| Line | Branch | Exec | Source |
|---|---|---|---|
| 1 | /* BEGIN software license | ||
| 2 | * | ||
| 3 | * MsXpertSuite - mass spectrometry software suite | ||
| 4 | * ----------------------------------------------- | ||
| 5 | * Copyright(C) 2009,...,2018 Filippo Rusconi | ||
| 6 | * | ||
| 7 | * http://www.msxpertsuite.org | ||
| 8 | * | ||
| 9 | * This file is part of the MsXpertSuite project. | ||
| 10 | * | ||
| 11 | * The MsXpertSuite project is the successor of the massXpert project. This | ||
| 12 | * project now includes various independent modules: | ||
| 13 | * | ||
| 14 | * - massXpert, model polymer chemistries and simulate mass spectrometric data; | ||
| 15 | * - mineXpert, a powerful TIC chromatogram/mass spectrum viewer/miner; | ||
| 16 | * | ||
| 17 | * This program is free software: you can redistribute it and/or modify | ||
| 18 | * it under the terms of the GNU General Public License as published by | ||
| 19 | * the Free Software Foundation, either version 3 of the License, or | ||
| 20 | * (at your option) any later version. | ||
| 21 | * | ||
| 22 | * This program is distributed in the hope that it will be useful, | ||
| 23 | * but WITHOUT ANY WARRANTY; without even the implied warranty of | ||
| 24 | * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the | ||
| 25 | * GNU General Public License for more details. | ||
| 26 | * | ||
| 27 | * You should have received a copy of the GNU General Public License | ||
| 28 | * along with this program. If not, see <http://www.gnu.org/licenses/>. | ||
| 29 | * | ||
| 30 | * END software license | ||
| 31 | */ | ||
| 32 | |||
| 33 | |||
| 34 | /////////////////////// Local includes | ||
| 35 | #include "ChemicalGroup.hpp" | ||
| 36 | |||
| 37 | |||
| 38 | namespace MsXpS | ||
| 39 | { | ||
| 40 | |||
| 41 | namespace libXpertMass | ||
| 42 | { | ||
| 43 | |||
| 44 | |||
| 45 | /*! | ||
| 46 | \class MsXpS::libXpertMass::ChemicalGroup | ||
| 47 | \inmodule libXpertMass | ||
| 48 | \ingroup PolChemDefBuildingdBlocks | ||
| 49 | \inheaderfile ChemicalGroup.hpp | ||
| 50 | |||
| 51 | \brief The ChemicalGroup class provides a model for specifying the | ||
| 52 | acido-basic behaviour of a chemical group of either a \l Monomer object or of a | ||
| 53 | \l Modif object. | ||
| 54 | |||
| 55 | If the ChemicalGroup does not prove sufficient to characterize precisely the | ||
| 56 | acido-basic properties of an entity, \l ChemicalGroupRule instances can be | ||
| 57 | added to that effect. | ||
| 58 | |||
| 59 | In an pkaphpidata definition file, the following xml structure | ||
| 60 | is encountered: | ||
| 61 | |||
| 62 | \code | ||
| 63 | <pkaphpidata> | ||
| 64 | <monomers> | ||
| 65 | <monomer> | ||
| 66 | <code>A</code> | ||
| 67 | <mnmchemgroup> | ||
| 68 | <name>N-term NH2</name> | ||
| 69 | <pka>9.6</pka> | ||
| 70 | <acidcharged>TRUE</acidcharged> | ||
| 71 | <polrule>left_trapped</polrule> | ||
| 72 | <chemgrouprule> | ||
| 73 | <entity>LE_PLM_MODIF</entity> | ||
| 74 | <name>Acetylation</name> | ||
| 75 | <outcome>LOST</outcome> | ||
| 76 | </chemgrouprule> | ||
| 77 | </mnmchemgroup> | ||
| 78 | <mnmchemgroup> | ||
| 79 | <name>C-term COOH</name> | ||
| 80 | <pka>2.35</pka> | ||
| 81 | <acidcharged>FALSE</acidcharged> | ||
| 82 | <polrule>right_trapped</polrule> | ||
| 83 | </mnmchemgroup> | ||
| 84 | </monomer> | ||
| 85 | <monomer> | ||
| 86 | <code>C</code> | ||
| 87 | <mnmchemgroup> | ||
| 88 | <name>N-term NH2</name> | ||
| 89 | <pka>9.6</pka> | ||
| 90 | <acidcharged>TRUE</acidcharged> | ||
| 91 | <polrule>left_trapped</polrule> | ||
| 92 | <chemgrouprule> | ||
| 93 | <entity>LE_PLM_MODIF</entity> | ||
| 94 | <name>Acetylation</name> | ||
| 95 | <outcome>LOST</outcome> | ||
