libpappsomspp
Library for mass spectrometry
Public Member Functions | Private Member Functions | Private Attributes | List of all members
pappso::ChemicalFormula Class Reference

#include <chemicalformula.h>

Inheritance diagram for pappso::ChemicalFormula:
pappso::AtomNumberInterface

Public Member Functions

 ChemicalFormula ()
 
 ChemicalFormula (const AtomNumberInterface &atom_interface)
 
 ChemicalFormula (const ChemicalFormula &other)
 
virtual ~ChemicalFormula ()
 
pappso::ChemicalFormula & operator= (const pappso::ChemicalFormula &other)
 
pappso::ChemicalFormula operator- () const
 
pappso::ChemicalFormula operator+ (const pappso::ChemicalFormula &to_add) const
 
int getNumberOfAtom (AtomIsotopeSurvey atom) const override
 get the number of atom C, O, N, H in the molecule More...
 
int getNumberOfIsotope (Isotope isotope) const override
 get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...
 
double getMass () const
 
void setOboPsiModTerm (const OboPsiModTerm &term)
 get formula from an Obo term More...
 
void addIsotopeCount (const IsotopeCount &isotope_count)
 add an atom or isotope to the forumla More...
 
const QString toString () const
 
void setFullIsotope (Isotope isotope)
 set full isotope labels More...
 
- Public Member Functions inherited from pappso::AtomNumberInterface
virtual int getNumberOfAtom (AtomIsotopeSurvey atom) const =0
 get the number of atom C, O, N, H in the molecule More...
 
virtual int getNumberOfIsotope (Isotope isotope) const =0
 get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule More...
 
virtual const ChemicalFormula getChemicalFormula () const
 

Private Member Functions

void setPsimodDiffFormula (const QString &diff_formula)
 
void setUnimodDiffFormula (const QString &diff_formula)
 
void addIsotopeNumberCount (const QString &atom_str, const QString &atom_isotope_number, std::int8_t count)
 
void simplify ()
 simplify chemical formula sort, group isotope, remove 0 More...
 

Private Attributes

std::vector< IsotopeCount > m_isotopeVector
 

Detailed Description

Definition at line 42 of file chemicalformula.h.

Constructor & Destructor Documentation

◆ ChemicalFormula() [1/3]

pappso::ChemicalFormula::ChemicalFormula ( )

Definition at line 88 of file chemicalformula.cpp.

89{
90}

◆ ChemicalFormula() [2/3]

pappso::ChemicalFormula::ChemicalFormula ( const AtomNumberInterface &  atom_interface)

Definition at line 102 of file chemicalformula.cpp.

