libpappsomspp
Library for mass spectrometry
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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 (Enums::AtomIsotopeSurvey atom) const override
 get the number of atom C, O, N, H in the molecule
 
int getNumberOfIsotope (Enums::Isotope isotope) const override
 get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
 
double getMass () const
 
void setOboPsiModTerm (const OboPsiModTerm &term)
 get formula from an Obo term
 
void addIsotopeCount (const IsotopeCount &isotope_count)
 add an atom or isotope to the forumla
 
const QString toString () const
 
void setFullIsotope (Enums::Isotope isotope)
 set full isotope labels
 
- Public Member Functions inherited from pappso::AtomNumberInterface
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
 

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}

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

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

References m_isotopeVector.

◆ ~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, pappso::IsotopeCount::isotope, and m_isotopeVector.

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({Enums::Isotope::C, count});
508 }
509 else if(atom_isotope_number == "13")
510 {
511 m_isotopeVector.push_back({Enums::Isotope::C13, count});
512 }
513 }
514 else if(atom_str == "H")
515 {
516 if(atom_isotope_number == "1")
517 {
518 m_isotopeVector.push_back({Enums::Isotope::H, count});
519 }
520 else if(atom_isotope_number == "2")
521 {
522 m_isotopeVector.push_back({Enums::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({Enums::Isotope::N, count});
531 }
532 else if(atom_isotope_number == "15")
533 {
534 m_isotopeVector.push_back({Enums::Isotope::N15, count});
535 }
536 }
537 else if(atom_str == "O")
538 {
539 if(atom_isotope_number == "16")
540 {
541 m_isotopeVector.push_back({Enums::Isotope::O, count});
542 }
543 else if(atom_isotope_number == "17")
544 {
545 m_isotopeVector.push_back({Enums::Isotope::O17, count});
546 }
547 else if(atom_isotope_number == "18")
548 {
549 m_isotopeVector.push_back({Enums::Isotope::O18, count});
550 }
551 }
552 else if(atom_str == "S")
553 {
554 if(atom_isotope_number == "32")
555 {
556 m_isotopeVector.push_back({Enums::Isotope::S, count});
557 }
558 else if(atom_isotope_number == "33")
559 {
560 m_isotopeVector.push_back({Enums::Isotope::S33, count});
561 }
562 else if(atom_isotope_number == "34")
563 {
564 m_isotopeVector.push_back({Enums::Isotope::S34, count});
565 }
566 else if(atom_isotope_number == "36")
567 {
568 m_isotopeVector.push_back({Enums::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::Enums::C, pappso::Enums::C13, pappso::Enums::H, pappso::Enums::H2, m_isotopeVector, pappso::Enums::N, pappso::Enums::N15, pappso::Enums::O, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::S, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

Referenced by setPsimodDiffFormula(), and setUnimodDiffFormula().

