OEFPDatabase

class OEFPDatabase

The OEFPDatabase class is designed to perform rapid in-memory fingerprint searches. Each OEFPDatabase object is associated with a fingerprint type (OEFPTypeBase) that is specified when the database is constructed. An OEFPDatabase object can only store fingerprints (OEFingerPrint) with this specified type.

Constructors¶

OEFPDatabase(unsigned int fptype)

Creates an OEFPDatabase object that can store OEFingerPrint objects with fptype type from the OEFPType namespace.

OEFPDatabase(const OEGraphSim::OEFPTypeBase *)

Creates an OEFPDatabase object that can store OEFingerPrint objects with OEFPTypeBase type.

Note

By default, an OEFPDatabase object is constructed with:

no cutoff value
Tanimoto similarity measure
descending order to return scores when calling the OEFPDatabase.GetSortedScores method

These default values can be altered by the following methods:

OEFPDatabase.SetCutoff
OEFPDatabase.SetSimFunc

AddFP¶

unsigned int AddFP(const OEChem::OEMolBase &mol)

Generates an OEFingerPrint object from the OEMolBase molecule with the fingerprint type of the OEFPDatabase. The generated OEFingerPrint object is then inserted into the database returning its index. This method will return -1, if the fingerprint generation was unsuccessful.

unsigned int AddFP(const OEGraphSim::OEFingerPrint &fp)

Creates a copy of the OEFingerPrint object, inserts it into the database, and then returns its index. If the type of the passed fingerprint was different from the type of the database, than the insertion is unsuccessful and this method will return -1.

Note

The index returned by the OEFPDatabase.AddFP method is a unique number starting from zero. This index can be used as a reference number to associate the fingerprint with the molecule from which is it generated.

ClearCutoff¶

void ClearCutoff()

Removes the cutoff value previously set by the OEFPDatabase.SetCutoff method. After clearing the cutoff value OEFPDatabase.HasCutoff method will return false.

See also

OEFPDatabase.GetCutoff
OEFPDatabase.HasCutoff
OEFPDatabase.SetCutoff

GetCutoff¶

float GetCutoff() const

Returns the cutoff value previously set by the OEFPDatabase.SetCutoff method.

See also

OEFPDatabase.ClearCutoff
OEFPDatabase.HasCutoff
OEFPDatabase.SetCutoff

GetFPTypeBase¶

const OEGraphSim::OEFPTypeBase *GetFPTypeBase() const

Returns the fingerprint type of the OEFPDatabase object.

GetFingerPrints¶

OESystem::OEIterBase<const OEGraphSim::OEFingerPrint> *GetFingerPrints() const

Returns a iterator pointer over fingerprints (OEFingerPrint) stored in the OEFPDatabase object. The returned OEFingerPrint objects can only be accessed by const methods or functions, i.e., they can not be modified.

GetScores¶

OESystem::OEIterBase<OEGraphSim::OESimScore> *
  GetScores(const OEChem::OEMolBase &mol, unsigned int bgn=0,
            unsigned int end=0) const

OESystem::OEIterBase<OEGraphSim::OESimScore> *
  GetScores(const OEGraphSim::OEFingerPrint &fp, unsigned int bgn=0,
            unsigned int end=0) const

Performs a similarity calculation between a given molecule or a fingerprint and the fingerprints stored in the OEFPDatabase object. It returns an iterator over the calculated similarity scores (OESimScore). Each OESimScore holds a similarity score and index of the corresponding fingerprint of the database.

If the method is called with an OEMolBase object, then a fingerprint is generated from this molecule before looping over the fingerprints of the database and calculating similarities. If it is called with an OEFingerPrint object, then its type has to match with the type of the OEFPDatabase.

The bgn and end arguments define the segment of the database on which the similarity calculation will take place. If both of these parameters are omitted (or set to zero), then the similarity calculation is performed on the entire fingerprint database.

Note

By default, the OEFPDatabase.GetScores methods calculates Tanimoto similarity scores and will always return these scores in order in which the corresponding OEFingerPrint objects are added to the database.

By using the OEFPDatabase.SetSimFunc method, similarity measures other than the default can be performed. The behavior of OEFPDatabase.GetScores is also influenced by the cutoff value (OEFPDatabase.SetCutoff) of the database and the order of the scores specified by the OEFPDatabase.SetSimFunc method. If a cutoff value was set, then the OEFPDatabase.GetScores method will

return scores that are equal to or larger than the specified cutoff value if the order is descending
return scores that are equal to or smaller than the specified cutoff value if the order is ascending

See also

OEFPDatabase.SetSimFunc method
OEFPDatabase.SetCutoff method

Examples:

Calculates the:oeconst:Tanimoto#OEGraphSim::OESimMeasure::Tanimoto# similarity on the first 100 entries of the database and returns scores that are equal to or larger than 0.1.

descending = True 
fpdb.SetSimFunc(OESimMeasure_Tanimoto, descending)
fpdb.SetCutoff(0.1)
for score in fpdb.GetScores(qfp, 0, 100):
    print "%.3f" % score.GetScore()

Calculates the Tversky similarity (with $\alpha=0.9$ and $\beta=0.1$ ) on the entire database and returns all scores.

fpdb.SetSimFunc(OETverskySim(0.9))
for score in fpdb.GetScores(qfp):
    print "%.3f" % score.GetScore()

Calculates the Dice similarity beginning at the 100th entry of the database and returns scores that are equal to or smaller than 0.5.

