35 #include "../exception/exceptionnotfound.h"
42 AaBase::AaBase(
char aa_letter) : m_aaLetter(aa_letter)
52 QObject::tr(
"amino acid %1 not found").arg(aa_letter));
71 AminoAcidCharList ret = {
96 ret.insert(std::pair<char, pappso_double>(
101 ret.insert(std::pair<char, pappso_double>(
107 ret.insert(std::pair<char, pappso_double>(
112 ret.insert(std::pair<char, pappso_double>(
117 ret.insert(std::pair<char, pappso_double>(
122 ret.insert(std::pair<char, pappso_double>(
127 ret.insert(std::pair<char, pappso_double>(
132 ret.insert(std::pair<char, pappso_double>(
137 ret.insert(std::pair<char, pappso_double>(
142 ret.insert(std::pair<char, pappso_double>(
147 ret.insert(std::pair<char, pappso_double>(
152 ret.insert(std::pair<char, pappso_double>(
157 ret.insert(std::pair<char, pappso_double>(
162 ret.insert(std::pair<char, pappso_double>(
168 ret.insert(std::pair<char, pappso_double>(
177 ret.insert(std::pair<char, pappso_double>(
182 ret.insert(std::pair<char, pappso_double>(
187 ret.insert(std::pair<char, pappso_double>(
192 ret.insert(std::pair<char, pappso_double>(
199 ret.insert(std::pair<char, pappso_double>(
205 ret.insert(std::pair<char, pappso_double>(
211 ret.insert(std::pair<char, pappso_double>(
226 ret.insert(std::pair<char, unsigned int>(
'W', 11));
227 ret.insert(std::pair<char, unsigned int>(
'G', 2));
228 ret.insert(std::pair<char, unsigned int>(
'A', 3));
229 ret.insert(std::pair<char, unsigned int>(
'S', 3));
230 ret.insert(std::pair<char, unsigned int>(
'P', 5));
231 ret.insert(std::pair<char, unsigned int>(
'V', 5));
232 ret.insert(std::pair<char, unsigned int>(
'T', 4));
233 ret.insert(std::pair<char, unsigned int>(
'L', 6));
234 ret.insert(std::pair<char, unsigned int>(
'I', 6));
235 ret.insert(std::pair<char, unsigned int>(
'N', 4));
236 ret.insert(std::pair<char, unsigned int>(
'D', 4));
237 ret.insert(std::pair<char, unsigned int>(
'K', 6));
238 ret.insert(std::pair<char, unsigned int>(
'Q', 5));
239 ret.insert(std::pair<char, unsigned int>(
'E', 5));
240 ret.insert(std::pair<char, unsigned int>(
'M', 5));
241 ret.insert(std::pair<char, unsigned int>(
'H', 6));
242 ret.insert(std::pair<char, unsigned int>(
'F', 9));
243 ret.insert(std::pair<char, unsigned int>(
'R', 6));
244 ret.insert(std::pair<char, unsigned int>(
'C', 3));
245 ret.insert(std::pair<char, unsigned int>(
'Y', 9));
247 ret.insert(std::pair<char, unsigned int>(
'U', 3));
249 ret.insert(std::pair<char, unsigned int>(
'O', 12));
258 ret.insert(std::pair<char, unsigned int>(
'A', 5));
259 ret.insert(std::pair<char, unsigned int>(
'C', 5));
260 ret.insert(std::pair<char, unsigned int>(
'D', 5));
261 ret.insert(std::pair<char, unsigned int>(
'E', 7));
262 ret.insert(std::pair<char, unsigned int>(
'F', 9));
263 ret.insert(std::pair<char, unsigned int>(
'G', 3));
264 ret.insert(std::pair<char, unsigned int>(
'H', 7));
265 ret.insert(std::pair<char, unsigned int>(
'I', 11));
266 ret.insert(std::pair<char, unsigned int>(
'K', 12));
267 ret.insert(std::pair<char, unsigned int>(
'L', 11));
268 ret.insert(std::pair<char, unsigned int>(
'M', 9));
269 ret.insert(std::pair<char, unsigned int>(
'N', 6));
270 ret.insert(std::pair<char, unsigned int>(
'P', 7));
271 ret.insert(std::pair<char, unsigned int>(
'Q', 8));
272 ret.insert(std::pair<char, unsigned int>(
'R', 12));
273 ret.insert(std::pair<char, unsigned int>(
'S', 5));
274 ret.insert(std::pair<char, unsigned int>(
'T', 7));
275 ret.insert(std::pair<char, unsigned int>(
'V', 9));
276 ret.insert(std::pair<char, unsigned int>(
'W', 10));
277 ret.insert(std::pair<char, unsigned int>(
'Y', 9));
279 ret.insert(std::pair<char, unsigned int>(
'U', 7));
281 ret.insert(std::pair<char, unsigned int>(
'O', 21));
290 ret.insert(std::pair<char, unsigned int>(
'A', 1));
291 ret.insert(std::pair<char, unsigned int>(
'C', 1));
292 ret.insert(std::pair<char, unsigned int>(
'D', 1));
293 ret.insert(std::pair<char, unsigned int>(
'E', 1));
294 ret.insert(std::pair<char, unsigned int>(
'F', 1));
295 ret.insert(std::pair<char, unsigned int>(
'G', 1));
296 ret.insert(std::pair<char, unsigned int>(
'H', 3));
297 ret.insert(std::pair<char, unsigned int>(
'I', 1));
298 ret.insert(std::pair<char, unsigned int>(
'K', 2));
299 ret.insert(std::pair<char, unsigned int>(
'L', 1));
300 ret.insert(std::pair<char, unsigned int>(
'M', 1));
301 ret.insert(std::pair<char, unsigned int>(
'N', 2));
302 ret.insert(std::pair<char, unsigned int>(