103{
104 qDebug();
105 std::int16_t count_iso = atom_interface.getNumberOfIsotope(Isotope::C13);
106 std::int16_t count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::C) - count_iso;
107 qDebug() << count;
108 if(count > 0)
109 {
110 m_isotopeVector.push_back({Isotope::C, count});
111 }
112
113 if(count_iso > 0)
114 {
115 m_isotopeVector.push_back({Isotope::C13, count_iso});
116 }
117
118 count_iso = atom_interface.getNumberOfIsotope(Isotope::H2);
119 count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::H) - count_iso;
120 if(count > 0)
121 {
122 m_isotopeVector.push_back({Isotope::H, count});
123 }
124
125 if(count_iso > 0)
126 {
127 m_isotopeVector.push_back({Isotope::H2, count_iso});
128 }
129
130 qDebug();
131 count_iso = atom_interface.getNumberOfIsotope(Isotope::O17);
132 std::int16_t count_iso2 = atom_interface.getNumberOfIsotope(Isotope::O18);
133 count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::O) - count_iso - count_iso2;
134 if(count > 0)
135 {
136 m_isotopeVector.push_back({Isotope::O, count});
137 }
138
139 if(count_iso > 0)
140 {
141 m_isotopeVector.push_back({Isotope::O17, count_iso});
142 }
143
144 if(count_iso2 > 0)
145 {
146 m_isotopeVector.push_back({Isotope::O18, count_iso2});
147 }
148
149 qDebug();
150
151 count_iso = atom_interface.getNumberOfIsotope(Isotope::N15);
152 count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::N) - count_iso;
153 if(count > 0)
154 {
155 m_isotopeVector.push_back({Isotope::N, count});
156 }
157
158 if(count_iso > 0)
159 {
160 m_isotopeVector.push_back({Isotope::N15, count_iso});
161 }
162
163 qDebug();
164
165 count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::S);
166 count_iso = atom_interface.getNumberOfIsotope(Isotope::S33);
167 if(count_iso > 0)
168 {
169 m_isotopeVector.push_back({Isotope::S33, count_iso});
170 }
171 count = count - count_iso;
172 qDebug();
173
174 count_iso = atom_interface.getNumberOfIsotope(Isotope::S34);
175 if(count_iso > 0)
176 {
177 m_isotopeVector.push_back({Isotope::S34, count_iso});
178 }
179 count = count - count_iso;
180 qDebug();
181
182 count_iso = atom_interface.getNumberOfIsotope(Isotope::S36);
183 if(count_iso > 0)
184 {
185 m_isotopeVector.push_back({Isotope::S36, count_iso});
186 }
187 count = count - count_iso;
188
189 if(count > 0)
190 {
191 m_isotopeVector.push_back({Isotope::S, count});
192 }
193 qDebug();
194 count = atom_interface.getNumberOfAtom(AtomIsotopeSurvey::P);
195 if(count > 0)
196 {
197 m_isotopeVector.push_back({Isotope::P, count});
198 }
199
200 qDebug() << m_isotopeVector.size();
201}
pappso::ChemicalFormula::m_isotopeVector
std::vector< IsotopeCount > m_isotopeVector
Definition: chemicalformula.h:88

References pappso::C, pappso::C13, pappso::AtomNumberInterface::getNumberOfAtom(), pappso::AtomNumberInterface::getNumberOfIsotope(), pappso::H, pappso::H2, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::P, pappso::S, pappso::S33, pappso::S34, and pappso::S36.

◆ ChemicalFormula() [3/3]

pappso::ChemicalFormula::ChemicalFormula ( const ChemicalFormula &  other)

Definition at line 96 of file chemicalformula.cpp.

97 : m_isotopeVector(other.m_isotopeVector)
98{
99}

◆ ~ChemicalFormula()

pappso::ChemicalFormula::~ChemicalFormula ( )
virtual

Definition at line 92 of file chemicalformula.cpp.

93{
94}

Member Function Documentation

◆ addIsotopeCount()

void pappso::ChemicalFormula::addIsotopeCount ( const IsotopeCount &  isotope_count)

add an atom or isotope to the forumla

Definition at line 641 of file chemicalformula.cpp.

642{
643 bool added = false;
644 for(IsotopeCount &iso_count : m_isotopeVector)
645 {
646 if(iso_count.isotope == isotope_count.isotope)
647 {
648 added = true;
649 iso_count.count += isotope_count.count;
650 }
651 }
652
653 if(!added)
654 m_isotopeVector.push_back(isotope_count);
655}

References pappso::IsotopeCount::count, and pappso::IsotopeCount::isotope.

Referenced by pappso::PeptideInterface::getChemicalFormulaCharge().

◆ addIsotopeNumberCount()

void pappso::ChemicalFormula::addIsotopeNumberCount ( const QString &  atom_str,
const QString &  atom_isotope_number,
std::int8_t  count 
)
private

Definition at line 498 of file chemicalformula.cpp.

