36 #ifndef OPENMS_CHEMISTRY_RESIDUE_H 
   37 #define OPENMS_CHEMISTRY_RESIDUE_H 
   50   class ResidueModification;
 
   75       return internal_to_full;
 
   80       static const DoubleReal internal_to_full_average_weight = getInternalToFull().getAverageWeight();
 
   81       return internal_to_full_average_weight;
 
   86       static const DoubleReal internal_to_full_mono_weight = getInternalToFull().getMonoWeight();
 
   87       return internal_to_full_mono_weight;
 
   94       return Nterminal_to_full;
 
   99       static const DoubleReal Nterminal_to_full_average_weight = getNTerminalToFull().getAverageWeight();
 
  100       return Nterminal_to_full_average_weight;
 
  105       static const DoubleReal Nterminal_to_full_mono_weight = getNTerminalToFull().getMonoWeight();
 
  106       return Nterminal_to_full_mono_weight;
 
  113       return Cterminal_to_full;
 
  118       static const DoubleReal Cterminal_to_full_average_weight = getCTerminalToFull().getAverageWeight();
 
  119       return Cterminal_to_full_average_weight;
 
  124       static const DoubleReal Cterminal_to_full_mono_weight = getCTerminalToFull().getMonoWeight();
 
  125       return Cterminal_to_full_mono_weight;
 
  132       return b_ion_to_full;
 
  137       static const DoubleReal b_ion_to_full_average_weight = getBIonToFull().getAverageWeight();
 
  138       return b_ion_to_full_average_weight;
 
  143       static const DoubleReal b_ion_to_full_mono_weight = getBIonToFull().getMonoWeight();
 
  144       return b_ion_to_full_mono_weight;
 
  151       return a_ion_to_full;
 
  156       static const DoubleReal a_ion_to_full_average_weight = getAIonToFull().getAverageWeight();
 
  157       return a_ion_to_full_average_weight;
 
  162       static const DoubleReal a_ion_to_full_mono_weight = getAIonToFull().getMonoWeight();
 
  163       return a_ion_to_full_mono_weight;
 
  170       return y_ion_to_full;
 
  175       static const DoubleReal y_ion_to_full_average_weight = getYIonToFull().getAverageWeight();
 
  176       return y_ion_to_full_average_weight;
 
  181       static const DoubleReal y_ion_to_full_mono_weight = getYIonToFull().getMonoWeight();
 
  182       return y_ion_to_full_mono_weight;
 
  189       return c_ion_to_full;
 
  194       static const DoubleReal c_ion_to_full_average_weight = getCIonToFull().getAverageWeight();
 
  195       return c_ion_to_full_average_weight;
 
  200       static const DoubleReal c_ion_to_full_mono_weight = getCIonToFull().getMonoWeight();
 
  201       return c_ion_to_full_mono_weight;
 
  208       return c_ion_to_full;
 
  213       static const DoubleReal c_ion_to_full_average_weight = getCIonMinusOneToFull().getAverageWeight();
 
  214       return c_ion_to_full_average_weight;
 
  219       static const DoubleReal c_ion_to_full_mono_weight = getCIonMinusOneToFull().getMonoWeight();
 
  220       return c_ion_to_full_mono_weight;
 
  227       return c_ion_to_full;
 
  232       static const DoubleReal c_ion_to_full_average_weight = getCIonPlusOneToFull().getAverageWeight();
 
  233       return c_ion_to_full_average_weight;
 
  238       static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusOneToFull().getMonoWeight();
 
  239       return c_ion_to_full_mono_weight;
 
  246       return c_ion_to_full;
 
  251       static const DoubleReal c_ion_to_full_average_weight = getCIonPlusTwoToFull().getAverageWeight();
 
  252       return c_ion_to_full_average_weight;
 
  257       static const DoubleReal c_ion_to_full_mono_weight = getCIonPlusTwoToFull().getMonoWeight();
 
  258       return c_ion_to_full_mono_weight;
 
  265       return x_ion_to_full;
 
  270       static const DoubleReal x_ion_to_full_average_weight = getXIonToFull().getAverageWeight();
 
  271       return x_ion_to_full_average_weight;
 
  276       static const DoubleReal x_ion_to_full_mono_weight = getXIonToFull().getMonoWeight();
 
  277       return x_ion_to_full_mono_weight;
 
  284       return z_ion_to_full;
 
  289       static const DoubleReal z_ion_to_full_average_weight = getZIonToFull().getAverageWeight();
 
  290       return z_ion_to_full_average_weight;
 
  295       static const DoubleReal z_ion_to_full_mono_weight = getZIonToFull().getMonoWeight();
 
  296       return z_ion_to_full_mono_weight;
 
  303       return z_ion_to_full;
 
  308       static const DoubleReal z_ion_to_full_average_weight = getZIonMinusOneToFull().getAverageWeight();
 
  309       return z_ion_to_full_average_weight;
 
  314       static const DoubleReal z_ion_to_full_mono_weight = getZIonMinusOneToFull().getMonoWeight();
 
  315       return z_ion_to_full_mono_weight;
 
  322       return z_ion_to_full;
 