| 96 | </chemgrouprule> | ||
| 97 | </mnmchemgroup> | ||
| 98 | <mnmchemgroup> | ||
| 99 | <name>C-term COOH</name> | ||
| 100 | <pka>2.35</pka> | ||
| 101 | <acidcharged>FALSE</acidcharged> | ||
| 102 | <polrule>right_trapped</polrule> | ||
| 103 | </mnmchemgroup> | ||
| 104 | <mnmchemgroup> | ||
| 105 | <name>Lateral SH2</name> | ||
| 106 | <pka>8.3</pka> | ||
| 107 | <acidcharged>FALSE</acidcharged> | ||
| 108 | <polrule>never_trapped</polrule> | ||
| 109 | </mnmchemgroup> | ||
| 110 | </monomer> | ||
| 111 | ..... | ||
| 112 | <modifs> | ||
| 113 | <modif> | ||
| 114 | <name>Phosphorylation</name> | ||
| 115 | <mdfchemgroup> | ||
| 116 | <name>none_set</name> | ||
| 117 | <pka>1.2</pka> | ||
| 118 | <acidcharged>FALSE</acidcharged> | ||
| 119 | </mdfchemgroup> | ||
| 120 | <mdfchemgroup> | ||
| 121 | <name>none_set</name> | ||
| 122 | <pka>6.5</pka> | ||
| 123 | <acidcharged>FALSE</acidcharged> | ||
| 124 | </mdfchemgroup> | ||
| 125 | </modif> | ||
| 126 | </modifs> | ||
| 127 | </pkaphpidata> | ||
| 128 | \endcode | ||
| 129 | |||
| 130 | \sa ChemicalGroupRule, | ||
| 131 | */ | ||
| 132 | |||
| 133 | /*! | ||
| 134 | \enum MsXpS::libXpertMass::ChemicalGroupTrapping | ||
| 135 | |||
| 136 | This enum specifies how the chemical group behaves when the chemical entity | ||
| 137 | that it holds polymerizes into a \l Polymer. | ||
| 138 | |||
| 139 | One example will clear things out: | ||
| 140 | |||
| 141 | An amino acid has a amino group and a carboxylic acid group. The amino group | ||
| 142 | gets entrapped in the monomer-to-monomer bond (the peptide bond) if the | ||
| 143 | polymerization occurs at the left of the monomer. That means that if the | ||
| 144 | Monomer holding this ChemicalGroup is N-terminal, then the amino group should | ||
| 145 | be accounted for because it is intact. Conversely, the carboxylic acid group | ||
| 146 | gets entrapped in the peptide bond if the polymerization occurs at the right of | ||
| 147 | the monomer. That means that if the Monomer holding this ChemicalGroup is | ||
| 148 | C-terminal, then the carboxylic acid group should be accounted for because it is | ||
| 149 | intact. | ||
| 150 | |||
| 151 | \value NEVER_TRAPPED | ||
| 152 | The chemical group is not lost upon polymerization, it should thus | ||
| 153 | always be accounted for. | ||
| 154 | |||
| 155 | \value LEFT_TRAPPED | ||
| 156 | The chemical group gets trapped in the inter-monomer bond if | ||
| 157 | polymerization occurs at left of the \l Monomer. | ||
| 158 | |||
| 159 | \value RIGHT_TRAPPED | ||
| 160 | The chemical group gets trapped in the inter-monomer bond if | ||
| 161 | polymerization occurs at right of the \l Monomer. | ||
| 162 | |||
| 163 | \omitvalue NOT_SET. | ||
| 164 | */ | ||
| 165 | |||
| 166 | /*! | ||
| 167 | \variable MsXpS::libXpertMass::ChemicalGroup::m_name | ||
| 168 | |||
| 169 | \brief The name of the ChemicalGroup instance. | ||
| 170 | */ | ||
| 171 | |||
| 172 | /*! | ||
| 173 | \variable MsXpS::libXpertMass::ChemicalGroup::m_pka | ||
| 174 | |||
| 175 | \brief The pKa of the ChemicalGroup instance. | ||
| 176 | */ | ||
| 177 | |||
| 178 | /*! | ||
| 179 | \variable MsXpS::libXpertMass::ChemicalGroup::m_acidCharged | ||
| 180 | |||
| 181 | \brief Tells if the group is charged when in acid conditions (that is, the pH | ||
| 182 | is less than the pKa). | ||
| 183 | */ | ||
| 184 | |||
| 185 | /*! | ||
| 186 | \variable MsXpS::libXpertMass::ChemicalGroup::m_polymerizationRule | ||
| 187 | |||
| 188 | \brief The way this ChemicalGroup behaves upon polymerization of the chemical | ||
| 189 | entity into a \l Polymer. | ||
| 190 | */ | ||
| 191 | |||
| 192 | /*! | ||
| 193 | \variable MsXpS::libXpertMass::ChemicalGroup::m_ruleList | ||
| 194 | |||
