OEInChIOptions

class OEInChIOptions

This class is used to control the output for the OEFormat_INCHI and OEFormat_INCHIKEY formats. The options have a direct mapping between the flavors in the OEOFlavor_INCHI and OEOFlavor_INCHIKEY. The options also have a direct mapping into the options provided by the InChI library.

See also

• InChI API Reference documentation

• InChI Technical Manual documentation

Constructors

OEInChIOptions(flavor: int) -> OEInChIOptions

The default constructor initializes the options class to the flavors indicated by the OEOFlavor_INCHI_Default constant.

OEInChIOptions(arg2: OEInChIOptions) -> OEInChIOptions

Copy constructor.

GetChiral

GetChiral() -> bool

Returns a bool stating whether to use absolute stereochemistry.

GetFixedHLayer

GetFixedHLayer() -> bool

Returns whether to include the fixed H-layer.

GetHydrogens

GetHydrogens() -> bool

Returns whether to add H according to usual valences.

GetNonPolymerPseudoAtoms

GetNonPolymerPseudoAtoms() -> bool

Returns the state of the flag that allows non-polymer *atoms (OEElemNo_Du) to be present in the structure used for InChI generation. Setting this flag results in a nonstandard InChI version. By default, no *atoms are allowed. Currently there is no support for polymer InChIs in OEChem.

GetRacemicStereo

GetRacemicStereo() -> bool

Returns whether to export all stereo as racemic stereo in the InChI string. By default, all stereo is exported as absolute stereo.

GetReconnectedMetals

GetReconnectedMetals() -> bool

Returns whether to include reconnected metals.

GetRelativeStereo

GetRelativeStereo() -> bool

Returns whether to export all stereo as relative stereo in the InChI string. By default, all stereo is exported as absolute stereo.

GetStereo

GetStereo() -> bool

Returns whether the stereo information in the input structure is ignored.

GetTimeout

GetTimeout() -> int

Returns the setting for the maximum number of seconds the InChI generation is allowed to take. By default, a 60 second execution limit is used.

GetUndefinedStereo

GetUndefinedStereo() -> bool

Returns the setting that controls explicit undefined stereo annotations in the generated InChI identifier. Default, false.

SetChiral

SetChiral(val: bool) -> None

If set to true, use absolute stereochemistry, else relative stereochemistry (corresponds to InChI option “ChiralFlagOn”).

SetFixedHLayer

SetFixedHLayer(val: bool) -> None

If set to true, do not allow for mobile hydrogens e.g. in tautomers (corresponds to InChI option “FixedH”).

SetHydrogens

SetHydrogens(val: bool) -> None

If set to true, hydrogens are added according to usual valences (corresponds to the inverse of the InChI option “DoNotAddH”).

SetNonPolymerPseudoAtoms

SetNonPolymerPseudoAtoms(val: bool) -> None

If set to true, non-polymer *atoms (OEElemNo_Du) are allowed to be present in the structure used for InChI generation. Setting this flag results in a nonstandard InChI version. By default, no *atoms are allowed. Currently there is no support for polymer InChIs in OEChem.

SetRacemicStereo

SetRacemicStereo(val: bool) -> None

If set to true, export all stereo as racemic stereo (corresponds to InChI option “SRac”). Enabling the racemic stereo option takes precedence over the option setting to disable OEInChIOptions.SetStereo.

SetReconnectedMetals

SetReconnectedMetals(val: bool) -> None

If set to true, include reconnected metals (corresponds to InChI option “RecMet”).

SetRelativeStereo

SetRelativeStereo(val: bool) -> None

If set to true, export all stereo as relative stereo (corresponds to InChI option “SRel”). Enabling the relative stereo option takes precedence over other option settings of OEInChIOptions.SetRacemicStereo or (disabled) OEInChIOptions.SetStereo.

SetStereo

SetStereo(val: bool) -> None

If set to true, stereo information is used from input structure (corresponds to the inverse of the InChI option “SNon”).

SetTimeout

SetTimeout(val: int) -> None

Sets the InChI execution time cutoff to val seconds. Setting a value of 0 means unlimited, and by default a 60 second limit is used.

SetUndefinedStereo

SetUndefinedStereo(val: bool) -> None

If set to true, requests explicit undefined stereo annotations in the generated InChI and InChIKey identifiers. Enabling this flag always results in a nonstandard InChI.