OEMolBuilderOptions

class OEMolBuilderOptions : public OESystem::OEOptions

This class provides an interface to set up options required for generating an initial 3D structure of a molecule by connecting pregenerated fragment coordinates that constitute the molecule.

Constructors

OEMolBuilderOptions() -> OEMolBuilderOptions
OEMolBuilderOptions(arg2: OEMolBuilderOptions) -> OEMolBuilderOptions

Default and copy constructors.

GetCanonOrder

GetCanonOrder() -> bool

See the SetCanonOrder method.

GetEnumNitrogen

GetEnumNitrogen() -> int

See the SetEnumNitrogen method.

GetEnumRing

GetEnumRing() -> bool

See the SetEnumRing method.

GetFragBuilderOptions

GetFragBuilderOptions() -> OEFragBuilderOptions

See the SetFragBuilderOptions method.

GetFromCT

GetFromCT() -> bool

See the SetFromCT method.

GetIgnoreStereo

GetIgnoreStereo() -> bool

See the SetIgnoreStereo method.

GetMaxEnumConfs

GetMaxEnumConfs() -> int

See the SetMaxEnumConfs method.

GetSampleHydrogens

GetSampleHydrogens() -> bool

See the SetSampleHydrogens method.

GetStrictAtomTypes

GetStrictAtomTypes() -> bool

See the SetStrictAtomTypes method.

SetCanonOrder

SetCanonOrder(value: bool) -> bool

This method can be used to enable/disable the automatic reordering of input molecules to a canonical atom and bond order. In order to obtain consistent results from different file formats and different connection table orders, OMEGA reorders the input connection table. If true, the atoms of the molecule are indexed in canonical order before building the molecule structure. Default: True

SetEnumNitrogen

SetEnumNitrogen(value: int) -> bool

Sets whether the generated initial conformation should be enumerated for invertible nitrogens. Default: OENitrogenEnumeration_Unspecified

SetEnumRing

SetEnumRing(value: bool) -> bool

Sets whether the generated initial conformation should be enumerated for ring stereo. If true, the builder will enumerate alternate ring conformations and generate multiple conformations, if available. Default: True

SetFragBuilderMode

SetFragBuilderMode(mode: int) -> bool

Sets the OEFragBuilderOptions parameter defaults corresponding to the specified mode.

SetFragBuilderOptions

SetFragBuilderOptions(opts: OEFragBuilderOptions) -> None

Sets OEFragBuilderOptions related to building fragment coordinates.

SetFromCT

SetFromCT(value: bool) -> bool

Sets whether the initial 3D coordinates should be generated from the connection table of the input molecule. If true, the initial 3D coordinates are generated from the connection table. Default: True

SetIgnoreStereo

SetIgnoreStereo(value: bool) -> bool

Sets whether conformer generation should continue even when specified stereo signatures in a molecule could not be honored. Default: False

SetMaxEnumConfs

SetMaxEnumConfs(value: int) -> bool

Sets the maximum number of conformers to be generated during enumeration. Default: 1024

SetSampleHydrogens

SetSampleHydrogens(value: bool) -> bool

Sets whether hydrogen sampling should be performed on generated structures. If true, hydrogen sampling is performed. Default: False

SetStrictAtomTypes

SetStrictAtomTypes(value: bool) -> bool

Sets whether strict definition of atom typing should be used. If true, a molecule will fail if any atom does not have a valid atom type. Calling this method with false will allow the atom typer to look for a different atom type of the same element and replace the failing atom type with a valid one that is “close enough.” Default: True