501{
502
503 if(atom_str == "C")
504 {
505 if(atom_isotope_number == "12")
506 {
507 m_isotopeVector.push_back({pappso::Isotope::C, count});
508 }
509 else if(atom_isotope_number == "13")
510 {
511 m_isotopeVector.push_back({pappso::Isotope::C13, count});
512 }
513 }
514 else if(atom_str == "H")
515 {
516 if(atom_isotope_number == "1")
517 {
518 m_isotopeVector.push_back({pappso::Isotope::H, count});
519 }
520 else if(atom_isotope_number == "2")
521 {
522 m_isotopeVector.push_back({pappso::Isotope::H2, count});
523 }
524 }
525 else if(atom_str == "N")
526 {
527
528 if(atom_isotope_number == "14")
529 {
530 m_isotopeVector.push_back({pappso::Isotope::N, count});
531 }
532 else if(atom_isotope_number == "15")
533 {
534 m_isotopeVector.push_back({pappso::Isotope::N15, count});
535 }
536 }
537 else if(atom_str == "O")
538 {
539 if(atom_isotope_number == "16")
540 {
541 m_isotopeVector.push_back({pappso::Isotope::O, count});
542 }
543 else if(atom_isotope_number == "17")
544 {
545 m_isotopeVector.push_back({pappso::Isotope::O17, count});
546 }
547 else if(atom_isotope_number == "18")
548 {
549 m_isotopeVector.push_back({pappso::Isotope::O18, count});
550 }
551 }
552 else if(atom_str == "S")
553 {
554 if(atom_isotope_number == "32")
555 {
556 m_isotopeVector.push_back({pappso::Isotope::S, count});
557 }
558 else if(atom_isotope_number == "33")
559 {
560 m_isotopeVector.push_back({pappso::Isotope::S33, count});
561 }
562 else if(atom_isotope_number == "34")
563 {
564 m_isotopeVector.push_back({pappso::Isotope::S34, count});
565 }
566 else if(atom_isotope_number == "36")
567 {
568 m_isotopeVector.push_back({pappso::Isotope::S36, count});
569 }
570 }
571 else
572 {
573 // not known
574
575 throw pappso::ExceptionNotFound(QObject::tr("atom string: [%1] with atom number %2 not found")
576 .arg(atom_str)
577 .arg(atom_isotope_number));
578 }
579}

References pappso::C, pappso::C13, pappso::H, pappso::H2, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.

◆ getMass()

double pappso::ChemicalFormula::getMass ( ) const

Definition at line 296 of file chemicalformula.cpp.

