OEUniMolecularRxnOptions

class OEUniMolecularRxnOptions

This class represents the OEUniMolecularRxnOptions options class that encapsulates properties to control transforms using OEUniMolecularRxn and OEGetUniMolecularRxnIter.

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Constructors

OEUniMolecularRxnOptions()

Default constructor that initializes an OEUniMolecularRxnOptions object with the following properties:

Default parameters of OEUniMolecularRxnOptions

Option

Default value

Strict SMIRKS

true

Validate Kekule

true

Clear Coordinates

false

Fix Valences

OEUniMolecularRxnFixValence.Explicit

Altered Tag

empty

Max Matches

10000

 
OEUniMolecularRxnOptions(const OEUniMolecularRxnOptions &rhs)

Copy constructor.

operator=

OEUniMolecularRxnOptions &operator=(const OEUniMolecularRxnOptions &rhs)

Assignment operator.

GetAlteredTag

std::string GetAlteredTag() const

Return the desired generic data tag that captures the boolean state indicating specific atoms that are modified by the transformation. If empty or blank, no generic data is returned on the transformation product atoms.

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GetClearCoordinates

bool GetClearCoordinates() const

Returns whether the coordinates of a molecule are cleared before performing the chemical transformation.

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GetFixValence

unsigned GetFixValence() const

Returns what type of valence corrections should be applied to the transformation products. The legal values are taken from OEUniMolecularRxnFixValence.

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GetMaxMatches

unsigned GetMaxMatches() const

The maximum number of transformations returned or applied. A value of 0 indicates there is no constraint. Note that if this value is low, the transformations returned will be arbitrarily truncated to this limit.

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GetStrictSmirks

bool GetStrictSmirks() const

Returns the current setting of the strict flag that controls how to interpret the SMIRKS for the transformation. This setting value controls the interpretation of the SMIRKS semantics. By default, the SMIRKS string is interpreted using strict semantics (i.e., with the setting value of true).

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GetValidateKekule

bool GetValidateKekule() const

Returns whether the transformation validates the Kekulé form of the returned products.

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SetAlteredTag

bool SetAlteredTag(const std::string &alteredtag)

Sets the desired generic data tag value used to capture boolean data indicating specific atoms that are modified by the transformation. If empty or blank, no generic data is returned on the transformation product atoms.

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SetClearCoordinates

bool SetClearCoordinates(bool clearcoords)

Sets whether the coordinates of a molecule should be cleared before performing the chemical transformation.

Note

The OEUniMolecularRxn modifies the molecular graph when applying the transformations. Generating valid 2D or 3D coordinates for the products is beyond the scope of the OEUniMolecularRxn class.

It is recommended to either clear the coordinates by invoking the OEUniMolecularRxn.SetClearCoordinates method or regenerate the coordinates of the molecule afterwards.

If no transformation is applied the molecule will not be changed.

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SetFixValence

unsigned SetFixValence(unsigned fixvalence)

Sets the type of valence corrections that should be applied to the transformation products. The legal values are taken from OEUniMolecularRxnFixValence.

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SetMaxMatches

bool SetMaxMatches(unsigned maxmatches)

Sets the maximum number of transformations that should be returned or applied. Setting the value to 0 removes the constraint. Note that if this value is low, the transformations returned will be arbitrarily truncated to this limit.

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SetStrictSmirks

bool SetStrictSmirks(bool strict)

Sets the desired value of the strict flag that controls how to interpret the SMIRKS for the transformation. This setting value controls the interpretation of the SMIRKS semantics. By default, the SMIRKS string is interpreted using strict semantics (i.e., with the setting value of true).

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SetValidateKekule

bool SetValidateKekule(bool validatekekule)

Sets whether the generated products are simply returned after a Kekulization attempt, or if the Kekulé form is validated more rigorously. If the extra validation is enabled and an invalid Kekulé form is identified, alternatives are tried by adding and removing implicit hydrogens from aromatic nitrogens to produce a valid Kekulé form. No further attempt is made to return the most reasonable or chemically sensible result. By default, the extra Kekulé validation is enabled.

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