Scine::Molassembler::Stereopermutators::Abstract Struct Reference

Class to compute the set of abstract permutations from ranking and shape. More...

#include <AbstractPermutations.h>

Public Member Functions
Constructors
	Abstract ()=default
	Empty initializer, all data members are nulled.
	Abstract (const RankingInformation &ranking, Shapes::Shape shape)
	Generates the set of abstract stereopermutations and intermediate data. More...

Static Public Member Functions
Static functions
static RankingInformation::RankedSitesType	canonicalize (RankingInformation::RankedSitesType rankedSites)
	Stably re-sort ranked site indices in decreasing set size. More...
static std::vector< char >	transferToSymbolicCharacters (const RankingInformation::RankedSitesType &canonicalSites)
	Condense site ranking information into canonical characters for symbolic computation. More...
static Stereopermutations::Stereopermutation::OrderedLinks	selfReferentialTransform (const std::vector< RankingInformation::Link > &rankingLinks, const RankingInformation::RankedSitesType &canonicalSites)
	Make site-index based links self-referential within canonical sites. More...
static std::vector< char >	makeStereopermutationCharacters (const RankingInformation::RankedSitesType &canonicalSites, const std::vector< char > &canonicalStereopermutationCharacters, const Temple::StrongIndexFlatMap< Shapes::Vertex, SiteIndex > &sitesAtShapeVertices)
	Generates the reduced character representation of sites at their current shape positions. More...

Data Fields
Data members
RankingInformation::RankedSitesType	canonicalSites
	Stably resorted (by set size) site ranking.
std::vector< char >	symbolicCharacters
	Character representation of bonding case.
Stereopermutations::Stereopermutation::OrderedLinks	selfReferentialLinks
	Self-referential representation of links.
Stereopermutations::Uniques	permutations
	Vector of rotationally unique stereopermutations with associated weights.

Detailed Description

Class to compute the set of abstract permutations from ranking and shape.

Constructor & Destructor Documentation

Scine::Molassembler::Stereopermutators::Abstract::Abstract	(	const RankingInformation &	ranking,
		Shapes::Shape	shape
	)

Generates the set of abstract stereopermutations and intermediate data.

Complexity The generation of permutations dominates: \(\Theta(S!)\)

Parameters

ranking	Ranking object indicating chemical differences between substituents and sites
shape	Shape name

Member Function Documentation

static RankingInformation::RankedSitesType Scine::Molassembler::Stereopermutators::Abstract::canonicalize ( RankingInformation::RankedSitesType  rankedSites )

static

Stably re-sort ranked site indices in decreasing set size.

Necessary to avoid treating e.g. AAB and ABB separately, although the resulting assignments are identical.

Complexity \(N \log N\)

Example:

* rankedSites = {5, 8}, {3}, {1, 2, 4}
* canonicalize(rankedSites) = {1, 2, 4}, {5, 8}, {3}
* 

static std::vector<char> Scine::Molassembler::Stereopermutators::Abstract::makeStereopermutationCharacters ( const RankingInformation::RankedSitesType &  canonicalSites, const std::vector< char > &  canonicalStereopermutationCharacters, const Temple::StrongIndexFlatMap< Shapes::Vertex, SiteIndex > &  sitesAtShapeVertices  )

static

Generates the reduced character representation of sites at their current shape positions.

Complexity \(O(S^2)\) worst case

static Stereopermutations::Stereopermutation::OrderedLinks Scine::Molassembler::Stereopermutators::Abstract::selfReferentialTransform ( const std::vector< RankingInformation::Link > &  rankingLinks, const RankingInformation::RankedSitesType &  canonicalSites  )

static

Make site-index based links self-referential within canonical sites.

Complexity \(\Theta(L)\)

Example:

* links = {sites = {5, 8}}
*
* self-refential idx: 0  1  2    3  4    5
* canonicalSites =   {1, 2, 4}, {5, 8}, {3} (this is output from canonicalize)
*
* selfReferentialTransform(links, canonicalSites) = {3, 4}
* 

static std::vector<char> Scine::Molassembler::Stereopermutators::Abstract::transferToSymbolicCharacters ( const RankingInformation::RankedSitesType &  canonicalSites )

static

Condense site ranking information into canonical characters for symbolic computation.

Use the output of canonicalize here as input:

Complexity \(\Theta(N)\)

Example:

* rankedSites = {5, 8}, {3}, {1, 2, 4}
* canonical = canonicalize(rankedSites = {1, 2, 4}, {5, 8}, {3}
* transferToSymbolicCharacetrs(canonical) = A, A, A, B, B, C
* 

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The documentation for this struct was generated from the following file:

• Molassembler/Stereopermutators/AbstractPermutations.h