OEExtrinsicPropOptions¶

Attention

This is a preliminary API and may be improved based on user feedback. It is currently available in C++ and Python.

class OEExtrinsicPropOptions : public OESystem::OEOptions

This class provides an interface to setup options related to medicinal chemistry property limits during fragment replacement scoring.

The OEExtrinsicPropOptions class defines the following public methods:

GetComplexity and SetComplexity
GetFrequency and SetFrequency
GetLipinski and SetLipinski
GetLipinskiAcc and SetLipinskiAcc
GetLipinskiDon and SetLipinskiDon
GetLogP and SetLogP
GetMartin and SetMartin

Constructors¶

OEExtrinsicPropOptions(const unsigned)
OEExtrinsicPropOptions(const OEExtrinsicPropOptions &)

Default and copy constructors.

operator=¶

OEExtrinsicPropOptions &operator=(const OEExtrinsicPropOptions &)=default

Assignment operator.

GetComplexity¶

double GetComplexity() const

See SetComplexity method.

GetFrequency¶

unsigned GetFrequency() const

See SetFrequency method.

GetLipinski¶

unsigned GetLipinski() const

See SetLipinski method.

GetLipinskiAcc¶

unsigned GetLipinskiAcc() const

See SetLipinskiAcc method.

GetLipinskiDon¶

unsigned GetLipinskiDon() const

See SetLipinskiDon method.

GetLogP¶

double GetLogP() const

See SetLogP method.

GetMartin¶

double GetMartin() const

See SetMartin method.

SetComplexity¶

bool SetComplexity(const double)

Sets the molecular complexity range for any selected analog. Default: [Min: 0.0, Max: 1.0]

SetFrequency¶

bool SetFrequency(const unsigned)

Sets the fragment frequency in the database for any selected analog. The frequency is a percentile number indicating the frequency of each fragment normalized relative to the frequency of fragments in the database. Frequency as assessed here is a measure of how common each fragment is among the source molecules. The most commonly occurring fragment would be in the 99th percentile, while the least commonly occurring fragments would be in the 1st percentile. Default: [Min: 0, Max: 100]

SetLipinski¶

bool SetLipinski(const unsigned)

Sets the allowed Lipinski violations for any selected analog. In order to segregate molecules that progressed through clinical trials, Lipinski determined that one violation was acceptable, but two were not [Lipinski-1997]. Default: [Min: 0 Max: 1]

SetLipinskiAcc¶

bool SetLipinskiAcc(const unsigned)

Sets the required number of Lipinski hydrogen bond acceptors for any selected analog. For the purpose of this measure, H-bond acceptors are determined by the method of Lipinski [Lipinski-1997]. Default: [Min: 2, Max: 11]

SetLipinskiDon¶

bool SetLipinskiDon(const unsigned)

Sets the required number of Lipinski hydrogen bond donors for any selected analog. For the purpose of this measure, H-bond donors are determined by the method of Lipinski [Lipinski-1997]. Default: [Min: 1, Max: 8]

SetLogP¶

bool SetLogP(const double)

Sets the required calculated LogP for any selected analog. Default: [Min: -1.0, Max: 5.0]

SetMartin¶

bool SetMartin(const double)

Sets the required Abbott Bioavailability Score (ABS) for any selected analog. This floating point ABS parameter (range 0.0-1.0) indicates the minimum allowable probability that F will be >10% in rats according the QSAR model developed and published by Yvonne Martin [Martin-2005]. A value of 0.0 will allow all compounds to pass. Default: [Min: 0.2, Max: 1.0]