OETautomerOptions

class OETautomerOptions

This class is used for setting options during tautomer enumeration with OEEnumerateTautomers.

By default, OEEnumerateTautomers will return the “canonical” tautomer, regardless of the tautomer submitted to the function. This “canonical” tautomer is extremely useful for efficient and reliable tautomer cheminformatics, such as database searching. The OETautomerOptions.SetRankTautomers method can be used to make OEEnumerateTautomers generate a tautomer more “reasonable” for depiction for chemists.

Constructors

OETautomerOptions(maxGenerated: int = 4096, rank: bool = True,
                  warts: bool = False, level: int = 0,
                  carbonHybrid: bool = True,
                  saveStereo: bool = False, maxZoneSize: int = 35,
                  maxTautomericAtoms: int = 70,
                  maxTime: float = 120, kekule: bool = False,
                  clearCoords: bool = False, hybridLevel: int,
                  maxToReturn: int = 256, racemicType: int) -> OETautomerOptions

Default constructor.

OETautomerOptions(rhs: OETautomerOptions) -> OETautomerOptions

Copy constructor.

GetApplyWarts

GetApplyWarts() -> bool

Returns setting for warts application of {title}_1, {title}_2, etc., on tautomers.

GetCarbonHybridization

GetCarbonHybridization() -> bool

Returns setting for whether or not carbon hybridization changes are allowed. Allowing sp2-sp3 changes of carbon atoms can significantly increase computation time.

GetClearCoordinates

bool GetClearCoordinates() const

Returns whether input coordinates are cleared. The default value is false.

GetHybridizationLevel

GetHybridizationLevel() -> int

Returns setting for the level of hybridization changes allowed when carbon hybridization is allowed. Allowing carbon hybridization significantly increase computation time. The returned value is from the OEHybridizationLevel namespace.

See also

OEHybridizationLevel namespace

GetKekule

GetKekule() -> bool

Returns setting for whether or not generated tautomers are kekule or have aromaticity perceived.

GetLevel

GetLevel() -> int

Returns level for tautomerization. Higher levels allow less likely atomic transitions to occur.

GetMaxSearchTime

GetMaxSearchTime() -> float

Returns the maximum search time in seconds allowed for a molecule.

GetMaxTautomericAtoms

GetMaxTautomericAtoms() -> int

Returns the maximum number of tautomeric atoms allowed in a molecule. The default value is 70.

GetMaxTautomersGenerated

GetMaxTautomersGenerated() -> int

Returns setting for maximum number of tautomers that may be generated for each input molecule.

See also

OETautomerOptions.GetMaxTautomersToReturn method

GetMaxTautomersToReturn

GetMaxTautomersToReturn() -> int

Returns setting for maximum number of tautomers that may be returned for each input molecule.

See also

OETautomerOptions.GetMaxTautomersGenerated method

GetMaxZoneSize

GetMaxZoneSize() -> int

Returns setting for maximum number of atoms allowed in a continuous tautomerization zone. The default zone size is 35.

GetRacemicType

GetRacemicType() -> int

Returns setting for the way to handle loss of stereocenters, if the OETautomerOptions.GetSaveStereo method returns false. If the OETautomerOptions.GetSaveStereo method returns true, this option is irrelevant. The returned value is from the OERacemicType namespace. The default value is OERacemicType_LocalSampled.

See also

OETautomerOptions.GetSaveStereo method
OERacemicType namespace

GetRankTautomers

GetRankTautomers() -> bool

Returns setting for whether or not tautomers are ranked and ordered before being returned. By default, this is false, i.e., the canonical tautomer is returned as the first molecule in the iterator. As opposed to the most “reasonable” tautomer being returned first.

GetSaveStereo

GetSaveStereo() -> bool

Returns setting for whether atoms and bonds with labeled stereochemistry are fixed or allowed to participate in tautomerization.

See also

OETautomerOptions.GetRacemicType method

SetApplyWarts
SetApplyWarts(warts: bool) -> None
Sets whether warts of {title}_1, {title}_2, etc., are added to tautomers.

SetCarbonHybridization
SetCarbonHybridization(carbonHybrid: bool) -> None
Sets whether carbon hybridization changes are allowed. Allowing sp2-sp3 changes of carbon atoms can significantly increase computation time.

See also

OETautomerOptions.SetHybridizationLevel method
SetClearCoordinates
bool SetClearCoordinates(bool clear_coordinates)
Sets whether input coordinates are cleared from generated tautomers.
SetHybridizationLevel
SetHybridizationLevel(level: int) -> None
Sets level of hybridization changes allowed for carbon atoms if the OETautomerOptions.GetCarbonHybridization method returns true. If the OETautomerOptions.GetCarbonHybridization method returns false, this option is irrelevant.

level
This value has to be from the OEHybridizationLevel namespace.

Note

The level of hybridization can have significantly impact on the computation time.

See also

OETautomerOptions.SetCarbonHybridization method

OEHybridizationLevel namespace
SetKekule
SetKekule(kekule: bool) -> None
Sets whether tautomers are returned in kekule format or have aromaticity perceived.
SetLevel
SetLevel(level: int) -> None
Sets level for tautomerization. Higher levels allow less likely atomic transitions to occur.

SetMaxSearchTime
SetMaxSearchTime(maxTime: float) -> None
Sets the maximum search time in seconds allowed for a molecule.

SetMaxTautomericAtoms
SetMaxTautomericAtoms(maxTautomericAtoms: int) -> None
Sets the maximum number of tautomeric atoms allowed in a molecule.

SetMaxTautomersGenerated
SetMaxTautomersGenerated(max: int) -> None
Sets the maximum number of tautomers that may be generated per input molecule.

See also

OETautomerOptions.SetMaxTautomersToReturn method

SetMaxTautomersToReturn
SetMaxTautomersToReturn(max: int) -> None
Sets the maximum number of tautomers that may be returned per input molecule.

See also

OETautomerOptions.SetMaxTautomersGenerated method

SetMaxZoneSize
SetMaxZoneSize(maxZoneSize: int) -> None
Sets the maximum number of atoms allowed in a continuous tautomerization zone.

SetRacemicType
SetRacemicType(raceType: int) -> None
Sets the racemic type for loss of stereocenters if the OETautomerOptions.GetSaveStereo method returns false. If the OETautomerOptions.GetSaveStereo method returns true, this option is irrelevant.

racemicType
This value has to be from the OERacemicType namespace.

See also

OETautomerOptions.SetSaveStereo method

OERacemicType namespace
SetRankTautomers
SetRankTautomers(rank: bool) -> None
Sets whether or not tautomers are ranked and ordered before being returned. Setting this argument to true will cause the most “reasonable” tautomer to be returned as the first tautomer, opposed to the “canonical” tautomer being returned first.

The “canonical” tautomer may or may not be a suitable representative tautomer for depiction. To fill this role, the SetRankTautomers(true) provides “reasonable” tautomer forms for any input molecule.

SetSaveStereo
SetSaveStereo(saveStereo: bool) -> None
Sets whether atoms and bonds with labeled stereochemistry are fixed or allowed to participate in tautomerization.

See also

OETautomerOptions.SetRacemicType method