OpenMS
EmpiricalFormula.h
Go to the documentation of this file.
1 // --------------------------------------------------------------------------
2 // OpenMS -- Open-Source Mass Spectrometry
3 // --------------------------------------------------------------------------
4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2023.
6 //
7 // This software is released under a three-clause BSD license:
8 // * Redistributions of source code must retain the above copyright
9 // notice, this list of conditions and the following disclaimer.
10 // * Redistributions in binary form must reproduce the above copyright
11 // notice, this list of conditions and the following disclaimer in the
12 // documentation and/or other materials provided with the distribution.
13 // * Neither the name of any author or any participating institution
14 // may be used to endorse or promote products derived from this software
15 // without specific prior written permission.
16 // For a full list of authors, refer to the file AUTHORS.
17 // --------------------------------------------------------------------------
18 // THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
19 // AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
20 // IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
21 // ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
22 // INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
23 // EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
24 // PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
25 // OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
26 // WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
27 // OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
28 // ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
29 //
30 // --------------------------------------------------------------------------
31 // $Maintainer: Chris Bielow, Ahmed Khalil $
32 // $Authors: Andreas Bertsch, Chris Bielow $
33 // --------------------------------------------------------------------------
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:
96  typedef MapType_::const_iterator ConstIterator;
97  typedef MapType_::const_iterator const_iterator;
98  typedef MapType_::iterator Iterator;
99  typedef MapType_::iterator iterator;
101 
107 
110 
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 
145  double getMonoWeight() const;
146 
148  double getAverageWeight() const;
149 
152 
166  bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P);
167 
181  bool estimateFromMonoWeightAndComp(double mono_weight, double C, double H, double N, double O, double S, double P);
182 
197  bool estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P);
198 
199 
208 
220  const std::set<UInt>& precursor_isotopes,
221  const CoarseIsotopePatternGenerator& method) const;
222 
224  SignedSize getNumberOf(const Element* element) const;
225 
228 
230  Int getCharge() const;
231 
233  void setCharge(Int charge);
234 
236  String toString() const;
237 
239  std::map<std::string, int> toMap() const;
241 
245 
248 
251 
254 
256  EmpiricalFormula operator*(const SignedSize& times) const;
257 
260 
263 
266 
268 
273  bool isEmpty() const;
274 
276  bool isCharged() const;
277 
279  bool hasElement(const Element* element) const;
280 
282  bool contains(const EmpiricalFormula& ef) const;
283 
285  bool operator==(const EmpiricalFormula& rhs) const;
286 
288  bool operator!=(const EmpiricalFormula& rhs) const;
289 
291  bool operator<(const EmpiricalFormula& rhs) const;
292 
294 
296  friend OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
297 
301  inline ConstIterator begin() const { return formula_.begin(); }
302 
303  inline ConstIterator end() const { return formula_.end(); }
304 
305  inline Iterator begin() { return formula_.begin(); }
306 
307  inline Iterator end() { return formula_.end(); }
309 
312  // @TODO: make these static member variables instead?
314  static EmpiricalFormula hydrogen(int n_atoms = 1);
316 
318  static EmpiricalFormula water(int n_molecules = 1);
320 
321 protected:
322 
325 
327 
329 
330  Int parseFormula_(std::map<const Element*, SignedSize>& ef, const String& formula) const;
331 
332  };
333 
334  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const EmpiricalFormula& formula);
335 
336 } // namespace OpenMS
Isotope pattern generator for coarse isotope distributions.
Definition: CoarseIsotopePatternGenerator.h:105
Representation of an element.
Definition: Element.h:58
Representation of an empirical formula.
Definition: EmpiricalFormula.h:85
Int parseFormula_(std::map< const Element *, SignedSize > &ef, const String &formula) const
bool hasElement(const Element *element) const
returns true if the formula contains the element
EmpiricalFormula operator*(const SignedSize &times) const
multiplies the elements and charge with a factor
EmpiricalFormula operator+(const EmpiricalFormula &rhs) const
adds the elements of the given formula and returns a new formula
bool estimateFromWeightAndComp(double average_weight, double C, double H, double N, double O, double S, double P)
Fills this EmpiricalFormula with an approximate elemental composition for a given average weight and ...
EmpiricalFormula(const String &rhs)
Iterator begin()
Definition: EmpiricalFormula.h:305
String toString() const
returns the formula as a string (charges are not included)
static EmpiricalFormula water(int n_molecules=1)
Efficiently generates a formula for water.
bool operator<(const EmpiricalFormula &rhs) const
less operator
double getMonoWeight() const
returns the mono isotopic weight of the formula (includes proton charges)
std::map< const Element *, SignedSize > MapType_
Internal typedef for the used map type.