| 195 | \brief The list of \l ChemicalGroupRule instances. | ||
| 196 | */ | ||
| 197 | |||
| 198 | /*! | ||
| 199 | \brief Constructs a ChemicalGroup instance. | ||
| 200 | |||
| 201 | \a name The name of this ChemicalGroup. | ||
| 202 | \a pka The pKa value of this ChemicalGroup. | ||
| 203 | \a is_acid_charged Tells if the ChemicalGroup bears a charge when in acidic | ||
| 204 | conditions. | ||
| 205 | \a polymerization_rule Specifies the polymerization rule. | ||
| 206 | */ | ||
| 207 | ✗ | ChemicalGroup::ChemicalGroup(QString name, | |
| 208 | float pka, | ||
| 209 | bool is_acid_charged, | ||
| 210 | ✗ | ChemicalGroupTrapping polymerization_rule) | |
| 211 | ✗ | : m_name(name), | |
| 212 | ✗ | m_pka(pka), | |
| 213 | ✗ | m_acidCharged(is_acid_charged), | |
| 214 | ✗ | m_polymerizationRule(polymerization_rule) | |
| 215 | { | ||
| 216 | ✗ | Q_ASSERT(m_pka > 0 && m_pka < 14); | |
| 217 | ✗ | } | |
| 218 | |||
| 219 | /*! | ||
| 220 | \brief Construct a ChemicalGroup instance as a copy of \a other. | ||
| 221 | */ | ||
| 222 | ✗ | ChemicalGroup::ChemicalGroup(const ChemicalGroup &other) | |
| 223 | ✗ | : m_name(other.m_name), | |
| 224 | ✗ | m_pka(other.m_pka), | |
| 225 | ✗ | m_acidCharged(other.m_acidCharged), | |
| 226 | ✗ | m_polymerizationRule(other.m_polymerizationRule) | |
| 227 | { | ||
| 228 | ✗ | } | |
| 229 | |||
| 230 | /*! | ||
| 231 | \brief Destructs this ChemicalGroup instance. | ||
| 232 | */ | ||
| 233 | ✗ | ChemicalGroup::~ChemicalGroup() | |
| 234 | { | ||
| 235 | ✗ | while(!m_ruleList.isEmpty()) | |
| 236 | ✗ | delete m_ruleList.takeFirst(); | |
| 237 | ✗ | } | |
| 238 | |||
| 239 | /*! | ||
| 240 | \brief Assigns \a other to this ChemicalGroup instance. | ||
| 241 | |||
| 242 | Returns a reference to this ChemicalGroup instance. | ||
| 243 | */ | ||
| 244 | ChemicalGroup & | ||
| 245 | ✗ | ChemicalGroup::operator=(const ChemicalGroup &other) | |
| 246 | { | ||
| 247 | ✗ | if(&other == this) | |
| 248 | ✗ | return *this; | |
| 249 | |||
| 250 | ✗ | m_name = other.m_name; | |
| 251 | ✗ | m_pka = other.m_pka; | |
| 252 | ✗ | m_acidCharged = other.m_acidCharged; | |
| 253 | ✗ | m_polymerizationRule = other.m_polymerizationRule; | |
| 254 | |||
| 255 | ✗ | qDeleteAll(m_ruleList); | |
| 256 | |||
| 257 | ✗ | for(int iter = 0; iter < other.m_ruleList.size(); ++iter) | |
| 258 | ✗ | m_ruleList.append(new ChemicalGroupRule(*other.m_ruleList.at(iter))); | |
| 259 | |||
| 260 | ✗ | return *this; | |
| 261 | } | ||
| 262 | |||
| 263 | /*! | ||
| 264 | \brief Sets the \a name. | ||
| 265 | */ | ||
| 266 | void | ||
| 267 | ✗ | ChemicalGroup::setName(QString name) | |
| 268 | { | ||
| 269 | ✗ | m_name = name; | |
| 270 | ✗ | } | |
| 271 | |||
| 272 | /*! | ||
| 273 | \brief Returns the name. | ||
| 274 | */ | ||
| 275 | QString | ||
| 276 | ✗ | ChemicalGroup::name() const | |
| 277 | { | ||
| 278 | ✗ | return m_name; | |
| 279 | } | ||
| 280 | |||
| 281 | /*! | ||
| 282 | \brief Sets the pKa to \a pka. | ||
| 283 | */ | ||
| 284 | void | ||
| 285 | ✗ | ChemicalGroup::setPka(float pka) | |
| 286 | { | ||
| 287 | ✗ | Q_ASSERT(pka > 0 && pka < 14); | |
| 288 | |||
| 289 | ✗ | m_pka = pka; | |
| 290 | ✗ | } | |
| 291 | |||
| 292 | /*! | ||
| 293 | \brief Returns the pKa. | ||
| 294 | */ | ||
| 295 | float | ||
| 296 | ✗ | ChemicalGroup::pka() const | |
| 297 | { | ||
| 298 | ✗ | return m_pka; | |
| 299 | } | ||
| 300 | |||
| 301 | /*! | ||
| 302 | \brief Sets the charge condition in acidic conditions to \a acid_charged. | ||
| 303 | |||
| 304 | If true, the group bears a charge when the pH is less than the pKa. | ||
| 305 | */ | ||
| 306 | void | ||
| 307 | ✗ | ChemicalGroup::setAcidCharged(bool acid_charged) | |
| 308 | { | ||
| 309 | ✗ | m_acidCharged = acid_charged; | |
