| OpenMS 2.5.0

EmpiricalFormula.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow $
32 // $Authors: Andreas Bertsch, Chris Bielow $
33 // --------------------------------------------------------------------------
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
103 EmpiricalFormula();
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
286 MapType_ formula_;
287
288 Int charge_;
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::SignedSize
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::operator<
bool operator<(const MultiplexDeltaMasses &dm1, const MultiplexDeltaMasses &dm2)
OpenMS::EmpiricalFormula::formula_
MapType_ formula_
Definition: EmpiricalFormula.h:286
OpenMS::IsotopeDistribution
Definition: IsotopeDistribution.h:64
OpenMS::StringConversions::toString
String toString(const T &i)
fallback template for general purpose using Boost::Karma; more specializations below ...
Definition: StringUtils.h:85
KDTree::operator!=
bool operator!=(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:824
Types.h
OpenMS::EmpiricalFormula::iterator
MapType_::iterator iterator
Definition: EmpiricalFormula.h:97
OpenMS::IsotopePatternGenerator
Provides an interface for different isotope pattern generator methods.
Definition: IsotopePatternGenerator.h:53
OpenMS::EmpiricalFormula::charge_
Int charge_
Definition: EmpiricalFormula.h:288
OpenMS::EmpiricalFormula::begin
Iterator begin()
Definition: EmpiricalFormula.h:276
OpenMS::Element
Representation of an element.
Definition: Element.h:53
OpenMS::operator<<
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::EmpiricalFormula
Representation of an empirical formula.
Definition: EmpiricalFormula.h:82
OpenMS::UInt
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
OpenMS::EmpiricalFormula::MapType_
std::map< const Element *, SignedSize > MapType_
Internal typedef for the used map type.
Definition: EmpiricalFormula.h:87
OpenMS::EmpiricalFormula::begin
ConstIterator begin() const
Definition: EmpiricalFormula.h:272
OpenMS::EmpiricalFormula::ConstIterator
MapType_::const_iterator ConstIterator
Iterators.
Definition: EmpiricalFormula.h:94
OpenMS::CoarseIsotopePatternGenerator
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:96
int
OpenMS::EmpiricalFormula::end
ConstIterator end() const
Definition: EmpiricalFormula.h:274
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::end
Iterator end()
Definition: EmpiricalFormula.h:278
OpenMS::EmpiricalFormula::const_iterator
MapType_::const_iterator const_iterator
Definition: EmpiricalFormula.h:95
OpenMS::EmpiricalFormula::Iterator
MapType_::iterator Iterator
Definition: EmpiricalFormula.h:96
KDTree::operator==
bool operator==(_Iterator< _Val, _Ref, _Ptr > const &, _Iterator< _Val, _Ref, _Ptr > const &)
Definition: KDTree.h:806