OEMolBuilderOptions

class OEMolBuilderOptions : public OESystem::OEOptions

This class provides an interface to setup options required for generating an initial 3D structure of a molecule, by connecting pre-generated fragment coordinates that constitute the molecule.

Constructors

OEMolBuilderOptions()
OEMolBuilderOptions(const OEMolBuilderOptions &)

Default and copy constructors.

operator=

OEMolBuilderOptions &operator=(const OEMolBuilderOptions &)

Assignment operator.

GetCanonOrder

bool GetCanonOrder() const

See SetCanonOrder method.

GetEnumNitrogen

unsigned int GetEnumNitrogen() const

See SetEnumNitrogen method.

GetEnumRing

bool GetEnumRing() const

See SetEnumRing method.

GetFragBuilderOptions

      OEFragBuilderOptions& GetFragBuilderOptions()
const OEFragBuilderOptions& GetFragBuilderOptions() const

See SetFragBuilderOptions method.

GetFromCT

bool GetFromCT() const

See SetFromCT method.

GetIgnoreStereo

bool GetIgnoreStereo() const

See SetIgnoreStereo method.

GetMaxEnumConfs

unsigned GetMaxEnumConfs() const

See SetMaxEnumConfs method.

GetSampleHydrogens

bool GetSampleHydrogens() const

See SetSampleHydrogens method.

GetStrictAtomTypes

bool GetStrictAtomTypes() const

See SetStrictAtomTypes method.

SetCanonOrder

bool SetCanonOrder(const bool)

This method can be used to enable/disable the automatic reordering of input molecules to a canonical atom and bond order. In order 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

bool SetEnumNitrogen(const unsigned int)

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

SetEnumRing

bool SetEnumRing(const 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

bool SetFragBuilderMode(const unsigned mode)

Sets the OEFragBuilderOptions parameter defaults corresponding to the specified mode.

SetFragBuilderOptions

void SetFragBuilderOptions(const OEFragBuilderOptions&)

Sets OEFragBuilderOptions related to building fragment coordinates.

SetFromCT

bool SetFromCT(const 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

bool SetIgnoreStereo(const bool)

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

SetMaxEnumConfs

bool SetMaxEnumConfs(const unsigned)

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

SetSampleHydrogens

bool SetSampleHydrogens(const bool)

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

SetStrictAtomTypes

bool SetStrictAtomTypes(const 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.