OEMolBuilderOptions

Attention

PRELIMINARY-IMAGE This is a preliminary API until 2019.Oct and may be improved based on user feedback. It is currently available in C++ and Python.

class OEMolBuilderOptions

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 constitutes 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.

GetSampleHydrogens

bool GetSampleHydrogens() const

See SetSampleHydrogens method.

GetStrictAtomTypes

bool GetStrictAtomTypes() const

See SetStrictAtomTypes method.

SetCanonOrder

void SetCanonOrder(const bool)

Sets whether the molecule should be indexed in canonical order. If true, the atoms of the molecule is indexed in canonical order before building the molecule structure. Default: True.

SetEnumNitrogen

void SetEnumNitrogen(const unsigned int)

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

See also

SetEnumRing

void SetEnumRing(const bool)

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

SetFragBuilderOptions

void SetFragBuilderOptions(const OEFragBuilderOptions&)

Sets options related to building fragment coordinates.

See also

SetFromCT

void 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.

SetSampleHydrogens

void SetSampleHydrogens(const bool)

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

SetStrictAtomTypes

void SetStrictAtomTypes(const bool)

Sets whether strict definition of atom typing should be used. If true, a molecule to 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.