The class representing a database of building blocks (bricks). More...

#include <cBricksDatabase.h>

Public Member Functions
bool	nextCombination (vector< int > &combarray, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass)
	Get next combination of bricks. More...

bool	nextCombinationFast (vector< int > &combarray, vector< int > &combcounts, vector< double > &combmasses, double &mass, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass)
	Get next combination of bricks. More...

bool	nextCombinationFastLimited (vector< int > &combarray, vector< int > &combcounts, vector< int > &comblimits, vector< double > &combmasses, double &mass, int numberofbasicbricks, int maximumbricksincombination, double maximumcumulativemass, double neutralprecursormass)
	Get next combination of bricks. More...

	cBricksDatabase ()
	The constructor.

int	loadFromPlainTextStream (ifstream &stream, string &errormessage, bool ignoreerrors, bool skiph2blocks)
	Load the database of bricks from a plain text stream. More...

void	storeToPlainTextStream (ofstream &stream)
	Store the database of bricks into a plain text stream. More...

int	size ()
	Get the number of bricks in the database. More...

void	print ()
	Print the database of bricks.

void	sortbyMass ()
	Sort the database of bricks by mass in ascending order.

cBrick &	operator[] (int position)
	Overloaded operator []. More...

double	getMassOfComposition (vector< int > &combarray, int numberofbasicbricks)
	Get the mass of a composition of bricks. More...

string	getRealName (string &composition)
	Get the real name of a peptide from a composition. More...

string	getAcronymName (string &composition, bool useHTMLReferences)
	Get the name of a peptide composed from acronyms of bricks. More...

string	getTagName (string &composition)
	Get a peptide sequence tag from a composition. More...

string	getAcronymNameOfTPeptide (const string &tcomposition, bool useHTMLReferences)
	Get the name of a branched peptide composed from acronyms of bricks. More...

string	getTagNameOfTPeptide (string &tcomposition)
	Get a peptide sequence tag of a branched peptide from a composition. More...

void	clear ()
	Clear the vector of bricks.

bool	replaceAcronymsByIDs (string &sequence, string &errormessage)
	Replace acronyms of bricks by ids. More...

void	push_back (cBrick &brick)
	Push a new brick into the vector of bricks. More...

void	removeLastBrick ()
	Remove the last brick from the vector of bricks if possible.

string	calculateSummaryFromComposition (int brickid)
	Calculate the summary formula of a composition. More...

void	store (ofstream &os)
	Store the structure into an output stream. More...

void	load (ifstream &is)
	Load the structure from an input stream. More...

bool	checkKetideBlocks (cBrick &brickseries, bool regularblocksorder)
	Check if the numbers of H2 loss and H2O loss blocks are correct. More...

double	getMassOfNeutralLosses (vector< int > &lossids)
	Get the summary mass of neutral losses. More...

string	getSummaryFormulaOfNeutralLosses (vector< int > &lossids)
	Get the summary formula of neutral losses. More...

void	getMapOfNeutralLosses (vector< int > &lossids, map< string, int > &summarymap)
	Get the summary map of neutral losses. More...

Detailed Description

The class representing a database of building blocks (bricks).

Member Function Documentation

◆ calculateSummaryFromComposition()

string cBricksDatabase::calculateSummaryFromComposition ( int brickid )

Calculate the summary formula of a composition.

Parameters

brickid brick id

Return values

string summary formula

◆ checkKetideBlocks()

bool cBricksDatabase::checkKetideBlocks	(	cBrick &	brickseries,
		bool	regularblocksorder
	)

Check if the numbers of H2 loss and H2O loss blocks are correct.

Parameters

brickseries	a tested combination of building blocks
regularblocksorder	check regular order of ketide blocks

Return values

bool	true when the numbers of blocks are correct

◆ getAcronymName()

string cBricksDatabase::getAcronymName	(	string &	composition,
		bool	useHTMLReferences
	)

Get the name of a peptide composed from acronyms of bricks.