descending = True
fpdb.SetSimFunc(OESimMeasure_Dice, not descending)
fpdb.SetCutoff(0.5)
for score in fpdb.GetScores(qfp, 100):
    print "%.3f" % score.GetScore()

GetSortedScores¶

OESystem::OEIterBase<OEGraphSim::OESimScore> *
  GetSortedScores(const OEChem::OEMolBase &mol, unsigned int limit=0,
                  unsigned int bgn=0, unsigned int end=0) const

OESystem::OEIterBase<OEGraphSim::OESimScore> *
  GetSortedScores(const OEGraphSim::OEFingerPrint &fp, unsigned int limit=0,
                  unsigned int bgn=0, unsigned int end=0) const

Performs similarity calculations between a molecule or a fingerprint and the fingerprints stored in the OEFPDatabase object. It returns a iterator over the calculated similarity scores (OESimScore) in sorted order. Each OESimScore holds a similarity score and index of the corresponding fingerprint of the database.

If the method is called with an OEMolBase object, then a fingerprint is generated from this molecule before looping over the fingerprints of the database and calculating similarities. If it is called with an OEFingerPrint object, then its type has to match with the type of the OEFPDatabase.

The bgn and end arguments define the segment of the database on which the similarity calculation will take place. If both of these parameters are omitted (or set to zero), then the similarity calculation is performed on the entire fingerprint database.

The limit argument defines the number of similarity scores returned by the OEFPDatabase.GetSortedScores method. If it is omitted (or set to zero) then all of the similarity scores are returned.

Note

By default, the OEFPDatabase.GetSortedScores method calculates Tanimoto similarity scores and returns them in descending order.

The OEFPDatabase.SetSimFunc method allows other similarity measures to be used. The behavior of OEFPDatabase.GetScores is also influenced by the cutoff value (OEFPDatabase.SetCutoff) of the database and the order of the scores specified by the OEFPDatabase.SetSimFunc method.

Examples:

Calculates the Tanimoto similarity on the entire database and returns the 10 best scores in descending order.
```
for score in fpdb.GetSortedScores(qfp, 10):
    print "%.3f" % score.GetScore()
```

Calculates the Dice similarity on the first 100 entries of the database and returns scores that are equal to or larger than 0.5 in descending order.

descending = True
fpdb.SetSimFunc(OESimMeasure_Dice, descending)
fpdb.SetCutoff(0.5)
for score in fpdb.GetSortedScores(qfp, 0 , 0, 100):
    print "%.3f" % score.GetScore()

Calculates Manhattan similarity beginning at the 100th entry of the database and returns the “worst” 5 scores that are equal to or smaller than 0.3 in ascending order.

descending = True
fpdb.SetSimFunc(OESimMeasure_Manhattan, not descending)
fpdb.SetCutoff(0.3)
for score in fpdb.GetSortedScores(qfp, 5, 100):
    print "%.3f" % score.GetScore()

HasCutoff¶

bool HasCutoff() const

Returns whether the cutoff value of the OEFPDatabase object has been set by the OEFPDatabase.SetCutoff method.

See also

OEFPDatabase.ClearCutoff
OEFPDatabase.GetCutoff
OEFPDatabase.SetCutoff

NumFingerPrints¶

unsigned int NumFingerPrints() const

Returns the number of OEFingerPrint objects stored in the database.

SetCutoff¶

void SetCutoff(float)

Sets the cutoff value of the OEFPDatabase object. The cutoff value influences the behavior of both the OEFPDatabase.GetScores and the OEFPDatabase.GetSortedScores methods.

See also

OEFPDatabase.ClearCutoff
OEFPDatabase.HasCutoff
OEFPDatabase.SetCutoff

SetSimFunc¶

Sets the method used to evaluate fingerprint similarity when calling either the OEFPDatabase.GetScores or the OEFPDatabase.GetSortedScores methods.

void SetSimFunc(unsigned int simtype, bool descending=true)

Sets the similarity calculation by specifying a similarity method with a constant from the OESimMeasure namespace. The second argument defines the order in which the calculated scores are returned by the OEFPDatabase.GetSortedScores method.

void SetSimFunc(const OEGraphSim::OESimFuncBase &, bool descending=true)

Creates a copy of the OESimFuncBase object and uses its OESimFuncBase.operator() method to evaluate similarity between two OEFingerPrint objects. The second argument defines the order in which the calculated scores are returned by the OEFPDatabase.GetSortedScores method.

Note

By default, both the OEFPDatabase.GetScores and the OEFPDatabase.GetSortedScores methods calculate Tanimoto similarity scores. While the OEFPDatabase.GetScores always returns these scores in order in which the corresponding OEFingerPrint objects are added to the database, the latter method returns them in descending order, by default.

See also

Searching with User-defined Similarity Measures section
User-defined Similarity Measures section
OESimMeasure namespace
OETanimotoSim class
OETverskySim class

OEFPDatabase

Constructors¶

AddFP¶

ClearCutoff¶

GetCutoff¶

GetFPTypeBase¶

GetFingerPrints¶

GetScores¶

GetSortedScores¶

HasCutoff¶

NumFingerPrints¶

SetCutoff¶

SetSimFunc¶

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OEFPDatabase

Constructors¶

AddFP¶

ClearCutoff¶

GetCutoff¶

GetFPTypeBase¶

GetFingerPrints¶

GetScores¶

GetSortedScores¶

HasCutoff¶

NumFingerPrints¶

SetCutoff¶

SetSimFunc¶

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