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.
OETautomerOptions(unsigned int maxGenerated=4096, bool rank=true, bool warts=false,
unsigned int level=0, bool carbonHybrid=true,
bool saveStereo=false, unsigned int maxZoneSize=35,
unsigned int maxTautomericAtoms = 70, float maxTime = 120,
bool kekule = false, bool clearCoords = false,
unsigned int hybridLevel = OEHybridizationLevel::EnolEnamine,
unsigned int maxToReturn = 256,
unsigned int racemicType = OERacemicType::LocalSampled)
Default constructor.
OETautomerOptions(const OETautomerOptions &rhs)
Copy constructor.
bool GetApplyWarts() const
Returns setting for warts application of {title}_1, {title}_2, etc, on tautomers.
bool GetCarbonHybridization() const
Returns setting for whether or not carbon hybridization changes are allowed. Allowing sp2-sp3 changes of carbon atoms can significantly increase computation time.
bool GetClearCoordinates() const
Returns whether input coordinates are cleared. The default value is false.
unsigned int GetHybridizationLevel() const
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
bool GetKekule() const
Returns setting for whether or not generated tautomers are kekule or have aromaticity perceived.
unsigned int GetLevel() const
Returns level for tautomerization. Higher levels allow less likely atomic transitions to occur.
float GetMaxSearchTime() const
Returns the maximum search time in seconds allowed for a molecule.
unsigned int GetMaxTautomericAtoms() const
Returns the maximum number of tautomeric atoms allowed in a molecule. The default value is 70.
unsigned int GetMaxTautomersGenerated() const
Returns setting for maximum number of tautomers that may be generated for each input molecule.
See also
unsigned int GetMaxTautomersToReturn() const
Returns setting for maximum number of tautomers that may be returned for each input molecule.
See also
unsigned int GetMaxZoneSize() const
Returns setting for maximum number of atoms allowed in a continuous tautomerization zone. The default zone size is 35.
unsigned int GetRacemicType() const
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
bool GetRankTautomers() const
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.
bool GetSaveStereo() const
Returns setting for whether atoms and bonds with labeled stereochemistry are fixed or allowed to participate in tautomerization.
See also
void SetApplyWarts(bool warts)
Sets whether warts of {title}_1, {title}_2, etc, are added to tautomers.
void SetCarbonHybridization(bool carbonHybrid)
Sets whether carbon hybridization changes are allowed. Allowing sp2-sp3 changes of carbon atoms can significantly increase computation time.
See also
void SetClearCoordinates(bool clear_coordinates)
Sets whether input coordinates are cleared from generated tautomers.
void SetHybridizationLevel(unsigned int level)
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.
Note
The level of hybridization can have significantly impact on the computation time.
See also
void SetKekule(bool kekule)
Sets whether tautomers are returned in kekule format or have aromaticity perceived.
void SetLevel(unsigned int level)
Sets level for tautomerization. Higher levels allow less likely atomic transitions to occur.
void SetMaxSearchTime(float maxSearchTime)
Sets the maximum search time in seconds allowed for a molecule.
void SetMaxTautomericAtoms(unsigned int maxTautomerAtoms)
Sets the maximum number of tautomeric atoms allowed in a molecule.
void SetMaxTautomersGenerated(unsigned int max)
Sets the maximum number of tautomers that may be generated per input molecule.
See also
void SetMaxTautomersToReturn(unsigned int max)
Sets the maximum number of tautomers that may be returned per input molecule.
See also
void SetMaxZoneSize(unsigned int maxZoneSize)
Sets the maximum number of atoms allowed in a continuous tautomerization zone.
void SetRacemicType(unsigned int racemicType)
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.
See also
void SetRankTautomers(bool rank)
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.
void SetSaveStereo(bool saveStereo)
Sets whether atoms and bonds with labeled stereochemistry are fixed or allowed to participate in tautomerization.
See also