Package chemaxon.marvin.calculations
Class TautomerizationPlugin
- java.lang.Object
-
- chemaxon.marvin.plugin.CalculatorPlugin
-
- chemaxon.marvin.calculations.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
-
-
Nested Class Summary
-
Nested classes/interfaces inherited from class chemaxon.marvin.plugin.CalculatorPlugin
CalculatorPlugin.HydrogenData
-
-
Field Summary
Fields Modifier and Type Field 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
-
-
Constructor Summary
Constructors Constructor Description TautomerizationPlugin()
Constructor.
-
Method Summary
All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods Modifier and Type Method 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.String
getErrorMessage()
Returns the calculation error information message or the empty string if there is no error.protected List<CalculatorPlugin.HydrogenData>
getExplicitHydrogenData(Molecule cmol, int n)
int[]
getNewOldIndexMap()
int[]
getOldNewIndexMap()
String
getProductName()
Returns the product identifier of the plugin as given byLicenseManager
.String
getRemark()
Returns a warning message if there are no tautomers,null
otherwise.Object
getResult(Object type, int index)
Returns the result item for the specified key and index.String
getResultAsString(Object type, int index, Object result)
Returns the specified result in String format.int
getResultCount(Object type)
Returns the number of result items for the given result key.int
getResultDomain(Object type)
Returns the calculation domain.chemaxon.marvin.plugin.PluginMDocSource
getResultSource()
Returns the result as a document source object.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 bygetStructure(int)
String
getTitle()
Returns the frame title.String
getWarningMessage()
Returns the calculation warning information message.boolean
handlesMultiFragmentMolecules()
Returnstrue
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 methodvoid
setDiaStereoIsomerMixtureAllowedState(boolean dsma)
void
setDominantTautomerDistributionCalculation(boolean distrib)
Sets dominant tautomer distribution calculation: iftrue
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.protected Molecule
setMolecule(Molecule mol, boolean st, boolean om, boolean storeExplicitHydrogens)
void
setNormalTautomerGenerationMode(boolean normal)
Generates only normal tautomers.void
setParameters(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 inrun()
to display progress status.void
setProtectAllTetrahedralStereoCenters(boolean protect)
Sets the protection of all tetrahedral stereo centers: iftrue
then all tetrahedral stereo information is preserved by the tautomer generator.void
setProtectAromaticity(boolean pa)
Sets aromaticity protection: iftrue
then aromatic bonds are not modified by the tautomer generator.void
setProtectCharge(boolean pc)
Sets charge protection: iftrue
then the charge of charged atoms are not modified by the tautomer generator.void
setProtectDoubleBondStereo(boolean protect)
Sets double bond stereo protection: iftrue
then double bonds stereo information is preserved by the tautomer generator.void
setProtectEsterGroups(boolean protect)
Sets the protection of ester groups: iftrue
then ester groups are excluded from the tautomerization.void
setProtectLabeledTetrahedralStereoCenters(boolean protect)
Sets the protection of labeled tetrahedral stereo centers: iftrue
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.
Defaulttrue
void
setSymmetryFiltering(boolean filtering)
Sets symmetry fitlering: iftrue
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
setTakeGenericTautomer(boolean generic, boolean nGeneric)
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
addHeavyAtomLimitChecker, addInputChecker, 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, standardizeIonicGroups, standardizeNeutralGroups
-
-
-
-
Method Detail
-
getProductName
public String getProductName()
Returns the product identifier of the plugin as given byLicenseManager
.- Specified by:
getProductName
in classCalculatorPlugin
- 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()
Returnstrue
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. Returnstrue
if parameter "single" is set to "false",false
otherwise (default:false
).- Overrides:
handlesMultiFragmentMolecules
in classCalculatorPlugin
- Returns:
- true if the plugin handles multifragment molecules, false otherwise
-
setProgressMonitor
public void setProgressMonitor(MProgressMonitor pmon)
Sets a progress observer to be used inrun()
to display progress status. Short calculations may ignore the observer object. The default implementation does nothing.- Overrides:
setProgressMonitor
in classCalculatorPlugin
- Parameters:
pmon
- is the progress monitor, may benull
-
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 classCalculatorPlugin
- Parameters:
params
- is the parameter table- Throws:
PluginException
- on error
-
setCleanResultStructures
@Deprecated public void setCleanResultStructures(boolean clean)
Deprecated.obsolate methodSets 2D cleaning of the result structures: iftrue
then the changed atoms in tautomers returned bygetStructure(int)
are partial cleaned in 2D. Should be called before setting input molecule. Default:false
.- Parameters:
clean
- iftrue
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 afterrun()
. Returnsnull
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: iftrue
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 thefiltering
parameter. Default:true
.- Parameters:
filtering
- istrue
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. Iflength = 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: iftrue
then aromatic bonds are not modified by the tautomer generator. Has no effect in case of generic tautomer. Default:true
.- Parameters:
pa
- istrue
if aromaticity should be protected- Since:
- Marvin 5.0.2
-
setProtectCharge
public void setProtectCharge(boolean pc)
Sets charge protection: iftrue
then the charge of charged atoms are not modified by the tautomer generator. Has no effect in case of generic tautomer. Default:false
.- Parameters:
pc
- istrue
if charges should be protected- Since:
- Marvin 5.0.1
-
setExcludeAntiAromaticCompounds
public void setExcludeAntiAromaticCompounds(boolean aa)
Sets whether antiaromatic compounds should be generated. Iftrue
then antiaromatic compounds are not generated. Has no effect in case of generic tautomer. Default:true
.- Parameters:
aa
- istrue
if antiaromatic compounds should not be generated- Since:
- Marvin 5.0.1
-
setProtectDoubleBondStereo
public void setProtectDoubleBondStereo(boolean protect)
Sets double bond stereo protection: iftrue
then double bonds stereo information is preserved by the tautomer generator. Has no effect in case of generic tautomer. Default:false
.- Parameters:
protect
- istrue
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: iftrue
then all tetrahedral stereo information is preserved by the tautomer generator. Default:false
.- Parameters:
protect
- istrue
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: iftrue
then labeled tetrahedral stereo centers are protected by the tautomer generator. Has no effect in case of generic tautomer. Default:false
.- Parameters:
protect
- istrue
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: iftrue
then ester groups are excluded from the tautomerization. Default:true
. Has no effect in case of generic tautomer.- Parameters:
protect
- istrue
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.