297{
298
299 double mass = 0;
300 for(auto &isotope_count : m_isotopeVector)
301 {
302 switch(isotope_count.isotope)
303 {
304 case pappso::Isotope::C13:
305 mass += ((DIFFC12C13 + MASSCARBON) * (double)isotope_count.count);
306 break;
307 case pappso::Isotope::C:
308 mass += (MASSCARBON * (double)isotope_count.count);
309 break;
310 case pappso::Isotope::H:
311 mass += (MPROTIUM * (double)isotope_count.count);
312 break;
313 case pappso::Isotope::H2:
314 mass += ((DIFFH1H2 + MPROTIUM) * (double)isotope_count.count);
315 break;
316 case pappso::Isotope::N:
317 mass += (MASSNITROGEN * (double)isotope_count.count);
318 break;
319 case pappso::Isotope::N15:
320 mass += ((MASSNITROGEN + DIFFN14N15) * (double)isotope_count.count);
321 break;
322 case pappso::Isotope::O:
323 mass += (MASSOXYGEN * (double)isotope_count.count);
324 break;
325 case pappso::Isotope::O17:
326 mass += ((DIFFO16O17 + MASSOXYGEN) * (double)isotope_count.count);
327 break;
328 case pappso::Isotope::O18:
329 mass += ((DIFFO16O18 + MASSOXYGEN) * (double)isotope_count.count);
330 break;
331 case pappso::Isotope::S:
332 mass += (MASSSULFUR * (double)isotope_count.count);
333 break;
334 case pappso::Isotope::S33:
335 mass += ((DIFFS32S33 + MASSSULFUR) * (double)isotope_count.count);
336 break;
337 case pappso::Isotope::S34:
338 mass += ((DIFFS32S34 + MASSSULFUR) * (double)isotope_count.count);
339 break;
340 case pappso::Isotope::S36:
341 mass += ((DIFFS32S36 + MASSSULFUR) * (double)isotope_count.count);
342 break;
343 case pappso::Isotope::P:
344 mass += (MASSPHOSPHORUS * (double)isotope_count.count);
345 break;
346 }
347 }
348 return mass;
349}
pappso::DIFFS32S33
const pappso_double DIFFS32S33(32.9714589101 - MASSSULFUR)
pappso::DIFFS32S34
const pappso_double DIFFS32S34(33.9678670300 - MASSSULFUR)
pappso::DIFFO16O17
const pappso_double DIFFO16O17(16.99913150 - MASSOXYGEN)
pappso::MASSCARBON
const pappso_double MASSCARBON(12)
pappso::MASSPHOSPHORUS
const pappso_double MASSPHOSPHORUS(30.973761998)
pappso::MASSSULFUR
const pappso_double MASSSULFUR(31.9720711741)
pappso::DIFFS32S36
const pappso_double DIFFS32S36(35.9670812000 - MASSSULFUR)
pappso::MPROTIUM
const pappso_double MPROTIUM(1.007825032241)
pappso::MASSNITROGEN
const pappso_double MASSNITROGEN(14.0030740048)
pappso::MASSOXYGEN
const pappso_double MASSOXYGEN(15.99491461956)
pappso::DIFFO16O18
const pappso_double DIFFO16O18(17.9991610 - MASSOXYGEN)
pappso::DIFFN14N15
const pappso_double DIFFN14N15(15.0001088982 - MASSNITROGEN)
pappso::DIFFC12C13
const pappso_double DIFFC12C13(1.0033548378)
pappso::DIFFH1H2
const pappso_double DIFFH1H2(2.0141017778 - MPROTIUM)

References pappso::C, pappso::C13, pappso::DIFFC12C13(), pappso::DIFFH1H2(), pappso::DIFFN14N15(), pappso::DIFFO16O17(), pappso::DIFFO16O18(), pappso::DIFFS32S33(), pappso::DIFFS32S34(), pappso::DIFFS32S36(), pappso::H, pappso::H2, pappso::MASSCARBON(), pappso::MASSNITROGEN(), pappso::MASSOXYGEN(), pappso::MASSPHOSPHORUS(), pappso::MASSSULFUR(), pappso::MPROTIUM(), pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::P, pappso::S, pappso::S33, pappso::S34, and pappso::S36.

Referenced by pappso::Peptide::getMass().

◆ getNumberOfAtom()

int pappso::ChemicalFormula::getNumberOfAtom ( AtomIsotopeSurvey  atom) const
overridevirtual

get the number of atom C, O, N, H in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 240 of file chemicalformula.cpp.

241{
242 int count = 0;
243 for(auto &isotope_count : m_isotopeVector)
244 {
245 switch(atom)
246 {
247 case pappso::AtomIsotopeSurvey::C:
248 if((isotope_count.isotope == pappso::Isotope::C) ||
249 (isotope_count.isotope == pappso::Isotope::C13))
250 count += isotope_count.count;
251 break;
252
253 case pappso::AtomIsotopeSurvey::H:
254 if((isotope_count.isotope == pappso::Isotope::H) ||
255 (isotope_count.isotope == pappso::Isotope::H2))
256 count += isotope_count.count;
257 break;
258 case pappso::AtomIsotopeSurvey::O:
259 if((isotope_count.isotope == pappso::Isotope::O) ||
260 (isotope_count.isotope == pappso::Isotope::O17) ||
261 (isotope_count.isotope == pappso::Isotope::O18))
262 count += isotope_count.count;
263 break;
264 case pappso::AtomIsotopeSurvey::N:
265 if((isotope_count.isotope == pappso::Isotope::N) ||
266 (isotope_count.isotope == pappso::Isotope::N15))
267 count += isotope_count.count;
268 break;
269 case pappso::AtomIsotopeSurvey::S:
270 if((isotope_count.isotope == pappso::Isotope::S) ||
271 (isotope_count.isotope == pappso::Isotope::S33) ||
272 (isotope_count.isotope == pappso::Isotope::S34) ||
273 (isotope_count.isotope == pappso::Isotope::S36))
274 count += isotope_count.count;
275 break;
276 default:
277 break;
278 }
279 }
280 return count;
281}