◆ 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 Enums::Isotope::C13:
305 mass += ((DIFFC12C13 + MASSCARBON) * (double)isotope_count.count);
306 break;
307 case Enums::Isotope::C:
308 mass += (MASSCARBON * (double)isotope_count.count);
309 break;
310 case Enums::Isotope::H:
311 mass += (MPROTIUM * (double)isotope_count.count);
312 break;
313 case Enums::Isotope::H2:
314 mass += ((DIFFH1H2 + MPROTIUM) * (double)isotope_count.count);
315 break;
316 case Enums::Isotope::N:
317 mass += (MASSNITROGEN * (double)isotope_count.count);
318 break;
319 case Enums::Isotope::N15:
320 mass += ((MASSNITROGEN + DIFFN14N15) * (double)isotope_count.count);
321 break;
322 case Enums::Isotope::O:
323 mass += (MASSOXYGEN * (double)isotope_count.count);
324 break;
325 case Enums::Isotope::O17:
326 mass += ((DIFFO16O17 + MASSOXYGEN) * (double)isotope_count.count);
327 break;
328 case Enums::Isotope::O18:
329 mass += ((DIFFO16O18 + MASSOXYGEN) * (double)isotope_count.count);
330 break;
331 case Enums::Isotope::S:
332 mass += (MASSSULFUR * (double)isotope_count.count);
333 break;
334 case Enums::Isotope::S33:
335 mass += ((DIFFS32S33 + MASSSULFUR) * (double)isotope_count.count);
336 break;
337 case Enums::Isotope::S34:
338 mass += ((DIFFS32S34 + MASSSULFUR) * (double)isotope_count.count);
339 break;
340 case Enums::Isotope::S36:
341 mass += ((DIFFS32S36 + MASSSULFUR) * (double)isotope_count.count);
342 break;
343 case Enums::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::Enums::C, pappso::Enums::C13, pappso::DIFFC12C13(), pappso::DIFFH1H2(), pappso::DIFFN14N15(), pappso::DIFFO16O17(), pappso::DIFFO16O18(), pappso::DIFFS32S33(), pappso::DIFFS32S34(), pappso::DIFFS32S36(), pappso::Enums::H, pappso::Enums::H2, m_isotopeVector, pappso::MASSCARBON(), pappso::MASSNITROGEN(), pappso::MASSOXYGEN(), pappso::MASSPHOSPHORUS(), pappso::MASSSULFUR(), pappso::MPROTIUM(), pappso::Enums::N, pappso::Enums::N15, pappso::Enums::O, pappso::Enums::O17, pappso::Enums::O18, pappso::Enums::P, pappso::Enums::S, pappso::Enums::S33, pappso::Enums::S34, and pappso::Enums::S36.

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

◆ getNumberOfAtom()

int pappso::ChemicalFormula::getNumberOfAtom ( Enums::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 Enums::AtomIsotopeSurvey::C:
248 if((isotope_count.isotope == Enums::Isotope::C) ||
249 (isotope_count.isotope == Enums::Isotope::C13))
250 count += isotope_count.count;
251 break;
252
253 case Enums::AtomIsotopeSurvey::H:
254 if((isotope_count.isotope == Enums::Isotope::H) ||
255 (isotope_count.isotope == Enums::Isotope::H2))
256 count += isotope_count.count;
257 break;
258 case Enums::AtomIsotopeSurvey::O:
259 if((isotope_count.isotope == Enums::Isotope::O) ||
260 (isotope_count.isotope == Enums::Isotope::O17) ||
261 (isotope_count.isotope == Enums::Isotope::O18))
262 count += isotope_count.count;
263 break;
264 case Enums::AtomIsotopeSurvey::N:
265 if((isotope_count.isotope == Enums::Isotope::N) ||
266 (isotope_count.isotope == Enums::Isotope::N15))
267 count += isotope_count.count;
268 break;
269 case Enums::AtomIsotopeSurvey::S:
270 if((isotope_count.isotope == Enums::Isotope::S) ||
271 (isotope_count.isotope == Enums::Isotope::S33) ||
272 (isotope_count.isotope == Enums::Isotope::S34) ||
273 (isotope_count.isotope == Enums::Isotope::S36))
274 count += isotope_count.count;
275 break;
276 default:
277 break;
278 }
279 }
280 return count;
281}

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

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

◆ getNumberOfIsotope()

int pappso::ChemicalFormula::getNumberOfIsotope ( Enums::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}

References m_isotopeVector.

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 ChemicalFormula(), 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 ChemicalFormula(), and 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 ( Enums::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 == Enums::Isotope::C13)
679 {
680 if(iso_count.isotope == Enums::Isotope::C)
681 {
682 cumul_count += iso_count.count;
683 iso_count.count = 0;
684 }
685 if(iso_count.isotope == Enums::Isotope::C13)
686 {
687 cumul_count += iso_count.count;
688 isotope_ref_p = &iso_count;
689 }
690 }
691 else if(isotope == Enums::Isotope::N15)
692 {
693 if(iso_count.isotope == Enums::Isotope::N)
694 {
695 cumul_count += iso_count.count;
696 iso_count.count = 0;
697 }
698 if(iso_count.isotope == Enums::Isotope::N15)
699 {
700 cumul_count += iso_count.count;
701 isotope_ref_p = &iso_count;
702 }
703 }
704 else if(isotope == Enums::Isotope::H2)
705 {
706 if(iso_count.isotope == Enums::Isotope::H)
707 {
708 cumul_count += iso_count.count;
709 iso_count.count = 0;
710 }
711 if(iso_count.isotope == Enums::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 == Enums::Isotope::C13)
721 {
722 m_isotopeVector.push_back({Enums::Isotope::C13, cumul_count});
723 }
724 else if(isotope == Enums::Isotope::N15)
725 {
726 m_isotopeVector.push_back({Enums::Isotope::N15, cumul_count});
727 }
728 else if(isotope == Enums::Isotope::H2)
729 {
730 m_isotopeVector.push_back({Enums::Isotope::H2, cumul_count});
731 }
732 }
733 else
734 {
735 isotope_ref_p->count = cumul_count;
736 }
737}

