text: /****************************************************************************
   * Copyright (C) from 2009 to Present EPAM Systems.
   *
   * This file is part of Indigo toolkit.
   *
   * Licensed under the Apache License, Version 2.0 (the "License");
   * you may not use this file except in compliance with the License.
   * You may obtain a copy of the License at
   *
   * http://www.apache.org/licenses/LICENSE-2.0
   *
   * Unless required by applicable law or agreed to in writing, software
   * distributed under the License is distributed on an "AS IS" BASIS,
   * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
   * See the License for the specific language governing permissions and
   * limitations under the License.
   ***************************************************************************/
  
  #ifndef __molecule_mass_h__
  #define __molecule_mass_h__
  #include <set>
  #include "base_cpp/red_black.h"
  #include "molecule/molecule_mass_options.h"
  namespace indigo
  {
  
      class Molecule;
  
      // Molecular mass calculation
      class MoleculeMass
      {
          DECL_ERROR;
  
      protected:
          struct _ElemCounter
          {
              int elem;
              double weight;
          };
  
          static int _cmp(_ElemCounter& ec1, _ElemCounter& ec2, void* context);
  
      public:
          MoleculeMass();
          MassOptions mass_options;
  
          const RedBlackMap<int, double>* relative_atomic_mass_map;
  
          /* Mass of a molecule calculated using the average mass of each
           * element weighted for its natural isotopic abundance
           */
          double molecularWeight(Molecule& mol );
  
          /* Mass of a molecule containing most likely
           * isotopic composition for a single random molecule.
           * Notes: in PubChem search engine it is called Exact Mass
           */
          double mostAbundantMass(Molecule& mol );
  
          /* Mass of a molecule calculated using the mass of
           * the most abundant isotope of each element.
           * Notes: in Marvin it is called Exact Mass
           */
          double monoisotopicMass( Molecule& mol );
  
          /* Sum of the mass numbers of all constituent atoms.
           */
          int nominalMass(Molecule& mol);
  
          /* Atom weight percentage like "C 77% H 13%"
           */
          void massComposition(Molecule& molecule, Array<char>& str );
      };
  
  } // namespace indigo
  
  #endif // __molecule_mass_h__
  