cBrick Class Reference

The class representing a building block (brick). More...

#include <cBrick.h>

Public Member Functions
	cBrick ()
	The constructor.
void	clear ()
	Clear all variables.
bool	empty ()
	Test whether the brick is empty. More...
string &	getName ()
	Access to a string variable which stores a full name of the brick. More...
void	setName (const string &name)
	Set a full name of the brick. More...
string &	getSummary ()
	Access to a string variable which stores a molecular formula of the brick. More...
map< string, int > &	getSummaryMap ()
	Access to a map which stores a molecular formula of the brick. More...
vector< string > &	getAcronyms ()
	Access to a vector of strings which stores acronyms of all izomers corresponding to the brick. More...
string &	getLosses ()
	Access to a string variable which stores a list of neutral losses. More...
vector< int > &	getLossIDs ()
	Access to a vector of identifiers of neutral losses. More...
vector< string > &	getReferences ()
	Access to a vector of strings which stores references (e.g., to ChemSpider) of all izomers corresponding to the brick. More...
string &	getComposition ()
	Access to a string containing composition of the brick (ids of bricks separated by '-') More...
string	getReverseComposition ()
	Reverse the composition of the brick. More...
double	getMass () const
	Get the mass of the brick. More...
void	setMass (double mass)
	Set the mass of the brick. More...
void	setComposition (const string &composition, bool normalize)
	Set the composition of the brick. More...
void	setSummary (const string &summary)
	Set the summary molecular formula of the brick. More...
void	createSummaryMap ()
	Create a map of atoms from the molecular formula.
void	setAcronyms (const string &acronyms)
	Set acronyms of all izomers corresponding to the brick. More...
void	setLosses (const string &str)
	Set the list of losses. More...
void	setLossIDs (vector< int > &lossids)
	Set a vector of identifiers of neutral losses. More...
void	setReferences (const string &references)
	Set references (e.g., to ChemSpider) of all izomers corresponding to the brick. More...
void	normalizeComposition ()
	Normalize the composition of the brick (ids of bricks are sorted in ascending order).
void	explodeToIntComposition (vector< int > &bricks)
	Explode the composition of the brick into a vector of intergers (ids of subbricks). More...
void	explodeToStringComposition (vector< string > &bricks)
	Explode the composition of the brick into a vector of strings (ids of subbricks). More...
string	getAcronymsAsString ()
	Get all acronyms. More...
string	getReferencesAsString ()
	Get all references. More...
string	getFirstAcronymAsString ()
	Get the first acronym. More...
string	getAcronymsWithReferencesAsHTMLString ()
	Get all acronyms with HTML links to theirs references. More...
void	setArtificial (bool artificial)
	Set a flag determining whether the brick is a calculated mass block or a regular brick. More...
bool	isArtificial ()
	Get a flag determining whether the brick is a calculated mass block or a regular brick. More...
void	setResidueLossType (eResidueLossType residuelosstype)
	Set the residue loss type. More...
eResidueLossType	getResidueLossType ()
	Get the residue loss type. 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...

Detailed Description

The class representing a building block (brick).

Member Function Documentation

empty()

bool cBrick::empty

(

)

Test whether the brick is empty.

Return values

true	if the brick is empty

explodeToIntComposition()

void cBrick::explodeToIntComposition

(

vector< int > &

bricks

)

Explode the composition of the brick into a vector of intergers (ids of subbricks).

Parameters

bricks

reference to a vector of integers

explodeToStringComposition()

void cBrick::explodeToStringComposition

(

vector< string > &

bricks

)

Explode the composition of the brick into a vector of strings (ids of subbricks).

Parameters

bricks

reference to a vector of strings

getAcronyms()

vector< string > & cBrick::getAcronyms

(

)

Access to a vector of strings which stores acronyms of all izomers corresponding to the brick.

Return values

reference

to a vector of strings

getAcronymsAsString()

string cBrick::getAcronymsAsString

(

)

Get all acronyms.

Return values

string

acronyms of all izomers separated by '/'

getAcronymsWithReferencesAsHTMLString()

string cBrick::getAcronymsWithReferencesAsHTMLString

(

)

Get all acronyms with HTML links to theirs references.

