OpenMS  3.0.0
EmpiricalFormula.h
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31 // $Maintainer: Chris Bielow, Ahmed Khalil $
32 // $Authors: Andreas Bertsch, Chris Bielow $
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34 //
35 #pragma once
36 
37 #include <iosfwd>
38 #include <map>
39 #include <set>
40 #include <string>
41 
42 #include <OpenMS/CONCEPT/Types.h>
43 
44 namespace OpenMS
45 {
46  class String;
47  class Element;
48  class ElementDB;
49  class IsotopeDistribution;
50  class IsotopePatternGenerator;
51  class CoarseIsotopePatternGenerator;
52 
84  class OPENMS_DLLAPI EmpiricalFormula
85  {
86 
87 protected:
89  typedef std::map<const Element*, SignedSize> MapType_;
90 
91 public:
95  typedef MapType_::const_iterator ConstIterator;
97  typedef MapType_::const_iterator const_iterator;
98  typedef MapType_::iterator Iterator;
99  typedef MapType_::iterator iterator;
101 
107 
109  EmpiricalFormula(const EmpiricalFormula&) = default;
110 
112  EmpiricalFormula(EmpiricalFormula&&) = default;
113 
119  explicit EmpiricalFormula(const String& rhs);
120 
122  EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge = 0);
123 
125  virtual ~EmpiricalFormula();
127 
135  static EmpiricalFormula fromString(const String& rhs)
136  {
137  EmpiricalFormula ef(rhs);
138  return ef;
139  }
140 
144  double getMonoWeight() const;
146 
148  double getAverageWeight() const;
149 
151  double calculateTheoreticalIsotopesNumber() const;
152 
166  bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);
167 
182  bool estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);
183 
184 
192  IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator& method) const;
193 
204  IsotopeDistribution getConditionalFragmentIsotopeDist(const EmpiricalFormula& precursor,
205  const std::set<UInt>& precursor_isotopes,
206  const CoarseIsotopePatternGenerator& method) const;
207 
209  SignedSize getNumberOf(const Element* element) const;
210 
212  SignedSize getNumberOfAtoms() const;
213 
215  Int getCharge() const;
216 
218  void setCharge(Int charge);
219 
221  String toString() const;
222 
224  std::map<std::string, int> toMap() const;
226 
230 
232  EmpiricalFormula& operator=(const EmpiricalFormula&) = default;
233 
235  EmpiricalFormula& operator=(EmpiricalFormula&&) & = default;
236 
238  EmpiricalFormula& operator+=(const EmpiricalFormula& rhs);
239 
241  EmpiricalFormula operator*(const SignedSize& times) const;
242 
244  EmpiricalFormula operator+(const EmpiricalFormula& rhs) const;
245 
247  EmpiricalFormula& operator-=(const EmpiricalFormula& rhs);
248 
250  EmpiricalFormula operator-(const EmpiricalFormula& rhs) const;
251 
253 
257  bool isEmpty() const;
259 
261  bool isCharged() const;
262 
264  bool hasElement(const Element* element) const;
265 
267  bool contains(const EmpiricalFormula& ef) const;
268 
270  bool operator==(const EmpiricalFormula& rhs) const;
271 
273  bool operator!=(const EmpiricalFormula& rhs) const;
274 
276  bool operator<(const EmpiricalFormula& rhs) const;
277 
279 
281  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
282 
286  inline ConstIterator begin() const { return formula_.begin(); }
287 
288  inline ConstIterator end() const { return formula_.end(); }
289 
290  inline Iterator begin() { return formula_.begin(); }
291 
292  inline Iterator end() { return formula_.end(); }
294 
297  // @TODO: make these static member variables instead?
299  static EmpiricalFormula hydrogen(int n_atoms = 1);
301 
303  static EmpiricalFormula water(int n_molecules = 1);
305 
306 protected:
307 
309  void removeZeroedElements_();
310 
312 
314 
315  Int parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;
316 
317  };
318 
319  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
320 
321 } // namespace OpenMS
OpenMS::EmpiricalFormula::MapType_
std::map< const Element *, SignedSize > MapType_
Internal typedef for the used map type.
Definition: EmpiricalFormula.h:89
OpenMS::toString
const std::string & toString(const DriftTimeUnit value)
Types.h
OpenMS::Element
Representation of an element.
Definition: Element.h:57
OpenMS::operator*
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:426
OpenMS::EmpiricalFormula::formula_
MapType_ formula_
Definition: EmpiricalFormula.h:311
OpenMS::String
A more convenient string class.
Definition: String.h:58
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:103
OpenMS::EmpiricalFormula::begin
Iterator begin()
Definition: EmpiricalFormula.h:290
OpenMS::EmpiricalFormula::iterator
MapType_::iterator iterator
Definition: EmpiricalFormula.h:99
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::EmpiricalFormula::begin
ConstIterator begin() const
Definition: EmpiricalFormula.h:286
OpenMS::operator+
FS_TV operator+(const TV_STATUS left, const TV_STATUS right)
allow + operations on the enum, e.g. 'HAS_CANVAS + HAS_LAYER + IS_1D_VIEW'
OpenMS::Int
int Int
Signed integer type.
Definition: Types.h:102
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::EmpiricalFormula::ConstIterator
MapType_::const_iterator ConstIterator
Iterators.
Definition: EmpiricalFormula.h:96
OpenMS::EmpiricalFormula::fromString
static EmpiricalFormula fromString(const String &rhs)
create EmpiricalFormular object by parsing an OpenMS string
Definition: EmpiricalFormula.h:135
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::IsotopePatternGenerator
Provides an interface for different isotope pattern generator methods.
Definition: IsotopePatternGenerator.h:67
OpenMS::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::EmpiricalFormula::const_iterator
MapType_::const_iterator const_iterator
Definition: EmpiricalFormula.h:97
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::Internal::operator==
bool operator==(const IDBoostGraph::ProteinGroup &lhs, const IDBoostGraph::ProteinGroup &rhs)
OpenMS::EmpiricalFormula::Iterator
MapType_::iterator Iterator
Definition: EmpiricalFormula.h:98
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:84
OpenMS::EmpiricalFormula::end
Iterator end()
Definition: EmpiricalFormula.h:292
OpenMS::StringUtils::number
static String number(double d, UInt n)
Definition: StringUtils.h:196
OpenMS::EmpiricalFormula::charge_
Int charge_
Definition: EmpiricalFormula.h:313
OpenMS::EmpiricalFormula::end
ConstIterator end() const
Definition: EmpiricalFormula.h:288