| 310 | ✗ | } | |
| 311 | |||
| 312 | /*! | ||
| 313 | \brief Returns the charge condition in acidic conditions. | ||
| 314 | |||
| 315 | If true, the group bears a charge when the pH is less than the pKa. | ||
| 316 | */ | ||
| 317 | bool | ||
| 318 | ✗ | ChemicalGroup::isAcidCharged() const | |
| 319 | { | ||
| 320 | ✗ | return m_acidCharged; | |
| 321 | } | ||
| 322 | |||
| 323 | /*! | ||
| 324 | \brief Sets the polymerization rule to \a pol_rule. | ||
| 325 | |||
| 326 | The polymerization rule determines if the chemical group is trapped upon | ||
| 327 | formation of a Monomer-to-Monomer bond. | ||
| 328 | */ | ||
| 329 | void | ||
| 330 | ✗ | ChemicalGroup::setPolRule(ChemicalGroupTrapping pol_rule) | |
| 331 | { | ||
| 332 | ✗ | m_polymerizationRule = pol_rule; | |
| 333 | ✗ | } | |
| 334 | |||
| 335 | /*! | ||
| 336 | \brief Returns the polymerization rule. | ||
| 337 | */ | ||
| 338 | ChemicalGroupTrapping | ||
| 339 | ✗ | ChemicalGroup::polRule() const | |
| 340 | { | ||
| 341 | ✗ | return m_polymerizationRule; | |
| 342 | } | ||
| 343 | |||
| 344 | /*! | ||
| 345 | \brief Returns the list of ChemicalGroupRule instances. | ||
| 346 | */ | ||
| 347 | QList<ChemicalGroupRule *> & | ||
| 348 | ✗ | ChemicalGroup::ruleList() | |
| 349 | { | ||
| 350 | ✗ | return m_ruleList; | |
| 351 | } | ||
| 352 | |||
| 353 | /*! | ||
| 354 | \brief Searches by \a entity for a ChemicalGroupRule instance. | ||
| 355 | |||
| 356 | Returns the \a index of the ChemicalGroupRule instance in the member list of | ||
| 357 | ChemicalGroupRule instances or -1 if not found. | ||
| 358 | */ | ||
| 359 | ChemicalGroupRule * | ||
| 360 | ✗ | ChemicalGroup::findRuleEntity(QString entity, int *index) const | |
| 361 | { | ||
| 362 | ✗ | int ruleIndex = 0; | |
| 363 | |||
| 364 | ✗ | if(!index) | |
| 365 | ✗ | ruleIndex = 0; | |
| 366 | else | ||
| 367 | { | ||
| 368 | ✗ | if(*index < 0) | |
| 369 | ✗ | return 0; | |
| 370 | ✗ | else if(*index > m_ruleList.size()) | |
| 371 | ✗ | return 0; | |
| 372 | ✗ | ruleIndex = *index; | |
| 373 | } | ||
| 374 | |||
| 375 | ✗ | if(entity.isEmpty()) | |
| 376 | ✗ | return 0; | |
| 377 | |||
| 378 | ✗ | for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter) | |
| 379 | { | ||
| 380 | ✗ | ChemicalGroupRule *rule = m_ruleList.at(iter); | |
| 381 | |||
| 382 | ✗ | if(rule->entity() == entity) | |
| 383 | { | ||
| 384 | ✗ | if(index) | |
| 385 | ✗ | *index = iter; | |
| 386 | |||
| 387 | ✗ | return rule; | |
| 388 | } | ||
| 389 | } | ||
| 390 | |||
| 391 | ✗ | return 0; | |
| 392 | } | ||
| 393 | |||
| 394 | /*! | ||
| 395 | \brief Searches by \a name for a ChemicalGroupRule instance. | ||
| 396 | |||
| 397 | Returns the \a index of the ChemicalGroupRule instance in the member list of | ||
| 398 | ChemicalGroupRule instances or -1 if not found. | ||
| 399 | */ | ||
| 400 | ChemicalGroupRule * | ||
| 401 | ✗ | ChemicalGroup::findRuleName(QString name, int *index) const | |
| 402 | { | ||
| 403 | ✗ | int ruleIndex = 0; | |
| 404 | |||
| 405 | ✗ | if(!index) | |
| 406 | ✗ | ruleIndex = 0; | |
| 407 | else | ||
| 408 | { | ||
| 409 | ✗ | if(*index < 0) | |
| 410 | ✗ | return 0; | |
| 411 | ✗ | else if(*index > m_ruleList.size()) | |
| 412 | ✗ | return 0; | |
| 413 | ✗ | ruleIndex = *index; | |
| 414 | } | ||
| 415 | |||
| 416 | ✗ | if(name.isEmpty()) | |
| 417 | ✗ | return 0; | |
| 418 | |||
| 419 | ✗ | for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter) | |
| 420 | { | ||
| 421 | ✗ | ChemicalGroupRule *rule = m_ruleList.at(iter); | |
| 422 | |||
| 423 | ✗ | if(rule->name() == name) | |
| 424 | { | ||
| 425 | ✗ | if(index) | |
| 426 | ✗ | *index = iter; | |
| 427 | |||
| 428 | ✗ | return rule; | |
| 429 | } | ||
| 430 | } | ||
