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
OEBroodGeneralOptions(arg2: OEBroodGeneralOptions) -> OEBroodGeneralOptions

Default and copy constructors.

operator=

Assignment operator.

GetAttachScale

GetAttachScale() -> float

See SetAttachScale method.

GetBumpRadius

GetBumpRadius() -> float

See SetBumpRadius method.

GetScoreType

GetScoreType() -> int

See SetScoreType method.

SetAttachScale

SetAttachScale(value: float) -> bool

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

SetBumpRadius(value: float) -> bool

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

SetScoreType(value: int) -> bool

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

GetIgnoreProtein() -> bool

See SetIgnoreProtein method.

GetIgnoreSelectionProtein

GetIgnoreSelectionProtein() -> bool

See SetIgnoreSelectionProtein method.

GetRangeSize

GetRangeSize() -> int

See SetRangeSize method.

GetRangeOffset

GetRangeOffset() -> int

See SetRangeOffset method.

GetRingOnly

GetRingOnly() -> int

See SetRingOnly method.

SetIgnoreProtein

SetIgnoreProtein(value: bool) -> 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

SetIgnoreSelectionProtein(value: bool) -> 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

SetRangeSize(value: int) -> bool

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

SetRangeOffset(value: int) -> bool

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

SetRingOnly(value: int) -> bool

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