OEBroodGeneralOptions

Attention

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

class OEBroodGeneralOptions : public OESystem::OEOptions

This class provides an interface to setup basic options related to bioisosteric fragment replacement.

The OEBroodGeneralOptions class defines the following public methods:

GetAttachScale and SetAttachScale
GetBumpRadius and SetBumpRadius
GetScoreType and SetScoreType
GetIgnoreProtein and SetIgnoreProtein
GetIgnoreSelectionProtein and SetIgnoreSelectionProtein
GetRangeSize and SetRangeSize
GetRangeOffset and SetRangeOffset
GetRingOnly and SetRingOnly

Constructors

OEBroodGeneralOptions()
OEBroodGeneralOptions(const OEBroodGeneralOptions &)

Default and copy constructors.

operator=

Assignment operator.

GetAttachScale

double GetAttachScale() const

See SetAttachScale method.

GetBumpRadius

double GetBumpRadius() const

See SetBumpRadius method.

GetScoreType

unsigned GetScoreType() const

See SetScoreType method.

SetAttachScale

bool SetAttachScale(const double)

Sets the scaling factor for attachment point scores. This value determines the balance between the chemical color score and the attachment point scores. Higher values indicate more weighting for the attachment-point alignment. Default: 1.5.

SetBumpRadius

bool SetBumpRadius(const double)

Sets the minimum distance defining clash between ligand heavy atoms and protein heavy atoms. New analogs with atoms closer than this cutoff to the active-site protein are marked as clashing, and eventually discarded from the hitlist. Default: 2.25.

SetScoreType

bool SetScoreType(const unsigned)

Sets the method to be used for scoring overlap between the query fragment and the replacement fragment. Possible choices of methods are described in OEBroodScoreType. Default: ROCS.

GetIgnoreProtein

bool GetIgnoreProtein() const

See SetIgnoreProtein method.

GetIgnoreSelectionProtein

bool GetIgnoreSelectionProtein() const

See SetIgnoreSelectionProtein method.

GetRangeSize

unsigned GetRangeSize() const

See SetRangeSize method.

GetRangeOffset

unsigned GetRangeOffset() const

See SetRangeOffset method.

GetRingOnly

int GetRingOnly() const

See SetRingOnly method.

SetIgnoreProtein

bool SetIgnoreProtein(const bool)

Sets whether the protein associated with the query should be ignored during scoring. When true, receptor clash and protein-select checks are skipped even if a protein was provided to OECreateBroodQuery. Default: False.

SetIgnoreSelectionProtein

bool SetIgnoreSelectionProtein(const bool)

Sets whether the selectivity protein associated with the query should be ignored during scoring. When true, protein-select scoring is skipped even if a selectivity protein was provided to OECreateBroodQuery. Default: False.

SetRangeSize

bool SetRangeSize(const unsigned)

Sets the range of heavy atom counts around the query fragment heavy atom count to examine from the database. Fragments whose heavy atom count falls outside [queryHeavy - rangeOffset - rangeSize, queryHeavy - rangeOffset + rangeSize] are skipped. Default: 6.

SetRangeOffset

bool SetRangeOffset(const unsigned)

Sets a bias toward smaller or larger fragments relative to the query. A positive offset shifts the search window toward larger fragments; a negative offset toward smaller fragments. Works together with SetRangeSize. Default: 0.

SetRingOnly

bool SetRingOnly(const int)

Sets the requirement for rings in selecting a fragment. This flag has to do with a count of the number of ring atoms in the shortest path between attachment points in a fragment. In cases with more than 2 attachment points, all shortest paths are calculated and the number of ring atoms is summed. Default: -2