| 431 | |||
| 432 | ✗ | return 0; | |
| 433 | } | ||
| 434 | |||
| 435 | |||
| 436 | /*! | ||
| 437 | \brief Searches by \a entity and \a name for a ChemicalGroupRule instance. | ||
| 438 | |||
| 439 | Returns the \a index of the ChemicalGroupRule instance in the member list of | ||
| 440 | ChemicalGroupRule instances or -1 if not found. | ||
| 441 | */ | ||
| 442 | ChemicalGroupRule * | ||
| 443 | ✗ | ChemicalGroup::findRule(QString entity, QString name, int *index) const | |
| 444 | { | ||
| 445 | ✗ | int ruleIndex = 0; | |
| 446 | |||
| 447 | ✗ | if(!index) | |
| 448 | ✗ | ruleIndex = 0; | |
| 449 | else | ||
| 450 | { | ||
| 451 | ✗ | if(*index < 0) | |
| 452 | ✗ | return 0; | |
| 453 | ✗ | else if(*index > m_ruleList.size()) | |
| 454 | ✗ | return 0; | |
| 455 | ✗ | ruleIndex = *index; | |
| 456 | } | ||
| 457 | |||
| 458 | ✗ | if(entity.isEmpty() || name.isEmpty()) | |
| 459 | ✗ | return 0; | |
| 460 | |||
| 461 | ✗ | for(int iter = ruleIndex; iter < m_ruleList.size(); ++iter) | |
| 462 | { | ||
| 463 | ✗ | ChemicalGroupRule *rule = m_ruleList.at(iter); | |
| 464 | |||
| 465 | ✗ | if(rule->entity() == entity && rule->name() == name) | |
| 466 | { | ||
| 467 | ✗ | if(index) | |
| 468 | ✗ | *index = iter; | |
| 469 | |||
| 470 | ✗ | return rule; | |
| 471 | } | ||
| 472 | } | ||
| 473 | |||
| 474 | ✗ | return 0; | |
| 475 | } | ||
| 476 | |||
| 477 | |||
| 478 | /*! | ||
| 479 | \brief Parses the ChemicalGroup XML \a element \e{related to a \l Monomer}. | ||
| 480 | |||
| 481 | Upon parsing of the \a element (tag \code{<mnmchemgroup>}), its data | ||
| 482 | are validated and set to this ChemicalGroup instance, thus essentially | ||
| 483 | initializing it. | ||
| 484 | |||
| 485 | In an pkaphpidata definition file, the following xml structure | ||
| 486 | is encountered: | ||
| 487 | |||
| 488 | \code | ||
| 489 | <pkaphpidata> | ||
| 490 | <monomers> | ||
| 491 | <monomer> | ||
| 492 | <code>A</code> | ||
| 493 | <mnmchemgroup> | ||
| 494 | <name>N-term NH2</name> | ||
| 495 | <pka>9.6</pka> | ||
| 496 | <acidcharged>TRUE</acidcharged> | ||
| 497 | <polrule>left_trapped</polrule> | ||
| 498 | <chemgrouprule> | ||
| 499 | <entity>LE_PLM_MODIF</entity> | ||
| 500 | <name>Acetylation</name> | ||
| 501 | <outcome>LOST</outcome> | ||
| 502 | </chemgrouprule> | ||
| 503 | </mnmchemgroup> | ||
| 504 | <mnmchemgroup> | ||
| 505 | <name>C-term COOH</name> | ||
| 506 | <pka>2.35</pka> | ||
| 507 | <acidcharged>FALSE</acidcharged> | ||
| 508 | <polrule>right_trapped</polrule> | ||
| 509 | </mnmchemgroup> | ||
| 510 | </monomer> | ||
| 511 | <monomer> | ||
| 512 | <code>C</code> | ||
| 513 | <mnmchemgroup> | ||
| 514 | <name>N-term NH2</name> | ||
| 515 | <pka>9.6</pka> | ||
| 516 | <acidcharged>TRUE</acidcharged> | ||
| 517 | <polrule>left_trapped</polrule> | ||
| 518 | <chemgrouprule> | ||
| 519 | <entity>LE_PLM_MODIF</entity> | ||
| 520 | <name>Acetylation</name> | ||
| 521 | <outcome>LOST</outcome> | ||
| 522 | </chemgrouprule> | ||
| 523 | </mnmchemgroup> | ||
| 524 | <mnmchemgroup> | ||
| 525 | <name>C-term COOH</name> | ||
| 526 | <pka>2.35</pka> | ||
| 527 | <acidcharged>FALSE</acidcharged> | ||
| 528 | <polrule>right_trapped</polrule> | ||
| 529 | </mnmchemgroup> | ||
| 530 | <mnmchemgroup> | ||
| 531 | <name>Lateral SH2</name> | ||
| 532 | <pka>8.3</pka> | ||
| 533 | <acidcharged>FALSE</acidcharged> | ||
| 534 | <polrule>never_trapped</polrule> | ||
| 535 | </mnmchemgroup> | ||
| 536 | </monomer> | ||
| 537 | \endcode | ||
| 538 | |||
| 539 | Upon parsing of the \a element, all the data are validated and set to this | ||
| 540 | ChemicalGroup instance, thus essentially initializing it. If there are | ||
| 541 | \l{ChemicalGroupRule}s associated to the ChemicalGroup element, these are | ||