Defaulttrue
- 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
- istrue
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 classCalculatorPlugin
- 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 classCalculatorPlugin
- Parameters:
mol
- is the input moleculeom
- 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 classCalculatorPlugin
- Parameters:
mol
- is the input molecule- Returns:
- the standardized molecule
- Throws:
PluginException
- on error- See Also:
#see #is InputMoleculeModified()
-
getExplicitHydrogenData
protected List<CalculatorPlugin.HydrogenData> getExplicitHydrogenData(Molecule cmol, int n)
- Overrides:
getExplicitHydrogenData
in classCalculatorPlugin
-
setMolecule
protected Molecule setMolecule(Molecule mol, boolean st, boolean om, boolean storeExplicitHydrogens) throws PluginException
- Overrides:
setMolecule
in classCalculatorPlugin
- Throws:
PluginException
-
setInputMolecule
protected void setInputMolecule(Molecule mol) throws PluginException
Sets the input molecule.- Specified by:
setInputMolecule
in classCalculatorPlugin
- 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
- iftrue
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
- iftrue
then wiggly bonds connected to double bonds are show as wiggly bonds, iffalse
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
- istrue
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
-
setDiaStereoIsomerMixtureAllowedState
public void setDiaStereoIsomerMixtureAllowedState(boolean dsma)
-
setRationalTautomerGenerationMode
@Deprecated public void setRationalTautomerGenerationMode(boolean rational)
Deprecated.Generates only rational tautomers. UsesetNormalTautomerGenerationMode(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
- istrue
if generic tautomer should be generated- Since:
- Marvin 5.1
- See Also:
getStructure(int)
,getStructures()
,getStructureCount()
,setProtectAllTetrahedralStereoCenters(boolean)
-
setTakeGenericTautomer
public void setTakeGenericTautomer(boolean generic, boolean nGeneric)
-
setTakeMostStableTautomer
@Deprecated public void setTakeMostStableTautomer(boolean mostStable)
Deprecated.Not used.Sets whether most stable tautomer should be generated. Default:false
.- Parameters:
mostStable
- istrue
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
- istrue
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
- istrue
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: iftrue
then dominant tautomer distribution is calculated. UsegetStructure(int)
to get the dominant tautomer structure andgetDominantTautomerDistribution(int)
to get its distribution.- Parameters:
distrib
- iftrue
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 classCalculatorPlugin
- 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. UsegetStructure(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 classCalculatorPlugin
- 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 bygetStructure(int)
Returns tautomers inMolecule[]
array..- Returns:
- tautomers
- See Also:
setTakeCanonicalForm(boolean)
,setTakeDominantTautomers(boolean)
-
getResultTypes
public Object[] getResultTypes()
Returns the result types.- Overrides:
getResultTypes
in classCalculatorPlugin
- Returns:
- the result types
-
getResultDomain
public int getResultDomain(Object type)
Returns the calculation domain.- Overrides:
getResultDomain
in classCalculatorPlugin
- Parameters:
type
- is the result type- Returns:
- the calculation domain
- See Also:
getResultTypes()
-
getResultCount
public int getResultCount(Object type)
Returns the number of result items for the given result key.- Overrides:
getResultCount
in classCalculatorPlugin
- Parameters:
type
- is the result type- Returns:
- the number of result items
- See Also:
getResultTypes()
-
getResult
public Object getResult(Object type, int index) throws PluginException
Returns the result item for the specified key and index.- Overrides:
getResult
in classCalculatorPlugin
- Parameters:
type
- is the result typeindex
- 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 String getResultAsString(Object type, int index, Object result) throws PluginException
Returns the specified result in String format.- Overrides:
getResultAsString
in classCalculatorPlugin
- Parameters:
type
- is the result typeindex
- is the result indexresult
- 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 classCalculatorPlugin
- 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 classCalculatorPlugin
- Returns:
- the calculation error information message
-
getTitle
public 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 classCalculatorPlugin
- Parameters:
mol
- is the molecule to be standardized
-
isMultiThreadedRunEnabled
public boolean isMultiThreadedRunEnabled()
For internal use only.- Overrides:
isMultiThreadedRunEnabled
in classCalculatorPlugin
- 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 classCalculatorPlugin
- Returns:
- the calculation warning information message
-
-