OEFragmentOptions

Attention

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

class OEFragmentOptions : public OESystem::OEOptions

This class provides an interface to set up options for fragmenting molecules when building a bioisosteric fragment database. These options control fragment generation, size constraints, and structural properties.

The OEFragmentOptions class defines the following public methods:

GetMaxChiral and SetMaxChiral
GetMaxDegree and SetMaxDegree
GetMaxHeavy and SetMaxHeavy
GetMaxMolWt and SetMaxMolWt
GetMinDegree and SetMinDegree
GetMinHeavy and SetMinHeavy
GetSingleSourceMol and SetSingleSourceMol
GetSmarts and SetSmarts
SetSmartsFile

Constructors

OEFragmentOptions()
OEFragmentOptions(const OEFragmentOptions &)

Default and copy constructors.

operator=

OEFragmentOptions &operator=(const OEFragmentOptions &)

Assignment operator.

GetMaxChiral

unsigned GetMaxChiral() const

See SetMaxChiral method.

GetMaxDegree

unsigned GetMaxDegree() const

See SetMaxDegree method.

GetMaxHeavy

unsigned GetMaxHeavy() const

See SetMaxHeavy method.

GetMaxMolWt

double GetMaxMolWt() const

See SetMaxMolWt method.

GetMinDegree

unsigned GetMinDegree() const

See SetMinDegree method.

GetMinHeavy

unsigned GetMinHeavy() const

See SetMinHeavy method.

GetSingleSourceMol

bool GetSingleSourceMol() const

See SetSingleSourceMol method.

GetSmarts

std::string GetSmarts() const

See SetSmarts method.

SetMaxChiral

bool SetMaxChiral(const unsigned)

Sets the maximum allowable number of chiral centers (atom and bond) in generated fragments. Default: 3.

SetMaxDegree

bool SetMaxDegree(const unsigned)

Sets the maximum allowed attachment points in generated fragments. Default: 3.

SetMaxHeavy

bool SetMaxHeavy(const unsigned)

Sets the maximum allowed heavy atoms in generated fragments. Default: 15.

SetMaxMolWt

bool SetMaxMolWt(const double)

Sets the maximum allowed molecular weight for generated fragments. Default: 350.

SetMinDegree

bool SetMinDegree(const unsigned)

Sets the minimum required attachment points in generated fragments. Default: 1.

SetMinHeavy

bool SetMinHeavy(const unsigned)

Sets the minimum required heavy atoms in generated fragments. Default: 1.

SetSingleSourceMol

bool SetSingleSourceMol(bool)

Sets whether to store only a single source molecule per fragment. When disabled (default), stores information for up to five source molecules. Default: false

SetSmarts

bool SetSmarts(const std::string value)

Sets the SMARTS pattern for bonds to break during fragmentation. Built-in options are recap, rlf, both (both rlf and recap), and all. Default: all

SetSmartsFile

bool SetSmartsFile(const std::string&)
bool SetSmartsFile(const OEPlatform::oeisstream value)

Sets SMARTS patterns for bonds to break from a file. The first overload accepts a filename and the second accepts an oeisstream. This method takes precedence over the SetSmarts method.