| 542 | rendered also. | ||
| 543 | |||
| 544 | Returns true if parsing and validation were successful, false otherwise. | ||
| 545 | */ | ||
| 546 | bool | ||
| 547 | ✗ | ChemicalGroup::renderXmlMnmElement(const QDomElement &element) | |
| 548 | { | ||
| 549 | // The element the parameter points to is: | ||
| 550 | // | ||
| 551 | // <mnmchemgroup> | ||
| 552 | // | ||
| 553 | // Which means that element.tagName() == "mnmchemgroup" and that we'll | ||
| 554 | // have to go one step down to the first child of the current node | ||
| 555 | // in order to get to the \code<name>\endcode element. | ||
| 556 | |||
| 557 | |||
| 558 | ✗ | QDomElement child; | |
| 559 | |||
| 560 | ✗ | if(element.tagName() != "mnmchemgroup") | |
| 561 | ✗ | return false; | |
| 562 | |||
| 563 | ✗ | child = element.firstChildElement("name"); | |
| 564 | |||
| 565 | ✗ | if(child.isNull()) | |
| 566 | ✗ | return false; | |
| 567 | |||
| 568 | ✗ | m_name = child.text(); | |
| 569 | |||
| 570 | ✗ | child = child.nextSiblingElement(); | |
| 571 | |||
| 572 | ✗ | if(child.isNull() || child.tagName() != "pka") | |
| 573 | ✗ | return false; | |
| 574 | |||
| 575 | ✗ | bool ok = false; | |
| 576 | ✗ | m_pka = child.text().toFloat(&ok); | |
| 577 | |||
| 578 | ✗ | if(!m_pka && !ok) | |
| 579 | ✗ | return false; | |
| 580 | |||
| 581 | ✗ | if(m_pka <= 0 || m_pka >= 14) | |
| 582 | ✗ | return false; | |
| 583 | |||
| 584 | ✗ | child = child.nextSiblingElement(); | |
| 585 | |||
| 586 | ✗ | if(child.isNull() || child.tagName() != "acidcharged") | |
| 587 | ✗ | return false; | |
| 588 | |||
| 589 | ✗ | if(child.text() != "FALSE" && child.text() != "TRUE") | |
| 590 | ✗ | return false; | |
| 591 | |||
| 592 | ✗ | m_acidCharged = (child.text() == "FALSE" ? false : true); | |
| 593 | |||
| 594 | // And now the polrule element. There should be one, here, in fact, | ||
| 595 | // because we are dealing with a monomer, and not a modification. | ||
| 596 | |||
| 597 | ✗ | child = child.nextSiblingElement(); | |
| 598 | |||
| 599 | ✗ | if(child.isNull() || child.tagName() != "polrule") | |
| 600 | ✗ | return false; | |
| 601 | |||
| 602 | ✗ | if(child.text() == "never_trapped") | |
| 603 | ✗ | m_polymerizationRule = ChemicalGroupTrapping::NEVER_TRAPPED; | |
| 604 | ✗ | else if(child.text() == "left_trapped") | |
| 605 | ✗ | m_polymerizationRule = ChemicalGroupTrapping::LEFT_TRAPPED; | |
| 606 | ✗ | else if(child.text() == "right_trapped") | |
| 607 | ✗ | m_polymerizationRule = ChemicalGroupTrapping::RIGHT_TRAPPED; | |
| 608 | else | ||
| 609 | ✗ | return false; | |
| 610 | |||
| 611 | // And finally the chemical group rules... There might be zero, one | ||
| 612 | // or more. | ||
| 613 | |||
| 614 | ✗ | QDomElement childChemGroupRule = child.nextSiblingElement("chemgrouprule"); | |
| 615 | |||
| 616 | ✗ | while(!childChemGroupRule.isNull()) | |
| 617 | { | ||
| 618 | ✗ | ChemicalGroupRule *rule = new ChemicalGroupRule(); | |
| 619 | |||
| 620 | ✗ | if(!rule->renderXmlElement(childChemGroupRule)) | |
| 621 | { | ||
| 622 | ✗ | delete rule; | |
| 623 | ✗ | return false; | |
| 624 | } | ||
| 625 | |||
| 626 | ✗ | m_ruleList.append(rule); | |
| 627 | |||
| 628 | ✗ | childChemGroupRule = childChemGroupRule.nextSiblingElement(); | |
| 629 | } | ||
| 630 | |||
| 631 | ✗ | return true; | |
| 632 | ✗ | } | |
| 633 | |||
| 634 | |||
| 635 | /*! | ||
| 636 | \brief Parses the ChemicalGroup XML \a element \e{related to a \l Modif}. | ||
| 637 | |||
| 638 | Upon parsing of the \a element (tag <mnmchemgroup>), its data are validated and | ||
| 639 | set to this ChemicalGroup instance, thus essentially initializing it. | ||
| 640 | |||
| 641 | In an pkaphpidata definition file, the following xml structure | ||