References pappso::C, pappso::C13, pappso::H, pappso::H2, pappso::N, pappso::N15, pappso::O, pappso::O17, pappso::O18, pappso::S, pappso::S33, pappso::S34, and pappso::S36.

Referenced by pappso::AaModification::setDiffFormula().

◆ getNumberOfIsotope()

int pappso::ChemicalFormula::getNumberOfIsotope ( Isotope  isotope) const
overridevirtual

get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule

Implements pappso::AtomNumberInterface.

Definition at line 284 of file chemicalformula.cpp.

285{
286 int count = 0;
287 for(auto &isotope_count : m_isotopeVector)
288 {
289 if(isotope_count.isotope == isotope)
290 count += isotope_count.count;
291 }
292 return count;
293}

Referenced by pappso::AaModification::setDiffFormula().

◆ operator+()

pappso::ChemicalFormula pappso::ChemicalFormula::operator+ ( const pappso::ChemicalFormula &  to_add) const

Definition at line 225 of file chemicalformula.cpp.

226{
227 ChemicalFormula new_formula(*this);
228
229 new_formula.m_isotopeVector.insert(new_formula.m_isotopeVector.end(),
230 to_add.m_isotopeVector.begin(),
231 to_add.m_isotopeVector.end());
232
233 new_formula.simplify();
234
235 return new_formula;
236}

References m_isotopeVector, and simplify().

◆ operator-()

pappso::ChemicalFormula pappso::ChemicalFormula::operator- ( ) const

Definition at line 211 of file chemicalformula.cpp.

212{
213 ChemicalFormula new_formula;
214
215 for(const IsotopeCount &isotope_count : m_isotopeVector)
216 {
217 std::int16_t count = isotope_count.count * -1;
218 new_formula.m_isotopeVector.push_back({isotope_count.isotope, count});
219 }
220
221 return new_formula;
222}

References m_isotopeVector.

◆ operator=()

pappso::ChemicalFormula & pappso::ChemicalFormula::operator= ( const pappso::ChemicalFormula &  other)

Definition at line 204 of file chemicalformula.cpp.

205{
206 m_isotopeVector = other.m_isotopeVector;
207 return *this;
208}

References m_isotopeVector.

◆ setFullIsotope()

void pappso::ChemicalFormula::setFullIsotope ( pappso::Isotope  isotope)

set full isotope labels

Definition at line 672 of file chemicalformula.cpp.

