OEFlipperOptions

class OEFlipperOptions : public OESystem::OEOptions

Constructors

OEFlipperOptions()
OEFlipperOptions(const OEFlipperOptions &)

Default and copy constructors.

GetAtomPredicate

const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>* GetAtomPredicate() const

See the SetAtomPredicate method.

GetBondPredicate

const OESystem::OEUnaryPredicate<OEChem::OEBondBase>* GetBondPredicate() const

See the SetBondPredicate method.

GetEnhancedStereo

bool GetEnhancedStereo() const

See the SetEnhancedStereo method.

GetEnumAtoms

bool GetEnumAtoms() const

See the SetEnumAtoms method.

GetEnumAtomSpecifiedStereo

bool GetEnumAtomSpecifiedStereo() const

See the SetEnumAtomSpecifiedStereo method.

GetEnumBonds

bool GetEnumBonds() const

See the SetEnumBonds method.

GetEnumBondSpecifiedStereo

bool GetEnumBondSpecifiedStereo() const

See the SetEnumBondSpecifiedStereo method.

GetEnumBridgehead

bool GetEnumBridgehead() const

See the SetEnumBridgehead method.

GetEnumEZ

bool GetEnumEZ() const

See the SetEnumEZ method.

GetEnumNitrogen

bool GetEnumNitrogen() const

See the SetEnumNitrogen method.

GetEnumRS

bool GetEnumRS() const

See the SetEnumRS method.

GetEnumRelativeAtomStereo

bool GetEnumRelativeAtomStereo() const

See the SetEnumRelativeAtomStereo method.

GetEnumSpecifiedStereo

bool GetEnumSpecifiedStereo() const

See the SetEnumSpecifiedStereo method.

GetMaxCenters

unsigned GetMaxCenters() const

See the SetMaxCenters method.

GetWarts

bool GetWarts() const

See the SetWarts method.

SetAtomPredicate

bool SetAtomPredicate(const OESystem::OEUnaryPredicate<OEChem::OEAtomBase>&)

Provides an input atom predicate to define the selection of the atom stereocenters which should be enumerated.

SetBondPredicate

bool SetBondPredicate(const OESystem::OEUnaryPredicate<OEChem::OEBondBase>&)

Provides an input bond predicate to define the selection of the bond stereocenters which should be enumerated.

SetEnhancedStereo

bool SetEnhancedStereo(const bool)

Sets whether to consider explicit MDL enhanced stereogroups during flipping. Enhanced stereogroups generally contain a collection of stereocenters which should be considered as a collective unit, where a “flip” implies that all centers in the group should be flipped, thus retaining the relative stereo parity between the grouped stereocenters. With this flag enabled, far fewer enantiomers will be generated than for individual stereocenter flipping activities, and relative stereo configurations will be retained. When enabled, explicitly marked absolute stereocenters are excluded from the flipping activities. Care should be taken to ensure that any custom atom predicate returns all atoms involved in enhanced stereogroups. Default: False

Note

The membership and type of existing enhanced stereogroups are not modified as a result of the flipping operation. That is, the explicit stereogroups of and and or are not promoted to abs groups as a result of stereocenter parity flips. This retains the source of original stereogroup(s) in the generated isomer(s) for post-flipping validations and processing. This behavior is true regardless of the setting of GetEnhancedStereo. Stereocenters can be explicitly promoted to abs centers by deletion of all stereogroups, or by deleting all stereogroups and adding marked stereocenters to a single new abs stereogroup.

SetEnumAtoms

bool SetEnumAtoms(const bool)

Sets whether to include R/S stereocenters in the enumeration or not. If false, disregards atom enumerations. Default: True

SetEnumAtomSpecifiedStereo

bool SetEnumAtomSpecifiedStereo(const bool)

Sets whether to force the modification of all R/S stereocenters in a molecule. If false, it will only enumerate stereocenters which do not already have a specified stereochemistry. Default: False

SetEnumBonds

bool SetEnumBonds(const bool)

Sets whether to include E/Z bonds in the enumeration. If false, disregards bond enumerations. Default: True

SetEnumBondSpecifiedStereo

bool SetEnumBondSpecifiedStereo(const bool)

Sets whether to force the modification of all E/Z stereocenters in a molecule. If false, it will only enumerate bonds which do not already have a specified stereochemistry. Default: False

SetEnumBridgehead

bool SetEnumBridgehead(const bool)

Sets whether to enumerate bridgehead stereocenters. Default: False

SetEnumEZ

bool SetEnumEZ(const bool)

Sets whether to enumerate E/Z stereocenters. Default: True

SetEnumNitrogen

bool SetEnumNitrogen(const bool)

Controls the behavior with respect to the enumeration of nonterminal nitrogens. Any nitrogen with pyramidal geometry in the initial model of the input molecule, and having no more than two ring bonds, is considered to be invertible. This will enumerate all possible puckers if set to true. Default: False

SetEnumRS

bool SetEnumRS(const bool)

Sets whether to enumerate R/S stereocenters. Default: True

SetEnumRelativeAtomStereo

bool SetEnumRelativeAtomStereo(const bool)

Sets whether to include enumeration of internally perceived relative atom stereocenters (e.g., 1,4-disubstituted cyclohexanes) in a molecule. If true, consider relative stereocenters during stereo enumeration. Default: False

SetEnumSpecifiedStereo

bool SetEnumSpecifiedStereo(const bool)

Sets whether to force the modification of all of the atom and bond stereocenters in a molecule. If false, it will only enumerate stereocenters which do not already have a specified stereochemistry. Default: False

SetMaxCenters

bool SetMaxCenters(const unsigned)

Sets the maximum number of stereocenters or groups of stereocenters which will be fully enumerated. Default: 12

SetWarts

bool SetWarts(const bool)

Sets whether to generate unique titles for molecules. Default: False