'P', 1));
303 ret.insert(std::pair<char, unsigned int>(
'Q', 2));
304 ret.insert(std::pair<char, unsigned int>(
'R', 4));
305 ret.insert(std::pair<char, unsigned int>(
'S', 1));
306 ret.insert(std::pair<char, unsigned int>(
'T', 1));
307 ret.insert(std::pair<char, unsigned int>(
'V', 1));
308 ret.insert(std::pair<char, unsigned int>(
'W', 2));
309 ret.insert(std::pair<char, unsigned int>(
'Y', 1));
311 ret.insert(std::pair<char, unsigned int>(
'U', 1));
313 ret.insert(std::pair<char, unsigned int>(
'O', 3));
321 ret.insert(std::pair<char, unsigned int>(
'A', 1));
322 ret.insert(std::pair<char, unsigned int>(
'C', 1));
323 ret.insert(std::pair<char, unsigned int>(
'D', 3));
324 ret.insert(std::pair<char, unsigned int>(
'E', 3));
325 ret.insert(std::pair<char, unsigned int>(
'F', 1));
326 ret.insert(std::pair<char, unsigned int>(
'G', 1));
327 ret.insert(std::pair<char, unsigned int>(
'H', 1));
328 ret.insert(std::pair<char, unsigned int>(
'I', 1));
329 ret.insert(std::pair<char, unsigned int>(
'K', 1));
330 ret.insert(std::pair<char, unsigned int>(
'L', 1));
331 ret.insert(std::pair<char, unsigned int>(
'M', 1));
332 ret.insert(std::pair<char, unsigned int>(
'N', 2));
333 ret.insert(std::pair<char, unsigned int>(
'P', 1));
334 ret.insert(std::pair<char, unsigned int>(
'Q', 2));
335 ret.insert(std::pair<char, unsigned int>(
'R', 1));
336 ret.insert(std::pair<char, unsigned int>(
'S', 2));
337 ret.insert(std::pair<char, unsigned int>(
'T', 2));
338 ret.insert(std::pair<char, unsigned int>(
'V', 1));
339 ret.insert(std::pair<char, unsigned int>(
'W', 1));
340 ret.insert(std::pair<char, unsigned int>(
'Y', 2));
342 ret.insert(std::pair<char, unsigned int>(
'U', 2));
344 ret.insert(std::pair<char, unsigned int>(
'O', 3));
352 ret.insert(std::pair<char, unsigned int>(
'A', 0));
353 ret.insert(std::pair<char, unsigned int>(
'C', 1));
354 ret.insert(std::pair<char, unsigned int>(
'D', 0));
355 ret.insert(std::pair<char, unsigned int>(
'E', 0));
356 ret.insert(std::pair<char, unsigned int>(
'F', 0));
357 ret.insert(std::pair<char, unsigned int>(
'G', 0));
358 ret.insert(std::pair<char, unsigned int>(
'H', 0));
359 ret.insert(std::pair<char, unsigned int>(
'I', 0));
360 ret.insert(std::pair<char, unsigned int>(
'K', 0));
361 ret.insert(std::pair<char, unsigned int>(
'L', 0));
362 ret.insert(std::pair<char, unsigned int>(
'M', 1));
363 ret.insert(std::pair<char, unsigned int>(
'N', 0));
364 ret.insert(std::pair<char, unsigned int>(
'P', 0));
365 ret.insert(std::pair<char, unsigned int>(
'Q', 0));
366 ret.insert(std::pair<char, unsigned int>(
'R', 0));
367 ret.insert(std::pair<char, unsigned int>(
'S', 0));
368 ret.insert(std::pair<char, unsigned int>(
'T', 0));
369 ret.insert(std::pair<char, unsigned int>(
'V', 0));
370 ret.insert(std::pair<char, unsigned int>(
'W', 0));
371 ret.insert(std::pair<char, unsigned int>(
'Y', 0));
373 ret.insert(std::pair<char, unsigned int>(
'U', 0));
375 ret.insert(std::pair<char, unsigned int>(
'O', 0));
413 qDebug() <<
"AaBase::getNumberOfAtom(AtomIsotopeSurvey atom) NOT IMPLEMENTED";
439 const std::vector<AminoAcidChar> &
std::vector< AminoAcidChar > AminoAcidCharList
static AaMassMap m_aaMassMap
std::map< char, unsigned int > AaIntMap
static AaIntMap m_aaNumberOfSulfurMap
static AaIntMap m_aaNumberOfCarbonMap
static AaIntMap m_aaNumberOfOxygenMap
virtual pappso_double getMass() const
static const std::vector< AminoAcidChar > & getAminoAcidCharList()
static pappso_double getAaMass(char aa_letter)
virtual void replaceLeucineIsoleucine()
std::map< char, pappso_double > AaMassMap
virtual const char & getLetter() const
static AminoAcidCharList m_aminoAcidCharList
static AaIntMap m_aaNumberOfNitrogenMap
static AaIntMap m_aaNumberOfHydrogenMap
virtual int getNumberOfAtom(AtomIsotopeSurvey atom) const override
get the number of atom C, O, N, H in the molecule
int getNumberOfIsotope(Isotope isotope) const override
get the number of isotopes C13, H2, O17, O18, N15, S33, S34, S36 in the molecule
tries to keep as much as possible monoisotopes, removing any possible C13 peaks and changes multichar...
const pappso_double MASSCARBON(12)
const pappso_double MASSSULFUR(31.9720711741)
const pappso_double MASSSELENIUM(79.916520)
double pappso_double
A type definition for doubles.
const pappso_double MPROTIUM(1.007825032241)
const pappso_double MASSNITROGEN(14.0030740048)
const pappso_double MASSOXYGEN(15.99491461956)