadedRunEnabled

getWarningMessage