Ranking data of substituents around a central vertex. More...

#include <RankingInformation.h>

Data Structures
struct	Link
	Information on links between substituents of a central atom. More...

Public Types
Member types
template<typename T >
using	NestedList = std::vector< std::vector< T > >
	ASC ordered list (via ranking) of atom index lists (sub-list atoms equal)

using	RankedSubstituentsType = NestedList< AtomIndex >
	ASC ordered list (via ranking) of atom index lists (sub-list atoms equal)

using	SiteListType = NestedList< AtomIndex >
	An unordered list of sets of atom indices that constitute binding sites.

using	RankedSitesType = NestedList< SiteIndex >
	Ascending ordered list of binding site indices (sub-list site indices equal)

Public Member Functions
Modification
void	applyPermutation (const std::vector< AtomIndex > &permutation)
	Applies an atom index permutation. More...

Information
SiteIndex	getSiteIndexOf (AtomIndex i) const
	Fetches the binding site index of a substituent. More...

unsigned	getRankedIndexOfSite (SiteIndex i) const
	Fetches the position of a binding site index within the site ranking. More...

bool	hasHapticSites () const
	Checks whether there are haptic binding sites. More...

Operators
bool	operator== (const RankingInformation &other) const

bool	operator!= (const RankingInformation &other) const

Static Public Member Functions
Static member functions
static std::vector< unsigned >	siteConstitutingAtomsRankedPositions (const std::vector< AtomIndex > &siteAtomList, const RankingInformation::RankedSubstituentsType &substituentRanking)
	Gets ranking positions of a binding site's constituting atoms in descending order. More...

static RankedSitesType	rankSites (const SiteListType &sites, const RankedSubstituentsType &substituentRanking)
	Combines the ranking of substituents with the binding site constitutions into a site-level ranking. More...

Data Fields
Data members
RankedSubstituentsType	substituentRanking
	Sorted substituents grouped by priority ascending.

SiteListType	sites
	Binding site atom index groupings. More...

RankedSitesType	siteRanking
	Site ranking. More...

std::vector< Link >	links
	A list of information on all links between binding sites. More...

Detailed Description

Ranking data of substituents around a central vertex.

Member Function Documentation

void Scine::Molassembler::RankingInformation::applyPermutation ( const std::vector< AtomIndex > & permutation )

Applies an atom index permutation.

Complexity \(\Theta(1)\)

Parameters

permutation The permutation to apply

unsigned Scine::Molassembler::RankingInformation::getRankedIndexOfSite ( SiteIndex i ) const

Fetches the position of a binding site index within the site ranking.

Complexity \(\Theta(1)\)

Parameters

i	The binding site index to find

Returns: The position within siteRanking of the supplied ligand index

SiteIndex Scine::Molassembler::RankingInformation::getSiteIndexOf ( AtomIndex i ) const

Fetches the binding site index of a substituent.

Complexity \(\Theta(1)\)

Exceptions

std::out_of_range If the specified atom index is not part of any binding site

bool Scine::Molassembler::RankingInformation::hasHapticSites ( ) const

Checks whether there are haptic binding sites.

Complexity \(\Theta(1)\)

Note: These are identified by the sites member having sets of substituents with more than one element

static RankedSitesType Scine::Molassembler::RankingInformation::rankSites	(	const SiteListType &	sites,
		const RankedSubstituentsType &	substituentRanking
	)

static

Combines the ranking of substituents with the binding site constitutions into a site-level ranking.

Site ordering is predicated on the following rules:

Larger sites precede smaller sites
Lexicographical comparison of the constituting atoms' ranking positions

Complexity \(\Theta(S^2)\) where \(S\) is the number of sites

Parameters

sites	List of atom index lists that each constitute a binding site
substituentRanking	The substituent-level ranking result

Returns: A ranked (ascending) nested list of ligand indices

static std::vector<unsigned> Scine::Molassembler::RankingInformation::siteConstitutingAtomsRankedPositions	(	const std::vector< AtomIndex > &	siteAtomList,
		const RankingInformation::RankedSubstituentsType &	substituentRanking
	)

static

Gets ranking positions of a binding site's constituting atoms in descending order.

*         Ranking position:     0     1       2      3
* Input:  substituentRanking: {{0}, {4, 3}, {1, 9}, {5}}
*         binding site indices: {5, 3, 0}
* Output: {3, 1, 0}
*

Complexity \(\Theta(S)\) where \(S\) is the number of substituents

Field Documentation

std::vector<Link> Scine::Molassembler::RankingInformation::links

A list of information on all links between binding sites.

Note: This list is sorted, enabling use of the RankingInformation comparison operators

RankedSitesType Scine::Molassembler::RankingInformation::siteRanking

Site ranking.

This is a ranked (ascending) nested list of site indices (indices into sites).

For any instance r, this member should merely be the cached result of a call to RankingInformation::rankSites with the arguments r.sites and r.substituentRanking.

SiteListType Scine::Molassembler::RankingInformation::sites

Binding site atom index groupings.

This is an unordered nested list of atom index lists that each constitute a binding site. If a nested list has only a single element, the site is 'normal'. If there are multiple elements in a nested list, the site is haptically bonded.

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

Molassembler/RankingInformation.h

Data Structures

Public Types

Public Member Functions

Static Public Member Functions

Data Fields

Detailed Description

Member Function Documentation

Field Documentation