Package chemaxon.marvin.calculations

Class TautomerizationPlugin

  • All Implemented Interfaces:
    chemaxon.license.Licensable
    @PublicAPI
public final 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

    • Field Detail

      • warningMsgOn

        public static boolean warningMsgOn

    • Constructor Detail

      • TautomerizationPlugin

        public TautomerizationPlugin()
        Constructor. Creates the tautomerization object.

    • Method Detail

      • 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​(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

      • 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

      • 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

      • setTakeGenericTautomer

        public void setTakeGenericTautomer​(boolean generic,
                                   boolean nGeneric)

      • 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

      • getResultCount

        public int getResultCount​(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()

      • getResultAsString

        public String getResultAsString​(Object type,
                                int index,
                                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 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 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 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 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