References pappso::Enums::C, pappso::Enums::C13, pappso::IsotopeCount::count, pappso::Enums::H, pappso::Enums::H2, m_isotopeVector, pappso::Enums::N, and pappso::Enums::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, m_isotopeVector, pappso::OboPsiModTerm::m_origin, setPsimodDiffFormula(), and setUnimodDiffFormula().

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({Enums::Isotope::C, count});
599 }
600 else if(match.captured(2) == "H")
601 {
602 m_isotopeVector.push_back({Enums::Isotope::H, count});
603 }
604 else if(match.captured(2) == "N")
605 {
606 m_isotopeVector.push_back({Enums::Isotope::N, count});
607 }
608 else if(match.captured(2) == "O")
609 {
610 m_isotopeVector.push_back({Enums::Isotope::O, count});
611 }
612 else if(match.captured(2) == "S")
613 {
614 m_isotopeVector.push_back({Enums::Isotope::S, count});
615 }
616 else if(match.captured(2) == "P")
617 {
618 m_isotopeVector.push_back({Enums::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 addIsotopeNumberCount(), pappso::Enums::C, pappso::Enums::H, m_isotopeVector, pappso::Enums::N, pappso::Enums::O, pappso::Enums::P, and pappso::Enums::S.

Referenced by setOboPsiModTerm().

◆ 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({Enums::Isotope::C, count});
404 }
405 else if(match.captured(2) == "H")
406 {
407 m_isotopeVector.push_back({Enums::Isotope::H, count});
408 }
409 else if(match.captured(2) == "N")
410 {
411 m_isotopeVector.push_back({Enums::Isotope::N, count});
412 }
413 else if(match.captured(2) == "O")
414 {
415 m_isotopeVector.push_back({Enums::Isotope::O, count});
416 }
417 else if(match.captured(2) == "S")
418 {
419 m_isotopeVector.push_back({Enums::Isotope::S, count});
420 }
421 else if(match.captured(2) == "P")
422 {
423 m_isotopeVector.push_back({Enums::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({Enums::Isotope::C, count});
442 }
443 else if(match.captured(2) == "H")
444 {
445 m_isotopeVector.push_back({Enums::Isotope::H, count});
446 }
447 else if(match.captured(2) == "N")
448 {
449 m_isotopeVector.push_back({Enums::Isotope::N, count});
450 }
451 else if(match.captured(2) == "O")
452 {
453 m_isotopeVector.push_back({Enums::Isotope::O, count});
454 }
455 else if(match.captured(2) == "S")
456 {
457 m_isotopeVector.push_back({Enums::Isotope::S, count});
458 }
459 else if(match.captured(2) == "P")
460 {
461 m_isotopeVector.push_back({Enums::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 addIsotopeNumberCount(), pappso::Enums::C, pappso::Enums::H, m_isotopeVector, pappso::Enums::N, pappso::Enums::O, pappso::Enums::P, and pappso::Enums::S.

Referenced by setOboPsiModTerm().

◆ 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::a, pappso::b, pappso::IsotopeCount::count, pappso::IsotopeCount::isotope, and m_isotopeVector.

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}

References m_isotopeVector.

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 ChemicalFormula(), ChemicalFormula(), addIsotopeCount(), addIsotopeNumberCount(), getMass(), getNumberOfAtom(), getNumberOfIsotope(), operator+(), operator-(), operator=(), setFullIsotope(), setOboPsiModTerm(), setPsimodDiffFormula(), setUnimodDiffFormula(), simplify(), and toString().

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