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.

See also

The OEMolBuilderOptions class defines the following public methods:

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.

See also

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.

See also

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.