| 642 | is encountered: | ||
| 643 | |||
| 644 | \code | ||
| 645 | <pkaphpidata> | ||
| 646 | <monomers> | ||
| 647 | <monomer> | ||
| 648 | <code>A</code> | ||
| 649 | <mnmchemgroup> | ||
| 650 | <name>N-term NH2</name> | ||
| 651 | <pka>9.6</pka> | ||
| 652 | <acidcharged>TRUE</acidcharged> | ||
| 653 | <polrule>left_trapped</polrule> | ||
| 654 | <chemgrouprule> | ||
| 655 | <entity>LE_PLM_MODIF</entity> | ||
| 656 | <name>Acetylation</name> | ||
| 657 | <outcome>LOST</outcome> | ||
| 658 | </chemgrouprule> | ||
| 659 | </mnmchemgroup> | ||
| 660 | <mnmchemgroup> | ||
| 661 | <name>C-term COOH</name> | ||
| 662 | <pka>2.35</pka> | ||
| 663 | <acidcharged>FALSE</acidcharged> | ||
| 664 | <polrule>right_trapped</polrule> | ||
| 665 | </mnmchemgroup> | ||
| 666 | </monomer> | ||
| 667 | ....... | ||
| 668 | </monomers> | ||
| 669 | <modifs> | ||
| 670 | <modif> | ||
| 671 | <name>Phosphorylation</name> | ||
| 672 | <mdfchemgroup> | ||
| 673 | <name>none_set</name> | ||
| 674 | <pka>1.2</pka> | ||
| 675 | <acidcharged>FALSE</acidcharged> | ||
| 676 | </mdfchemgroup> | ||
| 677 | <mdfchemgroup> | ||
| 678 | <name>none_set</name> | ||
| 679 | <pka>6.5</pka> | ||
| 680 | <acidcharged>FALSE</acidcharged> | ||
| 681 | </mdfchemgroup> | ||
| 682 | </modif> | ||
| 683 | </modifs> | ||
| 684 | </pkaphpidata> | ||
| 685 | \endcode | ||
| 686 | |||
| 687 | Upon parsing of the \a element, all the data are validated and set to this | ||
| 688 | ChemicalGroup instance, thus essentially initializing it. If there are | ||
| 689 | \l{ChemicalGroupRule}s associated to the ChemicalGroup element, these are | ||
| 690 | rendered also. | ||
| 691 | |||
| 692 | Returns true if parsing and validation were successful, false otherwise. | ||
| 693 | */ | ||
| 694 | bool | ||
| 695 | ✗ | ChemicalGroup::renderXmlMdfElement(const QDomElement &element) | |
| 696 | { | ||
| 697 | ✗ | QDomElement child; | |
| 698 | |||
| 699 | ✗ | if(element.tagName() != "mdfchemgroup") | |
| 700 | ✗ | return false; | |
| 701 | |||
| 702 | ✗ | child = element.firstChildElement("name"); | |
| 703 | |||
| 704 | ✗ | if(child.isNull()) | |
| 705 | ✗ | return false; | |
| 706 | |||
| 707 | ✗ | m_name = child.text(); | |
| 708 | |||
| 709 | ✗ | child = child.nextSiblingElement(); | |
| 710 | |||
| 711 | ✗ | if(child.isNull() || child.tagName() != "pka") | |
| 712 | ✗ | return false; | |
| 713 | |||
| 714 | ✗ | bool ok = false; | |
| 715 | ✗ | m_pka = child.text().toFloat(&ok); | |
| 716 | |||
| 717 | ✗ | if(!m_pka && !ok) | |
| 718 | ✗ | return false; | |
| 719 | |||
| 720 | ✗ | if(m_pka <= 0 || m_pka >= 14) | |
| 721 | ✗ | return false; | |
| 722 | |||
| 723 | ✗ | child = child.nextSiblingElement(); | |
| 724 | |||
| 725 | ✗ | if(child.isNull() || child.tagName() != "acidcharged") | |
| 726 | ✗ | return false; | |
| 727 | |||
| 728 | ✗ | if(child.text() != "FALSE" && child.text() != "TRUE") | |
| 729 | ✗ | return false; | |
| 730 | |||
| 731 | ✗ | m_acidCharged = (child.text() == "FALSE" ? false : true); | |
| 732 | |||
| 733 | ✗ | return true; | |
| 734 | ✗ | } | |
| 735 | |||
| 736 | |||
| 737 | //////////////////////// ChemicalGroupProp //////////////////////// | ||
| 738 | //////////////////////// ChemicalGroupProp //////////////////////// | ||
| 739 | |||
| 740 | |||
| 741 | /*! | ||
| 742 | \class MsXpS::libXpertMass::ChemicalGroupProp | ||
| 743 | \inmodule libXpertMass | ||
| 744 | \ingroup ThePropSystem | ||
| 745 | |||
| 746 | \brief The ChemicalGroupProp class provides a Prop instance of which the member | ||
| 747 | data points to a dynamically allocated \l ChemicalGroup instance. | ||
| 748 | */ | ||
| 749 | |||
| 750 | |||
| 751 | /*! | ||
| 752 | \brief Constructs a ChemicalGroupProp instance using \a data and \a name. | ||