Parameters

composition	reference to a string containing ids of bricks separated by '-'
useHTMLReferences	if true then each acronym is converted to a link to its reference (e.g., in ChemSpider)

Return values

string name of the peptide

◆ getAcronymNameOfTPeptide()

string cBricksDatabase::getAcronymNameOfTPeptide	(	const string &	tcomposition,
		bool	useHTMLReferences
	)

Get the name of a branched peptide composed from acronyms of bricks.

Parameters

tcomposition	reference to a string containing ids of bricks separated by '-', the branch is specified by '(' and ')'; example: 1-2-3(4-5)6-7
useHTMLReferences	if true then each acronym is converted to a link to its reference (e.g., in ChemSpider)

Return values

string name of the peptide

◆ getMapOfNeutralLosses()

void cBricksDatabase::getMapOfNeutralLosses	(	vector< int > &	lossids,
		map< string, int > &	summarymap
	)

Get the summary map of neutral losses.

Parameters

lossids	an input vector of ids of neutral losses
summarymap	an output map of atoms

◆ getMassOfComposition()

double cBricksDatabase::getMassOfComposition	(	vector< int > &	combarray,
		int	numberofbasicbricks
	)

Get the mass of a composition of bricks.

Parameters

combarray	reference to an input integer vector of ids
numberofbasicbricks	number of basic building blocks

Return values

double cumulative mass of the bricks in the combarray

◆ getMassOfNeutralLosses()

double cBricksDatabase::getMassOfNeutralLosses ( vector< int > & lossids )

Get the summary mass of neutral losses.

Parameters

lossids a vector of ids of neutral losses

Return values

double mass

◆ getRealName()

string cBricksDatabase::getRealName ( string & composition )

Get the real name of a peptide from a composition.

Parameters

composition reference to a string containing ids of bricks separated by '-'

Return values

string name of the peptide

◆ getSummaryFormulaOfNeutralLosses()

string cBricksDatabase::getSummaryFormulaOfNeutralLosses ( vector< int > & lossids )

Get the summary formula of neutral losses.

Parameters

lossids a vector of ids of neutral losses

Return values

string formula

◆ getTagName()

string cBricksDatabase::getTagName ( string & composition )

Get a peptide sequence tag from a composition.

Parameters

composition reference to a string containing ids of bricks separated by '-'

Return values

string sequence tag

◆ getTagNameOfTPeptide()

string cBricksDatabase::getTagNameOfTPeptide ( string & tcomposition )

Get a peptide sequence tag of a branched peptide from a composition.

Parameters

tcomposition reference to a string containing ids of bricks separated by '-', the branch is specified by '(' and ')'; example: 1-2-3(4-5)6-7

Return values

string sequence tag

◆ load()

void cBricksDatabase::load ( ifstream & is )

Load the structure from an input stream.

Parameters

is	an input stream

◆ loadFromPlainTextStream()

int cBricksDatabase::loadFromPlainTextStream	(	ifstream &	stream,
		string &	errormessage,
		bool	ignoreerrors,
		bool	skiph2blocks
	)

Load the database of bricks from a plain text stream.

Parameters

stream	reference to an input file stream
errormessage	reference to a string where an error message might be stored
ignoreerrors	if true errors are ignored
skiph2blocks	ignore ketide 2H loss blocks

Return values

int	0 when the database was successfully loaded, -1 when an error occurred (errormessage is filled up)

◆ nextCombination()

bool cBricksDatabase::nextCombination	(	vector< int > &	combarray,
		int	numberofbasicbricks,
		int	maximumbricksincombination,
		double	maximumcumulativemass,
		double	neutralprecursormass
	)

Get next combination of bricks.

Parameters

combarray	reference to an input/output vector of integers
numberofbasicbricks	initial number of bricks in a database
maximumbricksincombination	maximum number of combined bricks
maximumcumulativemass	maximum cummulative mass of combined bricks
neutralprecursormass	neutral precursor mass

Return values

bool	true when a valid vector is stored in combarray, false when all valid vectors were already generated

◆ nextCombinationFast()

bool cBricksDatabase::nextCombinationFast	(	vector< int > &	combarray,
		vector< int > &	combcounts,
		vector< double > &	combmasses,
		double &	mass,
		int	numberofbasicbricks,
		int	maximumbricksincombination,
		double	maximumcumulativemass,
		double	neutralprecursormass
	)

Get next combination of bricks.

