OEMatchedPairTransformExtractOptions

class OEMatchedPairTransformExtractOptions

This class represents the OEMatchedPairTransformExtractOptions class that encapsulates properties that control extraction of matched molecular pair transformations.

Constructors

OEMatchedPairTransformExtractOptions()

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

Default parameters of OEMatchedPairTransformExtractOptions
Property Default value
transformation context OEMatchedPairContext::Default
extraction options OEMatchedPairTransformExtractMode::Default
maximum matched pair core structure substituents 200
skip maximum matched pair core index nodes exceeding substituent limit false
OEMatchedPairTransformExtractOptions(const OEMatchedPairTransformExtractOptions &rhs)

Copy constructor.

operator=

OEMatchedPairTransformExtractOptions &operator=(const OEMatchedPairTransformExtractOptions &rhs)

Assignment operator.

GetAttachmentPoints

bool GetAttachmentPoints() const

Returns the setting that requests the addition of attachment points on the matched pair transformation.

GetContext

int GetContext() const

Returns the setting that controls the amount of core chemistry adjacent to the substituent attachment site for the matched pairs.

GetDirection

unsigned int GetDirection() const

Returns the setting that controls the direction for the returned matched pair transformation. One of OEMatchedPairTransformExtractMode::Forward, OEMatchedPairTransformExtractMode::Backward, ( OEMatchedPairTransformExtractMode::Forward | OEMatchedPairTransformExtractMode::Backward )`` (both) or OEMatchedPairTransformExtractMode::Sorted are supported. For OEMatchedPairTransformExtractMode::Sorted, the transformation is lexically sorted based on the reactants and products and may need to be inverted to have the transformation represent driving an arbitrary data property associated with the matched pair in a desired direction.

GetIsotopes

bool GetIsotopes() const

Returns the setting that controls the generalization of the returned transformations for isotopic substitutions.

GetMCSCorrespondence

bool GetMCSCorrespondence() const

Returns the setting that requests the addition of atom-atom mapping correspondence to the core of the matched pair transformation.

GetMatchedPairData

bool GetMatchedPairData() const

Returns whether the matched pair data is included in the matched pair transformation. If only the transformation itself is required, there may not be a need for extraction of related matched pair indexed data.

GetMatchedPairs

bool GetMatchedPairs() const

Returns whether the matched pair data ids are returned for the matched pair transformation. If only the transformation itself is required, there may not be a need for extraction of related matched pair indices.

GetMaxMMPLimit

unsigned int GetMaxMMPLimit() const

Returns the requested upper limit of matched pairs for the extracted transformations.

GetMaxSubstituentLimit

unsigned int GetMaxSubstituentLimit() const

Returns the setting for the maximum number of indexed core substituents that should be processed into matched pair transformations.

Warning

Setting this limit to 0 will suppress any core structure truncation or skipping activities, but may result in extremely poor transformation extraction performance owing to the combinatorial explosion of generating all NxM combinations of matched pairs.

GetMaxSubstituentLimitSkip

bool GetMaxSubstituentLimitSkip() const

Returns whether the matched pair core strucures in the index that have more than the OEMatchedPairTransformExtractOptions::GetMaxSubstituentLimit number of substituents are processed into matched pair transformation entries. If the setting is true, cores that exceed the limit are skipped, and if false, the substituent list is truncated to the first OEMatchedPairTransformExtractOptions::GetMaxSubstituentLimit substituents, if non-zero.

GetMinMMPLimit

unsigned int GetMinMMPLimit() const

Returns the requested lower limit of matched pairs for the extracted transformations.

GetMinSubstituentLimit

unsigned int GetMinSubstituentLimit() const

Returns the setting for the minimum number of core structure substituents for index nodes that should be processed into matched pair transformations.

GetOptions

unsigned int GetOptions() const

Returns the bit option settings for the extraction options.

GetSMARTS

bool GetSMARTS() const

Returns whether the matched pair transformations are annotated with additional SMARTS qualifiers to make the transfromations more chemically relevant when used for generating chemical transformations from extracted matched pairs.

SetAttachmentPoints

bool SetAttachmentPoints(bool val)

Set the option that controls the addition of attachment points on the matched pair transformation.

SetContext

bool SetContext(int context) const

Sets the option that that controls the amount of core chemistry adjacent to the substituent attachment site in then matched pair transformation.

SetDirection

bool SetDirection(unsigned int direction) const

Sets the specified transformation direction for the returned matched pair transformation. One of Forward, Backward, (Forward | Backward) (both) or Sorted are supported. For Sorted, the transformation is lexically sorted based on the reactants and products and may need to be inverted to have the transformation represent driving an arbitrary data property associated with the matched pair in a desired direction.

SetIsotopes

bool SetIsotopes(bool require)

Sets the option that controls whether the transformation is allowed to be generalized for isotopic substitutions. If true, isotopic information will be included in the transformations for the chemical modifications.

SetMCSCorrespondence

bool SetMCSCorrespondence(bool add)

Sets the option that requests the addition of atom-atom mapping correspondence to the core of the matched pair transformation.

SetMatchedPairData

bool SetMatchedPairData(bool enable)

Sets the option that requests matched pair data be included in the matched pair transformation. If only the transformation itself is required, there may not be a need for extraction of related matched pair indexed data, so the data extraction can be disabled.

SetMatchedPairs

bool SetMatchedPairs(bool enable)

Sets the option that requests that matched pair structure ids are returned for the matched pair transformation. If only the transformation itself is required, there may not be a need for extraction of related matched pair structure indices.

SetMaxSubstituentLimitSkip

bool SetMaxSubstituentLimitSkip(bool skip)

Sets the option that controls whether the matched pair core strucures in the index that have more than the OEMatchedPairTransformExtractOptions::GetMaxSubstituentLimit number of substituents are processed into matched pair transformation entries. If the setting is true, cores that exceed the limit are skipped, and if false, the substituent list is truncated to the first OEMatchedPairTransformExtractOptions::GetMaxSubstituentLimit substituents, if non-zero.

SetMMPLimit

bool SetMMPLimit(unsigned int atLeast, unsigned int atMost=0)

Sets the requested range limits for the number matched pairs in the extracted transformations.

SetSubstituentLimit

bool SetSubstituentLimit(unsigned int atLeast, unsigned int atMost=0)

Sets the requested range limits for the core structure index nodes to constrain processing to core index nodes matching the specified range.

Warning

Setting the maximum limit to 0 will suppress any core structure truncation or skipping activities, but may result in extremely poor transformation extraction performance owing to the combinatorial explosion of generating all NxM combinations of matched pairs and their associated transformations and data.

SetOptions

bool SetOptions(unsigned int options)

Sets the bit option settings that control the transformation extraction activities.

SetSMARTS

bool SetSMARTS(bool enable) const

Sets the option that indicates that matched pair transformations should be annotated with additional SMARTS qualifiers to make the transfromations more chemically relevant when used for generating chemical transformations from extracted matched pairs.