Return values

string

acronyms of all izomers with HTML references separated by '/'

getComposition()

string & cBrick::getComposition

(

)

Access to a string containing composition of the brick (ids of bricks separated by '-')

Return values

reference

to a string

getFirstAcronymAsString()

string cBrick::getFirstAcronymAsString

(

)

Get the first acronym.

Return values

string

acronym of the first izomer

getLosses()

string & cBrick::getLosses

(

)

Access to a string variable which stores a list of neutral losses.

Return values

reference

to a string

getLossIDs()

vector< int > & cBrick::getLossIDs

(

)

Access to a vector of identifiers of neutral losses.

Return values

reference

to a vector of identifiers of neutral losses

getMass()

double cBrick::getMass

(

)

const

Get the mass of the brick.

Return values

double

mass

getName()

string & cBrick::getName

(

)

Access to a string variable which stores a full name of the brick.

Return values

reference

to a string

getReferences()

vector< string > & cBrick::getReferences

(

)

Access to a vector of strings which stores references (e.g., to ChemSpider) of all izomers corresponding to the brick.

Return values

reference

to a vector of strings

getReferencesAsString()

string cBrick::getReferencesAsString

(

)

Get all references.

Return values

string

references of all izomers separated by '/'

getResidueLossType()

eResidueLossType cBrick::getResidueLossType

(

)

Get the residue loss type.

Return values

eResidueLossType

the residue loss type.

getReverseComposition()

string cBrick::getReverseComposition

(

)

Reverse the composition of the brick.

Return values

string

with reverted composition of bricks (ids of bricks separated by '-')

getSummary()

string & cBrick::getSummary

(

)

Access to a string variable which stores a molecular formula of the brick.

Return values

reference

to a string

getSummaryMap()

map< string, int > & cBrick::getSummaryMap

(

)

Access to a map which stores a molecular formula of the brick.

Return values

map<string,int>

reference to a map

isArtificial()

bool cBrick::isArtificial

(

)

Get a flag determining whether the brick is a calculated mass block or a regular brick.

Return values

bool	true when the brick is a calculated mass block; false when the brick is a regular brick.

load()

void cBrick::load

(

ifstream &

is

)

Load the structure from an input stream.

Parameters

is	an input stream

setAcronyms()

void cBrick::setAcronyms

(

const string &

acronyms

)

Set acronyms of all izomers corresponding to the brick.

Parameters

acronyms

reference to a string where the acronyms are separated by '/'

setArtificial()

void cBrick::setArtificial

(

bool

artificial

)

Set a flag determining whether the brick is a calculated mass block or a regular brick.

Parameters

artificial

true when the brick is a calculated mass block; false when the brick is a regular brick.

setComposition()

void cBrick::setComposition	(	const string &	composition,
		bool	normalize
	)

Set the composition of the brick.

Parameters

composition	reference to a string with composition (ids of bricks separated by '-')
normalize	if true then ids of bricks are sorted in ascending order

setLosses()

void cBrick::setLosses

(

const string &

str

)

Set the list of losses.

Parameters

str	reference to a string

setLossIDs()

void cBrick::setLossIDs

(

vector< int > &

lossids

)

Set a vector of identifiers of neutral losses.

Parameters

lossids

a vector of identifiers of neutral losses

setMass()

void cBrick::setMass

(

double

mass

)

Set the mass of the brick.

Parameters

mass	mass of the brick

setName()

void cBrick::setName

(

const string &

name

)

Set a full name of the brick.

Parameters

name	reference to a string

setReferences()

void cBrick::setReferences

(

const string &

references

)

Set references (e.g., to ChemSpider) of all izomers corresponding to the brick.

Parameters

references

reference to a string where references to izomers are separated by '/'

setResidueLossType()

void cBrick::setResidueLossType

(

eResidueLossType

residuelosstype

)

Set the residue loss type.

Parameters

residuelosstype

the residue loss type.

setSummary()

void cBrick::setSummary

(

const string &

summary

)

Set the summary molecular formula of the brick.

Parameters

summary

reference to a string

store()

void cBrick::store

(

ofstream &

os

)

Store the structure into an output stream.

Parameters

os	an output stream

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

• core/cBrick.h
• core/cBrick.cpp