  327       static const DoubleReal z_ion_to_full_average_weight = getZIonPlusOneToFull().getAverageWeight();
 
  328       return z_ion_to_full_average_weight;
 
  333       static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusOneToFull().getMonoWeight();
 
  334       return z_ion_to_full_mono_weight;
 
  341       return z_ion_to_full;
 
  346       static const DoubleReal z_ion_to_full_average_weight = getZIonPlusTwoToFull().getAverageWeight();
 
  347       return z_ion_to_full_average_weight;
 
  352       static const DoubleReal z_ion_to_full_mono_weight = getZIonPlusTwoToFull().getMonoWeight();
 
  353       return z_ion_to_full_mono_weight;
 
  386     static String getResidueTypeName(
const ResidueType res_type);
 
  400             const String & three_letter_code,
 
  401             const String & one_letter_code,
 
  418     void setName(
const String & name);
 
  422     const String & getName() 
const;
 
  425     void setShortName(
const String & short_name);
 
  428     const String & getShortName() 
const;
 
  431     void setSynonyms(
const std::set<String> & synonyms);
 
  434     void addSynonym(
const String & synonym);
 
  437     const std::set<String> & getSynonyms() 
const;
 
  440     void setThreeLetterCode(
const String & three_letter_code);
 
  443     const String & getThreeLetterCode() 
const;
 
  446     void setOneLetterCode(
const String & one_letter_code);
 
  449     const String & getOneLetterCode() 
const;
 
  455     void setLossFormulas(
const std::vector<EmpiricalFormula> &);
 
  461     void setNTermLossFormulas(
const std::vector<EmpiricalFormula> &);
 
  464     const std::vector<EmpiricalFormula> & getLossFormulas() 
const;
 
  467     const std::vector<EmpiricalFormula> & getNTermLossFormulas() 
const;
 
  470     void setLossNames(
const std::vector<String> & name);
 
  473     void setNTermLossNames(
const std::vector<String> & name);
 
  476     void addLossName(
const String & name);
 
  479     void addNTermLossName(
const String & name);
 
  482     const std::vector<String> & getLossNames() 
const;
 
  485     const std::vector<String> & getNTermLossNames() 
const;
 
  497     DoubleReal getAverageWeight(ResidueType res_type = Full) 
const;
 
  503     DoubleReal getMonoWeight(ResidueType res_type = Full) 
const;
 
  509     const String & getModification() 
const;
 
  512     void setLowMassIons(
const std::vector<EmpiricalFormula> & low_mass_ions);
 
  515     const std::vector<EmpiricalFormula> & getLowMassIons() 
const;
 
  518     void setResidueSets(
const std::set<String> & residues_sets);
 
  521     void addResidueSet(
const String & residue_sets);
 
  524     const std::set<String> & getResidueSets() 
const;
 
  530     bool hasNeutralLoss() 
const;
 
  534     bool hasNTermNeutralLosses() 
const;
 
  537     bool operator==(
const Residue & residue) 
const;
 
  540     bool operator!=(
const Residue & residue) 
const;
 
  543     bool operator==(
char one_letter_code) 
const;
 
  546     bool operator!=(
char one_letter_code) 
const;
 
  579     void setBackboneBasicityLeft(
DoubleReal gb_bb_l);
 
  585     void setBackboneBasicityRight(
DoubleReal gb_bb_r);
 
  588     bool isModified() 
const;
 
  591     bool isInResidueSet(
const String & residue_set);
 
  595     friend OPENMS_DLLAPI std::ostream & 
operator<<(std::ostream & os, 
const Residue & residue);
 
