OpenMS  2.6.0
EmpiricalFormula.h
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31 // $Maintainer: Chris Bielow $
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 <algorithm>
41 #include <string>
42 
43 #include <OpenMS/CONCEPT/Types.h>
44 
45 namespace OpenMS
46 {
47  class String;
48  class Element;
49  class ElementDB;
50  class IsotopeDistribution;
51  class IsotopePatternGenerator;
52  class CoarseIsotopePatternGenerator;
53 
82  class OPENMS_DLLAPI EmpiricalFormula
83  {
84 
85 protected:
87  typedef std::map<const Element*, SignedSize> MapType_;
88 
89 public:
93  typedef MapType_::const_iterator ConstIterator;
95  typedef MapType_::const_iterator const_iterator;
96  typedef MapType_::iterator Iterator;
97  typedef MapType_::iterator iterator;
99 
105 
107  EmpiricalFormula(const EmpiricalFormula&) = default;
108 
110  EmpiricalFormula(EmpiricalFormula&&) = default;
111 
117  explicit EmpiricalFormula(const String& rhs);
118 
119 
121  EmpiricalFormula(SignedSize number, const Element* element, SignedSize charge = 0);
122 
124  virtual ~EmpiricalFormula();
126 
130  double getMonoWeight() const;
132 
134  double getAverageWeight() const;
135 
137  double calculateTheoreticalIsotopesNumber() const;
138 
152  bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);
153 
168  bool estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);
169 
170 
178  IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator& method) const;
179 
190  IsotopeDistribution getConditionalFragmentIsotopeDist(const EmpiricalFormula& precursor,
191  const std::set<UInt>& precursor_isotopes,
192  const CoarseIsotopePatternGenerator& method) const;
193 
195  SignedSize getNumberOf(const Element* element) const;
196 
198  SignedSize getNumberOfAtoms() const;
199 
201  Int getCharge() const;
202 
204  void setCharge(Int charge);
205 
207  String toString() const;
208 
210  std::map<std::string, int> toMap() const;
212 
216 
218  EmpiricalFormula& operator=(const EmpiricalFormula&) = default;
219 
221  EmpiricalFormula& operator=(EmpiricalFormula&&) & = default;
222 
224  EmpiricalFormula& operator+=(const EmpiricalFormula& rhs);
225 
227  EmpiricalFormula operator*(const SignedSize& times) const;
228 
230  EmpiricalFormula operator+(const EmpiricalFormula& rhs) const;
231 
233  EmpiricalFormula& operator-=(const EmpiricalFormula& rhs);
234 
236  EmpiricalFormula operator-(const EmpiricalFormula& rhs) const;
237 
239 
243  bool isEmpty() const;
245 
247  bool isCharged() const;
248 
250  bool hasElement(const Element* element) const;
251 
253  bool contains(const EmpiricalFormula& ef);
254 
256  bool operator==(const EmpiricalFormula& rhs) const;
257 
259  bool operator!=(const EmpiricalFormula& rhs) const;
260 
262  bool operator<(const EmpiricalFormula& rhs) const;
263 
265 
267  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
268 
272  inline ConstIterator begin() const { return formula_.begin(); }
273 
274  inline ConstIterator end() const { return formula_.end(); }
275 
276  inline Iterator begin() { return formula_.begin(); }
277 
278  inline Iterator end() { return formula_.end(); }
280 
281 protected:
282 
284  void removeZeroedElements_();
285 
287 
289 
290  Int parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;
291 
292  };
293 
294  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
295 
296 } // namespace OpenMS
OpenMS::EmpiricalFormula::MapType_
std::map< const Element *, SignedSize > MapType_
Internal typedef for the used map type.
Definition: EmpiricalFormula.h:87
Types.h
OpenMS::Element
Representation of an element.
Definition: Element.h:53
OpenMS::operator*
DPosition< D, TCoordinateType > operator*(DPosition< D, TCoordinateType > position, typename DPosition< D, TCoordinateType >::CoordinateType scalar)
Scalar multiplication (a bit inefficient)
Definition: DPosition.h:427
OpenMS::EmpiricalFormula::formula_
MapType_ formula_
Definition: EmpiricalFormula.h:286
OpenMS::String
A more convenient string class.
Definition: String.h:59
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:96
OpenMS::EmpiricalFormula::begin
Iterator begin()
Definition: EmpiricalFormula.h:276
OpenMS::EmpiricalFormula::iterator
MapType_::iterator iterator
Definition: EmpiricalFormula.h:97
OpenMS::operator<
bool operator<(const QTCluster &q1, const QTCluster &q2)
OpenMS::EmpiricalFormula::begin
ConstIterator begin() const
Definition: EmpiricalFormula.h:272
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
int
OpenMS::EmpiricalFormula::ConstIterator
MapType_::const_iterator ConstIterator
Iterators.
Definition: EmpiricalFormula.h:94
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:53
OpenMS::StringConversions::toString
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below
Definition: StringUtils.h:127
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:95
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:96
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::EmpiricalFormula::end
Iterator end()
Definition: EmpiricalFormula.h:278
OpenMS::EmpiricalFormula::charge_
Int charge_
Definition: EmpiricalFormula.h:288
OpenMS::EmpiricalFormula::end
ConstIterator end() const
Definition: EmpiricalFormula.h:274