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(unsigned int flavor = OEOFlavor::INCHI::Default)

The default constructor initializes the options class to the flavors indicated by the OEOFlavor.INCHI.Default constant.

OEInChIOptions(const OEInChIOptions &)

Copy constructor.

operator=

OEInChIOptions &operator=(const OEInChIOptions &rhs)

Assignment operator.

GetChiral

bool GetChiral() const

Returns a bool stating whether to use absolute stereochemistry.

GetFixedHLayer

bool GetFixedHLayer() const

Returns whether to include the fixed H-layer.

GetHydrogens

bool GetHydrogens() const

Returns whether to add H according to usual valences.

GetNonPolymerPseudoAtoms

bool GetNonPolymerPseudoAtoms() const

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

bool GetRacemicStereo() const

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

GetReconnectedMetals

bool GetReconnectedMetals() const

Returns whether to include reconnected metals.

GetRelativeStereo

bool GetRelativeStereo() const

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

GetStereo

bool GetStereo() const

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

GetTimeout

unsigned int GetTimeout() const

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

bool GetUndefinedStereo() const

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

SetChiral

void SetChiral(bool val)

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

SetFixedHLayer

void SetFixedHLayer(bool val)

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

SetHydrogens

void SetHydrogens(bool val)

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

SetNonPolymerPseudoAtoms

bool SetNonPolymerPseudoAtoms(bool val)

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

void SetRacemicStereo(bool val)

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

void SetReconnectedMetals(bool val)

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

SetRelativeStereo

void SetRelativeStereo(bool val) const

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

void SetStereo(bool val)

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

SetTimeout

void SetTimeout(unsigned int val)

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

void SetUndefinedStereo(bool val)

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.