  661   OPENMS_DLLAPI std::ostream & 
operator<<(std::ostream & os, 
const Residue & residue);
 
Definition: Residue.h:367
static const EmpiricalFormula & getZIonPlusTwoToFull()
Definition: Residue.h:338
static const EmpiricalFormula & getBIonToFull()
Definition: Residue.h:129
static DoubleReal getCIonToFullAverageWeight()
Definition: Residue.h:192
Definition: Residue.h:374
DoubleReal pka_
Definition: Residue.h:642
std::vector< String > loss_names_
Definition: Residue.h:626
static DoubleReal getCIonMinusOneToFullMonoWeight()
Definition: Residue.h:217
A more convenient string class. 
Definition: String.h:56
static DoubleReal getZIonToFullAverageWeight()
Definition: Residue.h:287
static DoubleReal getNTerminalToFullMonoWeight()
Definition: Residue.h:103
std::vector< String > NTerm_loss_names_
Definition: Residue.h:630
static DoubleReal getAIonToFullMonoWeight()
Definition: Residue.h:160
Definition: Residue.h:364
DoubleReal pkb_
Definition: Residue.h:645
Definition: Residue.h:365
DoubleReal loss_average_weight_
Definition: Residue.h:634
DoubleReal gb_bb_r_
Definition: Residue.h:654
static const EmpiricalFormula & getInternalToFull()
Definition: Residue.h:72
static const EmpiricalFormula & getYIonToFull()
Definition: Residue.h:167
DoubleReal average_weight_
Definition: Residue.h:614
static DoubleReal getZIonMinusOneToFullMonoWeight()
Definition: Residue.h:312
static DoubleReal getCIonPlusTwoToFullMonoWeight()
Definition: Residue.h:255
std::ostream & operator<<(std::ostream &os, const ItraqQuantifier::ItraqQuantifierStats &stats)
Definition: Residue.h:366
static const EmpiricalFormula & getCIonPlusOneToFull()
Definition: Residue.h:224
static const EmpiricalFormula & getCIonToFull()
Definition: Residue.h:186
static const EmpiricalFormula & getZIonMinusOneToFull()
Definition: Residue.h:300
Representation of a residue. 
Definition: Residue.h:64
std::vector< EmpiricalFormula > loss_formulas_
Definition: Residue.h:628
static DoubleReal getZIonPlusOneToFullMonoWeight()
Definition: Residue.h:331
DoubleReal gb_sc_
Definition: Residue.h:650
static DoubleReal getCTerminalToFullAverageWeight()
Definition: Residue.h:116
std::vector< EmpiricalFormula > low_mass_ions_
Definition: Residue.h:639
Definition: Residue.h:378
DoubleReal pkc_
Definition: Residue.h:648
Definition: Residue.h:376
Definition: Residue.h:372
void setModification(int location, int max_size, String modification, OpenMS::AASequence &aas)
helper function that sets a modifiction on a AASequence object 
static DoubleReal getCIonPlusTwoToFullAverageWeight()
Definition: Residue.h:249
static const EmpiricalFormula & getZIonToFull()
Definition: Residue.h:281
static DoubleReal getZIonPlusTwoToFullAverageWeight()
Definition: Residue.h:344
static const EmpiricalFormula & getZIonPlusOneToFull()
Definition: Residue.h:319
static const EmpiricalFormula & getAIonToFull()
Definition: Residue.h:148
static const EmpiricalFormula & getCIonMinusOneToFull()
Definition: Residue.h:205
DoubleReal loss_mono_weight_
Definition: Residue.h:636
static DoubleReal getYIonToFullAverageWeight()
Definition: Residue.h:173
static DoubleReal getAIonToFullAverageWeight()
Definition: Residue.h:154
static const EmpiricalFormula & getCIonPlusTwoToFull()
Definition: Residue.h:243
String short_name_
Definition: Residue.h:602
Definition: Residue.h:373
Definition: Residue.h:377
static DoubleReal getXIonToFullAverageWeight()
Definition: Residue.h:268
static const EmpiricalFormula & getCTerminalToFull()
Definition: Residue.h:110
EmpiricalFormula internal_formula_
Definition: Residue.h:612
static DoubleReal getZIonToFullMonoWeight()
Definition: Residue.h:293
static DoubleReal getCIonMinusOneToFullAverageWeight()
Definition: Residue.h:211
String name_
Definition: Residue.h:600
String three_letter_code_
Definition: Residue.h:606
static DoubleReal getZIonPlusTwoToFullMonoWeight()
Definition: Residue.h:350
static DoubleReal getInternalToFullMonoWeight()
Definition: Residue.h:84
ResidueType
Definition: Residue.h:361
bool is_modified_
Definition: Residue.h:619
static DoubleReal getInternalToFullAverageWeight()
Definition: Residue.h:78
Definition: Residue.h:368
Definition: Residue.h:369
static const EmpiricalFormula & getXIonToFull()
Definition: Residue.h:262
std::set< String > synonyms_
Definition: Residue.h:604
static DoubleReal getCIonPlusOneToFullMonoWeight()
Definition: Residue.h:236
static DoubleReal getCIonToFullMonoWeight()
Definition: Residue.h:198
String pre_mod_name_
Definition: Residue.h:621
static DoubleReal getCTerminalToFullMonoWeight()
Definition: Residue.h:122
EmpiricalFormula formula_
Definition: Residue.h:610
static DoubleReal getBIonToFullAverageWeight()
Definition: Residue.h:135
String modification_
Definition: Residue.h:623
static DoubleReal getXIonToFullMonoWeight()
Definition: Residue.h:274
static DoubleReal getBIonToFullMonoWeight()
Definition: Residue.h:141
static const EmpiricalFormula & getNTerminalToFull()
Definition: Residue.h:91
DoubleReal gb_bb_l_
Definition: Residue.h:652
static DoubleReal getZIonMinusOneToFullAverageWeight()
Definition: Residue.h:306
DoubleReal mono_weight_
Definition: Residue.h:616
Definition: Residue.h:375
std::set< String > residue_sets_
Definition: Residue.h:657
Definition: Residue.h:371
std::vector< EmpiricalFormula > NTerm_loss_formulas_
Definition: Residue.h:632
static DoubleReal getCIonPlusOneToFullAverageWeight()
Definition: Residue.h:230
String one_letter_code_
Definition: Residue.h:608
static DoubleReal getYIonToFullMonoWeight()
Definition: Residue.h:179
static DoubleReal getNTerminalToFullAverageWeight()
Definition: Residue.h:97
Definition: Residue.h:370
static DoubleReal getZIonPlusOneToFullAverageWeight()
Definition: Residue.h:325