673{
674 IsotopeCount *isotope_ref_p = nullptr;
675 std::int16_t cumul_count = 0;
676 for(IsotopeCount &iso_count : m_isotopeVector)
677 {
678 if(isotope == Isotope::C13)
679 {
680 if(iso_count.isotope == Isotope::C)
681 {
682 cumul_count += iso_count.count;
683 iso_count.count = 0;
684 }
685 if(iso_count.isotope == Isotope::C13)
686 {
687 cumul_count += iso_count.count;
688 isotope_ref_p = &iso_count;
689 }
690 }
691 else if(isotope == Isotope::N15)
692 {
693 if(iso_count.isotope == Isotope::N)
694 {
695 cumul_count += iso_count.count;
696 iso_count.count = 0;
697 }
698 if(iso_count.isotope == Isotope::N15)
699 {
700 cumul_count += iso_count.count;
701 isotope_ref_p = &iso_count;
702 }
703 }
704 else if(isotope == Isotope::H2)
705 {
706 if(iso_count.isotope == Isotope::H)
707 {
708 cumul_count += iso_count.count;
709 iso_count.count = 0;
710 }
711 if(iso_count.isotope == Isotope::H2)
712 {
713 cumul_count += iso_count.count;
714 isotope_ref_p = &iso_count;
715 }
716 }
717 }
718 if(isotope_ref_p == nullptr)
719 {
720 if(isotope == Isotope::C13)
721 {
722 m_isotopeVector.push_back({Isotope::C13, cumul_count});
723 }
724 else if(isotope == Isotope::N15)
725 {
726 m_isotopeVector.push_back({Isotope::N15, cumul_count});
727 }
728 else if(isotope == Isotope::H2)
729 {
730 m_isotopeVector.push_back({Isotope::H2, cumul_count});
731 }
732 }
733 else
734 {
735 isotope_ref_p->count = cumul_count;
736 }
737}

References pappso::C, pappso::C13, pappso::IsotopeCount::count, pappso::H, pappso::H2, pappso::N, and pappso::N15.

Referenced by pappso::Peptide::getChemicalFormulaCharge().

◆ setOboPsiModTerm()

void pappso::ChemicalFormula::setOboPsiModTerm ( const OboPsiModTerm &  term)

get formula from an Obo term

Definition at line 352 of file chemicalformula.cpp.

353{
354 m_isotopeVector.clear();
355
356 if(term.isUnimod())
357 {
358 qDebug();
359 setUnimodDiffFormula(term.m_diffFormula);
360 }
361 else
362 {
363 qDebug() << "is_a " << term.m_isA.join(" ");
364 if(term.isA("MOD:01441"))
365 {
366 qDebug() << "term.isA(MOD:01441)";
367 if(term.m_origin.isEmpty())
368 {
369 throw pappso::ExceptionNotFound(
370 QObject::tr("origin not found for term : [%1]").arg(term.getAccession()));
371 }
372 setPsimodDiffFormula(term.m_formula);
373 qDebug();
374 // new_mod->m_mass = AaBase::getAaMass(term.m_origin[0].toLatin1());
375 }
376 else
377 {
378 setPsimodDiffFormula(term.m_diffFormula);
379 }
380 }
381 qDebug();
382}
pappso::ChemicalFormula::setPsimodDiffFormula
void setPsimodDiffFormula(const QString &diff_formula)
Definition: chemicalformula.cpp:583
pappso::ChemicalFormula::setUnimodDiffFormula
void setUnimodDiffFormula(const QString &diff_formula)
Definition: chemicalformula.cpp:385

References pappso::OboPsiModTerm::getAccession(), pappso::OboPsiModTerm::isA(), pappso::OboPsiModTerm::isUnimod(), pappso::OboPsiModTerm::m_diffFormula, pappso::OboPsiModTerm::m_formula, pappso::OboPsiModTerm::m_isA, and pappso::OboPsiModTerm::m_origin.

Referenced by pappso::AaModification::createInstance().

◆ setPsimodDiffFormula()

void pappso::ChemicalFormula::setPsimodDiffFormula ( const QString &  diff_formula)
private

Definition at line 583 of file chemicalformula.cpp.