Parameters

combarray	reference to an input/output vector of integers
combcounts	reference to an input/output vector containing counts of elements in combarray
combmasses	reference to an input vector containing masses of elements in combarray
mass	sum of masses of blocks
numberofbasicbricks	initial number of bricks in a database
maximumbricksincombination	maximum number of combined bricks
maximumcumulativemass	maximum cummulative mass of combined bricks
neutralprecursormass	neutral precursor mass

Return values

bool	true when a valid vector is stored in combarray, false when all valid vectors were already generated

◆ nextCombinationFastLimited()

bool cBricksDatabase::nextCombinationFastLimited	(	vector< int > &	combarray,
		vector< int > &	combcounts,
		vector< int > &	comblimits,
		vector< double > &	combmasses,
		double &	mass,
		int	numberofbasicbricks,
		int	maximumbricksincombination,
		double	maximumcumulativemass,
		double	neutralprecursormass
	)

Get next combination of bricks.

Parameters

combarray	reference to an input/output vector of integers
combcounts	reference to an input/output vector containing counts of elements in combarray
comblimits	reference to an input vector containing maximum allowed numbers of elements in combarray
combmasses	reference to an input vector containing masses of elements in combarray
mass	sum of masses of blocks
numberofbasicbricks	initial number of bricks in a database
maximumbricksincombination	maximum number of combined bricks
maximumcumulativemass	maximum cummulative mass of combined bricks
neutralprecursormass	neutral precursor mass

Return values

bool	true when a valid vector is stored in combarray, false when all valid vectors were already generated

◆ operator[]()

cBrick & cBricksDatabase::operator[] ( int position )

Overloaded operator [].

Parameters

position of the brick in the vector of bricks

Return values

cBrick reference to a brick

◆ push_back()

void cBricksDatabase::push_back ( cBrick & brick )

Push a new brick into the vector of bricks.

Parameters

brick an inserted brick

◆ replaceAcronymsByIDs()

bool cBricksDatabase::replaceAcronymsByIDs	(	string &	sequence,
		string &	errormessage
	)

Replace acronyms of bricks by ids.

Parameters

sequence	reference to an input/output string containing acronyms/ids of bricks
errormessage	reference to a string where an error message is stored when sequence contains an unknown building block

Return values

bool	true when the replacement was successful, false when an acronym of a brick is unknown

◆ size()

int cBricksDatabase::size ( )

Get the number of bricks in the database.

Return values

int	number of bricks

◆ store()

void cBricksDatabase::store ( ofstream & os )

Store the structure into an output stream.

Parameters

os	an output stream

◆ storeToPlainTextStream()

void cBricksDatabase::storeToPlainTextStream ( ofstream & stream )

Store the database of bricks into a plain text stream.

Parameters

stream reference to an output file stream

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

core/cBricksDatabase.h
core/cBricksDatabase.cpp

Public Member Functions

Detailed Description

Member Function Documentation

◆ calculateSummaryFromComposition()

◆ checkKetideBlocks()

◆ getAcronymName()

◆ getAcronymNameOfTPeptide()

◆ getMapOfNeutralLosses()

◆ getMassOfComposition()

◆ getMassOfNeutralLosses()

◆ getRealName()

◆ getSummaryFormulaOfNeutralLosses()

◆ getTagName()

◆ getTagNameOfTPeptide()

◆ load()

◆ loadFromPlainTextStream()

◆ nextCombination()

◆ nextCombinationFast()

◆ nextCombinationFastLimited()

◆ operator[]()

◆ push_back()

◆ replaceAcronymsByIDs()

◆ size()

◆ store()

◆ storeToPlainTextStream()