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CycloBranch
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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... | |
The class representing a building block (brick).
| bool cBrick::empty | ( | ) |
Test whether the brick is empty.
| true | if the brick is empty |
| void cBrick::explodeToIntComposition | ( | vector< int > & | bricks | ) |
Explode the composition of the brick into a vector of intergers (ids of subbricks).
| bricks | reference to a vector of integers |
| void cBrick::explodeToStringComposition | ( | vector< string > & | bricks | ) |
Explode the composition of the brick into a vector of strings (ids of subbricks).
| bricks | reference to a vector of strings |
| vector< string > & cBrick::getAcronyms | ( | ) |
Access to a vector of strings which stores acronyms of all izomers corresponding to the brick.
| reference | to a vector of strings |
| string cBrick::getAcronymsAsString | ( | ) |
Get all acronyms.
| string | acronyms of all izomers separated by '/' |
| string cBrick::getAcronymsWithReferencesAsHTMLString | ( | ) |
Get all acronyms with HTML links to theirs references.
| string | acronyms of all izomers with HTML references separated by '/' |
| string & cBrick::getComposition | ( | ) |
Access to a string containing composition of the brick (ids of bricks separated by '-')
| reference | to a string |
| string cBrick::getFirstAcronymAsString | ( | ) |
Get the first acronym.
| string | acronym of the first izomer |
| string & cBrick::getLosses | ( | ) |
Access to a string variable which stores a list of neutral losses.
| reference | to a string |
| vector< int > & cBrick::getLossIDs | ( | ) |
Access to a vector of identifiers of neutral losses.
| reference | to a vector of identifiers of neutral losses |
| double cBrick::getMass | ( | ) | const |
Get the mass of the brick.
| double | mass |
| string & cBrick::getName | ( | ) |
Access to a string variable which stores a full name of the brick.
| reference | to a string |
| vector< string > & cBrick::getReferences | ( | ) |
Access to a vector of strings which stores references (e.g., to ChemSpider) of all izomers corresponding to the brick.
| reference | to a vector of strings |
| string cBrick::getReferencesAsString | ( | ) |
Get all references.
| string | references of all izomers separated by '/' |
| eResidueLossType cBrick::getResidueLossType | ( | ) |
Get the residue loss type.
| eResidueLossType | the residue loss type. |
| string cBrick::getReverseComposition | ( | ) |
Reverse the composition of the brick.
| string | with reverted composition of bricks (ids of bricks separated by '-') |
| string & cBrick::getSummary | ( | ) |
Access to a string variable which stores a molecular formula of the brick.
| reference | to a string |
| map< string, int > & cBrick::getSummaryMap | ( | ) |
Access to a map which stores a molecular formula of the brick.
| map<string,int> | reference to a map |
| bool cBrick::isArtificial | ( | ) |
Get a flag determining whether the brick is a calculated mass block or a regular brick.
| bool | true when the brick is a calculated mass block; false when the brick is a regular brick. |
| void cBrick::load | ( | ifstream & | is | ) |
Load the structure from an input stream.
| is | an input stream |
| void cBrick::setAcronyms | ( | const string & | acronyms | ) |
Set acronyms of all izomers corresponding to the brick.
| acronyms | reference to a string where the acronyms are separated by '/' |
| void cBrick::setArtificial | ( | bool | artificial | ) |
Set a flag determining whether the brick is a calculated mass block or a regular brick.
| artificial | true when the brick is a calculated mass block; false when the brick is a regular brick. |
| void cBrick::setComposition | ( | const string & | composition, |
| bool | normalize | ||
| ) |
Set the composition of the brick.
| composition | reference to a string with composition (ids of bricks separated by '-') |
| normalize | if true then ids of bricks are sorted in ascending order |
| void cBrick::setLosses | ( | const string & | str | ) |
Set the list of losses.
| str | reference to a string |
| void cBrick::setLossIDs | ( | vector< int > & | lossids | ) |
Set a vector of identifiers of neutral losses.
| lossids | a vector of identifiers of neutral losses |
| void cBrick::setMass | ( | double | mass | ) |
Set the mass of the brick.
| mass | mass of the brick |
| void cBrick::setName | ( | const string & | name | ) |
Set a full name of the brick.
| name | reference to a string |
| void cBrick::setReferences | ( | const string & | references | ) |
Set references (e.g., to ChemSpider) of all izomers corresponding to the brick.
| references | reference to a string where references to izomers are separated by '/' |
| void cBrick::setResidueLossType | ( | eResidueLossType | residuelosstype | ) |
Set the residue loss type.
| residuelosstype | the residue loss type. |
| void cBrick::setSummary | ( | const string & | summary | ) |
Set the summary molecular formula of the brick.
| summary | reference to a string |
| void cBrick::store | ( | ofstream & | os | ) |
Store the structure into an output stream.
| os | an output stream |