584{
585 QRegularExpression rx("(^|\\s)([C,H,O,N,S,P])\\s([-]{0,1}\\d+)");
586 QRegularExpressionMatchIterator i = rx.globalMatch(diff_formula);
587
588 while(i.hasNext())
589 {
590 QRegularExpressionMatch match = i.next();
591
592 qDebug() << match.captured(2) << " " << match.captured(2) << " " << match.captured(3);
593 std::int8_t count = match.captured(3).toInt();
594
595 qDebug() << count;
596 if(match.captured(2) == "C")
597 {
598 m_isotopeVector.push_back({pappso::Isotope::C, count});
599 }
600 else if(match.captured(2) == "H")
601 {
602 m_isotopeVector.push_back({pappso::Isotope::H, count});
603 }
604 else if(match.captured(2) == "N")
605 {
606 m_isotopeVector.push_back({pappso::Isotope::N, count});
607 }
608 else if(match.captured(2) == "O")
609 {
610 m_isotopeVector.push_back({pappso::Isotope::O, count});
611 }
612 else if(match.captured(2) == "S")
613 {
614 m_isotopeVector.push_back({pappso::Isotope::S, count});
615 }
616 else if(match.captured(2) == "P")
617 {
618 m_isotopeVector.push_back({pappso::Isotope::P, count});
619 }
620 }
621
622 // look for isotopes :
623 rx.setPattern("\\((\\d+)\\)([C,H,O,N,S])\\s([-]{0,1}\\d+)");
624
625 i = rx.globalMatch(diff_formula);
626
627 while(i.hasNext())
628 {
629 QRegularExpressionMatch match = i.next();
630
631 qDebug() << match.captured(1) << " " << match.captured(2) << " " << match.captured(3);
632
633 std::int8_t number_of_isotopes = match.captured(3).toInt();
634
635
636 addIsotopeNumberCount(match.captured(2), match.captured(1), number_of_isotopes);
637 }
638}
pappso::ChemicalFormula::addIsotopeNumberCount
void addIsotopeNumberCount(const QString &atom_str, const QString &atom_isotope_number, std::int8_t count)
Definition: chemicalformula.cpp:498

References pappso::C, pappso::H, pappso::N, pappso::O, pappso::P, and pappso::S.

◆ setUnimodDiffFormula()

void pappso::ChemicalFormula::setUnimodDiffFormula ( const QString &  diff_formula)
private

Definition at line 385 of file chemicalformula.cpp.

386{
387 // C(-6) 13C(6) N(-2) 15N(2)
388
389 // atom alone
390 QRegularExpression rx("(^|\\s)([C,H,O,N,S,P])($|\\s)");
391 QRegularExpressionMatchIterator i = rx.globalMatch(diff_formula);
392
393 while(i.hasNext())
394 {
395 QRegularExpressionMatch match = i.next();
396
397 qDebug() << match.captured(2) << " " << match.captured(2);
398 std::int8_t count = 1;
399
400 qDebug() << count;
401 if(match.captured(2) == "C")
402 {
403 m_isotopeVector.push_back({pappso::Isotope::C, count});
404 }
405 else if(match.captured(2) == "H")
406 {
407 m_isotopeVector.push_back({pappso::Isotope::H, count});
408 }
409 else if(match.captured(2) == "N")
410 {
411 m_isotopeVector.push_back({pappso::Isotope::N, count});
412 }
413 else if(match.captured(2) == "O")
414 {
415 m_isotopeVector.push_back({pappso::Isotope::O, count});
416 }
417 else if(match.captured(2) == "S")
418 {
419 m_isotopeVector.push_back({pappso::Isotope::S, count});
420 }
421 else if(match.captured(2) == "P")
422 {
423 m_isotopeVector.push_back({pappso::Isotope::P, count});
424 }
425 }
426
427 // C(-6) 13C(6) N(-2) 15N(2)
428 rx.setPattern("(^|\\s)([C,H,O,N,S,P])\\(([-]{0,1}\\d+)\\)");
429 i = rx.globalMatch(diff_formula);
430
431 while(i.hasNext())
432 {
433 QRegularExpressionMatch match = i.next();
434
435 qDebug() << match.captured(2) << " " << match.captured(3);
436 std::int8_t count = match.captured(3).toInt();
437
438 qDebug() << count;
439 if(match.captured(2) == "C")
440 {
441 m_isotopeVector.push_back({pappso::Isotope::C, count});
442 }
443 else if(match.captured(2) == "H")
444 {
445 m_isotopeVector.push_back({pappso::Isotope::H, count});
446 }
447 else if(match.captured(2) == "N")
448 {
449 m_isotopeVector.push_back({pappso::Isotope::N, count});
450 }
451 else if(match.captured(2) == "O")
452 {
453 m_isotopeVector.push_back({pappso::Isotope::O, count});
454 }
455 else if(match.captured(2) == "S")
456 {
457 m_isotopeVector.push_back({pappso::Isotope::S, count});
458 }
459 else if(match.captured(2) == "P")
460 {
461 m_isotopeVector.push_back({pappso::Isotope::P, count});
462 }
463 }
464
465 // C(-6) 13C(6) N(-2) 15N(2)
466 // look for isotopes :
467 rx.setPattern("(^|\\s)(\\d+)([C,H,O,N,S])($|\\s)");
468
469 i = rx.globalMatch(diff_formula);
470
471 while(i.hasNext())
472 {
473 QRegularExpressionMatch match = i.next();
474
475 qDebug() << match.captured(2) << " " << match.captured(3);
476
477 addIsotopeNumberCount(match.captured(3), match.captured(2), 1);
478 }
479 // C(-6) 13C(6) N(-2) 15N(2)
480 // look for isotopes :
481 rx.setPattern("(^|\\s)(\\d+)([C,H,O,N,S])\\(([-]{0,1}\\d+)\\)");
482
483 i = rx.globalMatch(diff_formula);
484
485 while(i.hasNext())
486 {
487 QRegularExpressionMatch match = i.next();
488
489 qDebug() << match.captured(2) << " " << match.captured(3) << " " << match.captured(4);
490
491 std::int8_t number_of_isotopes = match.captured(4).toInt();
492
493 addIsotopeNumberCount(match.captured(3), match.captured(2), number_of_isotopes);
494 }
495}

