MultimerHandler Class Reference

#include <multimerHandler.h>

Public Member Functions
	MultimerHandler (std::string _stoichiom)
	// Constructor to initialize the stoichiometry
std::string	chainIndexToStoichiomLetter (int index)
	Map chain index to stoichiometry letter.
bool	getHeteromerMSAs (const std::vector< std::vector< int > > &vectors)
	Verify if the MSA is in the form of a paired MSA (sequences followed by the MSA of each chain)
bool	isHeteromerFormat ()
	Check if stoichiometry follows the pattern of a heteromer (e.g., A2B2C1)
bool	isHomomerFormat ()
	Check if the stoichiometry is in homomer format (e.g., A3)
std::vector< std::vector< int > >	getHomomerIndividualMSA (const std::vector< std::vector< int > > &sequences2num)
	Get individual MSA for homomer format.
std::vector< std::vector< std::vector< int > > >	getHetoromerMSAs (const std::vector< std::vector< int > > &sequences2num, const std::vector< int > &chainLengths)
	Get individual MSA for heteromer format.

Private Member Functions
std::vector< int >	getSequenceSegment (const std::vector< int > &row, int chainIndex, int repeat=1) const
	// Extract the sequence segment from the row that corresponds to the chain specified by the given chainIndex.
std::vector< int >	checkRepeatedChainAndReturnOneSegment (const std::vector< int > &row, int rowIndex, int chainIndex)
	Verify if all segments of the repeated chains in the given row are identical, and if so, return a single segment.
bool	includesInPairedMSA (const std::vector< int > &row)
	Check if the row is for the paired MSA, i.e, it includes at least two sequence segements corresponding to two chains with non-gap elements.
int	checkRowCorrespondsOnlyToOneChainAndReturnChainIndex (const std::vector< int > &row, int row_index)
	// Find index of the chain corrsponding to given row; it should correspond exactly to one chain
std::vector< int >	checkMSAFormatAndReturnRowIndexIntervalsCorrespondingToChains (const std::vector< int > &chainIndexOfRows)
	Check MSA format and return MSA row index intervals corresponding to each chain.

Private Attributes
std::string	stoichiom
std::vector< int >	numbers
int	chainsCount
std::vector< int >	chainIntervals

Constructor & Destructor Documentation

MultimerHandler()

MultimerHandler::MultimerHandler

(

std::string

_stoichiom

)

// Constructor to initialize the stoichiometry

Parameters

_stoichiom

Member Function Documentation

chainIndexToStoichiomLetter()

string MultimerHandler::chainIndexToStoichiomLetter

(

int

index

)

Map chain index to stoichiometry letter.

Parameters

index

Returns

stoichiometry letter

checkMSAFormatAndReturnRowIndexIntervalsCorrespondingToChains()

vector< int > MultimerHandler::checkMSAFormatAndReturnRowIndexIntervalsCorrespondingToChains ( const std::vector< int > & chainIndexOfRows )

private

Check MSA format and return MSA row index intervals corresponding to each chain.

Parameters

chainIndexOfRows

Returns

checkRepeatedChainAndReturnOneSegment()

vector< int > MultimerHandler::checkRepeatedChainAndReturnOneSegment ( const std::vector< int > & row, int rowIndex, int chainIndex )

private

Verify if all segments of the repeated chains in the given row are identical, and if so, return a single segment.

Parameters

row
rowIndex
chainIndex

Returns

chainSegment

checkRowCorrespondsOnlyToOneChainAndReturnChainIndex()

int MultimerHandler::checkRowCorrespondsOnlyToOneChainAndReturnChainIndex ( const std::vector< int > & row, int row_index )

private

// Find index of the chain corrsponding to given row; it should correspond exactly to one chain

Parameters

row
row_index

Returns

getHeteromerMSAs()

bool MultimerHandler::getHeteromerMSAs

(

const std::vector< std::vector< int > > &

vectors

)

Verify if the MSA is in the form of a paired MSA (sequences followed by the MSA of each chain)

Parameters

msa

Returns

getHetoromerMSAs()

vector< vector< vector< int > > > MultimerHandler::getHetoromerMSAs	(	const std::vector< std::vector< int > > &	sequences2num,
		const std::vector< int > &	chainLengths )

Get individual MSA for heteromer format.

Parameters

sequences2num
chain_lengths

Returns

individual MSAs

getHomomerIndividualMSA()

vector< vector< int > > MultimerHandler::getHomomerIndividualMSA

(

const std::vector< std::vector< int > > &

sequences2num

)

Get individual MSA for homomer format.

Returns

individual MSA

getSequenceSegment()

vector< int > MultimerHandler::getSequenceSegment ( const std::vector< int > & row, int chainIndex, int repeat = 1 ) const

private

// Extract the sequence segment from the row that corresponds to the chain specified by the given chainIndex.

Parameters

row
chainIndex
repeat

Returns

includesInPairedMSA()

bool MultimerHandler::includesInPairedMSA ( const std::vector< int > & row )

private

Check if the row is for the paired MSA, i.e, it includes at least two sequence segements corresponding to two chains with non-gap elements.

Parameters

row

Returns

isHeteromerFormat()

bool MultimerHandler::isHeteromerFormat

(

)

Check if stoichiometry follows the pattern of a heteromer (e.g., A2B2C1)

Returns

isHomomerFormat()

bool MultimerHandler::isHomomerFormat

(

)

Check if the stoichiometry is in homomer format (e.g., A3)

Returns

Member Data Documentation

chainIntervals

std::vector<int> MultimerHandler::chainIntervals

private

chainsCount

int MultimerHandler::chainsCount

private

numbers

std::vector<int> MultimerHandler::numbers

private

stoichiom

std::string MultimerHandler::stoichiom

private

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The documentation for this class was generated from the following files:

• code/multimerHandler.h
• code/multimerHandler.cpp