chemaxon.marvin.calculations
Class TautomerizationPlugin

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

All Implemented Interfaces:

chemaxon.license.Licensable

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 5.5, 04/06/2011

Author:

Nora Mate, Zsolt Mohacsi

Nested Class Summary

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

CalculatorPlugin.HydrogenData

Field Summary

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

TautomerizationPlugin()
Constructor.

Method Summary

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.
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)
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.
boolean	isMultiThreadedRunEnabled() For internal use only.
boolean	run() Calculates the tautomers.
void	setCleanResultStructures(boolean clean) Sets 2D cleaning of the result structures: if true then tautomers returned by getStructure(int) and getStructures() methods are cleaned in 2D.
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	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(chemaxon.common.util.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) Generates only rational tautomers
void	setRingChainTautomerizationAllowed(boolean allowed) Sets if ring tautomers are allowed or not.
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	setWigglyBondVisibility(boolean vis) Sets how wiggly bonds connected to double bonds are displayed.
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, getCalcMolecule, getDisplayMolecule, getDocument, getDoublePrecision, getInputMolDim, getMainMolecule, 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, 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

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

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(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

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

public void setCleanResultStructures(boolean clean)

Sets 2D cleaning of the result structures: if true then tautomers returned by getStructure(int) and getStructures() methods are 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

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. 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)

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

setRationalTautomerGenerationMode

public void setRationalTautomerGenerationMode(boolean rational)

Generates only rational tautomers

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)

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