References pappso::C, pappso::H, pappso::N, pappso::O, pappso::P, and pappso::S.

◆ simplify()

void pappso::ChemicalFormula::simplify ( )
private

simplify chemical formula sort, group isotope, remove 0

Definition at line 741 of file chemicalformula.cpp.

742{
743 std::vector<IsotopeCount> new_vector;
744 std::sort(m_isotopeVector.begin(), m_isotopeVector.end(), [](IsotopeCount &a, IsotopeCount &b) {
745 return a.isotope < b.isotope;
746 });
747
748 auto it = m_isotopeVector.begin();
749 while(it != m_isotopeVector.end())
750 {
751 IsotopeCount current_element = *it;
752 it++;
753 if(it != m_isotopeVector.end())
754 {
755 if(it->isotope != current_element.isotope)
756 {
757 new_vector.push_back(current_element);
758 }
759 else
760 {
761 while((it != m_isotopeVector.end()) && (it->isotope == current_element.isotope))
762 {
763 current_element.count += it->count;
764 it++;
765 }
766 if(current_element.count != 0)
767 {
768 new_vector.push_back(current_element);
769 }
770 }
771 }
772 }
773 m_isotopeVector = new_vector;
774}

References pappso::IsotopeCount::count, and pappso::IsotopeCount::isotope.

Referenced by operator+().

◆ toString()

const QString pappso::ChemicalFormula::toString ( ) const

Definition at line 659 of file chemicalformula.cpp.

660{
661 QStringList str_formula;
662 for(const IsotopeCount &iso_count : m_isotopeVector)
663 {
664 if(iso_count.count != 0)
665 str_formula << iso_count.toString();
666 }
667 str_formula.sort();
668 return str_formula.join(" ");
669}

Referenced by pappso::Peptide::getChemicalFormulaCharge().

Member Data Documentation

◆ m_isotopeVector

std::vector<IsotopeCount> pappso::ChemicalFormula::m_isotopeVector
private

Definition at line 88 of file chemicalformula.h.

Referenced by operator+(), operator-(), and operator=().

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