| 753 | |||
| 754 | The \a data pointer is set to the \l mpa_data member. | ||
| 755 | */ | ||
| 756 | ✗ | ChemicalGroupProp::ChemicalGroupProp(const QString &name, ChemicalGroup *data) | |
| 757 | { | ||
| 758 | ✗ | if(!name.isEmpty()) | |
| 759 | ✗ | m_name = name; | |
| 760 | else | ||
| 761 | ✗ | m_name = QString(); | |
| 762 | |||
| 763 | ✗ | mpa_data = static_cast<void *>(data); | |
| 764 | ✗ | } | |
| 765 | |||
| 766 | |||
| 767 | /*! | ||
| 768 | \brief Constructs a ChemicalGroupProp instance as a copy of \a other. | ||
| 769 | |||
| 770 | The data in \a other are duplicated and set to this ChemicalGroupProp instance. | ||
| 771 | */ | ||
| 772 | ✗ | ChemicalGroupProp::ChemicalGroupProp(const ChemicalGroupProp &other) | |
| 773 | ✗ | : Prop(other) | |
| 774 | { | ||
| 775 | ✗ | if(other.mpa_data != nullptr) | |
| 776 | { | ||
| 777 | ✗ | ChemicalGroup *chemicalGroup = | |
| 778 | static_cast<ChemicalGroup *>(other.mpa_data); | ||
| 779 | |||
| 780 | ✗ | mpa_data = static_cast<void *>(new ChemicalGroup(*chemicalGroup)); | |
| 781 | } | ||
| 782 | else | ||
| 783 | ✗ | mpa_data = nullptr; | |
| 784 | ✗ | } | |
| 785 | |||
| 786 | /*! | ||
| 787 | \brief Destructs this ChemicalGroupProp instance. | ||
| 788 | |||
| 789 | The deletion of the data are delegated to \l deleteData(). | ||
| 790 | */ | ||
| 791 | ✗ | ChemicalGroupProp::~ChemicalGroupProp() | |
| 792 | { | ||
| 793 | ✗ | deleteData(); | |
| 794 | ✗ | } | |
| 795 | |||
| 796 | /*! | ||
| 797 | \brief Deletes the member data. | ||
| 798 | */ | ||
| 799 | void | ||
| 800 | ✗ | ChemicalGroupProp::deleteData() | |
| 801 | { | ||
| 802 | ✗ | if(mpa_data != nullptr) | |
| 803 | { | ||
| 804 | ✗ | delete static_cast<ChemicalGroup *>(mpa_data); | |
| 805 | ✗ | mpa_data = nullptr; | |
| 806 | } | ||
| 807 | ✗ | } | |
| 808 | |||
| 809 | /*! | ||
| 810 | \brief Assigns \a other to this ChemicalGroupProp instance. | ||
| 811 | |||
| 812 | The member data are first deleted and then set to a copy of those in \a other. | ||
| 813 | */ | ||
| 814 | ChemicalGroupProp & | ||
| 815 | ✗ | ChemicalGroupProp::operator=(const ChemicalGroupProp &other) | |
| 816 | { | ||
| 817 | ✗ | if(&other == this) | |
| 818 | ✗ | return *this; | |
| 819 | |||
| 820 | ✗ | Prop::operator=(other); | |
| 821 | |||
| 822 | ✗ | if(mpa_data != nullptr) | |
| 823 | ✗ | deleteData(); | |
| 824 | |||
| 825 | ✗ | if(other.mpa_data != nullptr) | |
| 826 | { | ||
| 827 | ✗ | ChemicalGroup *chemicalGroup = | |
| 828 | static_cast<ChemicalGroup *>(other.mpa_data); | ||
| 829 | |||
| 830 | ✗ | mpa_data = static_cast<void *>(new ChemicalGroup(*chemicalGroup)); | |
| 831 | } | ||
| 832 | else | ||
| 833 | ✗ | mpa_data = nullptr; | |
| 834 | |||
| 835 | ✗ | return *this; | |
| 836 | } | ||
| 837 | |||
| 838 | |||
| 839 | /*! | ||
| 840 | \brief Duplicates this ChemicalGroupProp instance and returns its pointer. | ||
| 841 | */ | ||
| 842 | ChemicalGroupProp * | ||
| 843 | ✗ | ChemicalGroupProp::cloneOut() const | |
| 844 | { | ||
| 845 | ✗ | ChemicalGroupProp *new_p = new ChemicalGroupProp(*this); | |
| 846 | |||
| 847 | ✗ | return new_p; | |
| 848 | } | ||
| 849 | |||
| 850 | bool | ||
| 851 | ✗ | ChemicalGroupProp::renderXmlElement([[maybe_unused]] const QDomElement &element, | |
| 852 | [[maybe_unused]] int version) | ||
| 853 | { | ||
| 854 | ✗ | return false; | |
| 855 | } | ||
| 856 | |||
| 857 | QString * | ||
| 858 | ✗ | ChemicalGroupProp::formatXmlElement([[maybe_unused]] int offset, | |
| 859 | [[maybe_unused]] const QString &indent) | ||
| 860 | { | ||
| 861 | ✗ | return nullptr; | |
| 862 | } | ||
| 863 | |||
| 864 | } // namespace libXpertMass | ||
| 865 | |||
| 866 | } // namespace MsXpS | ||
| 867 |