Definition: EmpiricalFormula.h:89
MapType_::const_iterator ConstIterator
Iterators.
Definition: EmpiricalFormula.h:96
friend std::ostream & operator<<(std::ostream &os, const EmpiricalFormula &formula)
writes the formula to a stream
EmpiricalFormula & operator=(const EmpiricalFormula &)=default
Assignment operator.
EmpiricalFormula & operator-=(const EmpiricalFormula &rhs)
subtracts the elements of a formula
EmpiricalFormula(EmpiricalFormula &&)=default
Move constructor.
EmpiricalFormula()
Default constructor.
bool isCharged() const
returns true if charge != 0
EmpiricalFormula(const EmpiricalFormula &)=default
Copy constructor.
ConstIterator end() const
Definition: EmpiricalFormula.h:303
EmpiricalFormula operator-(const EmpiricalFormula &rhs) const
subtracts the elements of a formula an returns a new formula
Int getCharge() const
returns the charge
IsotopeDistribution getIsotopeDistribution(const IsotopePatternGenerator &method) const
returns the isotope distribution of the formula The details of the calculation of the isotope distrib...
void removeZeroedElements_()
remove elements with count 0
MapType_ formula_
Definition: EmpiricalFormula.h:326
SignedSize getNumberOf(const Element *element) const
returns the number of atoms for a certain element (can be negative)
bool operator!=(const EmpiricalFormula &rhs) const
returns true if the formulas differ in elements composition
double getAverageWeight() const
returns the average weight of the formula (includes proton charges)
bool estimateFromMonoWeightAndComp(double mono_weight, double C, double H, double N, double O, double S, double P)
Fills this EmpiricalFormula with an approximate elemental composition for a given monoisotopic weight...
bool operator==(const EmpiricalFormula &rhs) const
returns true if the formulas contain equal elements in equal quantities
MapType_::iterator iterator
Definition: EmpiricalFormula.h:99
bool estimateFromWeightAndCompAndS(double average_weight, UInt S, double C, double H, double N, double O, double P)
Fills this EmpiricalFormula with an approximate elemental composition for a given average weight,...
EmpiricalFormula(SignedSize number, const Element *element, SignedSize charge=0)
Constructor with element pointer and number.
SignedSize getNumberOfAtoms() const
returns the atoms total (not absolute: negative counts for certain elements will reduce the overall c...
Iterator end()
Definition: EmpiricalFormula.h:307
double calculateTheoreticalIsotopesNumber() const
returns the total number of discrete isotopes
void setCharge(Int charge)
sets the charge
MapType_::const_iterator const_iterator
Definition: EmpiricalFormula.h:97
bool isEmpty() const
returns true if the formula does not contain a element
IsotopeDistribution getConditionalFragmentIsotopeDist(const EmpiricalFormula &precursor, const std::set< UInt > &precursor_isotopes, const CoarseIsotopePatternGenerator &method) const
returns the fragment isotope distribution of this given a precursor formula and conditioned on a set ...
ConstIterator begin() const
Definition: EmpiricalFormula.h:301
EmpiricalFormula & operator+=(const EmpiricalFormula &rhs)
adds the elements of the given formula
virtual ~EmpiricalFormula()
Destructor.
EmpiricalFormula & operator=(EmpiricalFormula &&) &=default
Move assignment operator.
MapType_::iterator Iterator
Definition: EmpiricalFormula.h:98
Int charge_
Definition: EmpiricalFormula.h:328
std::map< std::string, int > toMap() const
returns the formula as a map (charges are not included)
static EmpiricalFormula fromString(const String &rhs)
create EmpiricalFormular object by parsing an OpenMS string
Definition: EmpiricalFormula.h:135
bool contains(const EmpiricalFormula &ef) const
returns true if all elements from ef are LESS abundant (negative allowed) than the corresponding elem...
Definition: IsotopeDistribution.h:65
Provides an interface for different isotope pattern generator methods.
Definition: IsotopePatternGenerator.h:68
A more convenient string class.
Definition: String.h:60
int Int
Signed integer type.
Definition: Types.h:102
unsigned int UInt
Unsigned integer type.
Definition: Types.h:94
ptrdiff_t SignedSize
Signed Size type e.g. used as pointer difference.
Definition: Types.h:134
static String number(double d, UInt n)
Definition: StringUtils.h:217
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48
std::ostream & operator<<(std::ostream &os, const AccurateMassSearchResult &amsr)