Candidate_v1.7.0
        stable
      
      
        
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            Last change
 on this file since 1e490ec was             999eaf, checked in by Frederik Heber <frederik.heber@…>, 5 years ago           | 
        
        
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Added EvaluateStabilityAction to estimate a molecule's stability. 
 
- removes every bond and checks the energies of the products against the
educt equipped with enough hydrogen molecules to compensate for the
cut bond times its degree.
 - outputs a CSV file with entries per bond.
 - extended HomologyGraph to allow direct use of AtomIdSet, i.e. atomic
ids coming from a selection in the World or from the molecule.
 - DOCU: Added subsection on this action to section homology.
 - TEST: Added regression test case.
  
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            File size:
            1.4 KB
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| [999eaf] | 1 | /*
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 | 2 |  * StabilityEvaluator.hpp
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 | 3 |  *
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 | 4 |  *  Created on: Apr 18, 2021
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 | 5 |  *      Author: heber
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 | 6 |  */
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 | 7 | 
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 | 8 | 
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 | 9 | #ifndef FRAGMENTATION_EVALUATION_STABILITYEVALUATOR_HPP_
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 | 10 | #define FRAGMENTATION_EVALUATION_STABILITYEVALUATOR_HPP_
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 | 11 | 
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 | 12 | // include config.h
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 | 13 | #ifdef HAVE_CONFIG_H
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 | 14 | #include <config.h>
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 | 15 | #endif
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 | 16 | 
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 | 17 | #include <iosfwd>
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 | 18 | #include <string>
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 | 19 | #include <vector>
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 | 20 | 
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 | 21 | class HomologyContainer;
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 | 22 | class HomologyGraph;
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 | 23 | class molecule;
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 | 24 | 
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 | 25 | /**
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 | 26 |  * Evaluates the stability for a given molecule by removing each bond
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 | 27 |  * and computing the energy of the products.
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 | 28 |  */
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 | 29 | class StabilityEvaluator {
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 | 30 | public:
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 | 31 |   StabilityEvaluator(const molecule * _mol);
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 | 32 | 
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 | 33 |   /**
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 | 34 |    * Contains all information on a single removed bond.
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 | 35 |    */
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 | 36 |   struct StabilityCriterion {
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 | 37 |     std::string formula_educt1;
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 | 38 |     std::string formula_educt2;
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 | 39 |     double energy_educts;
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 | 40 |     std::string formula_product1;
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 | 41 |     std::string formula_product2;
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 | 42 |     double energy_products;
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 | 43 |     bool isStable;  //!< states whether energy_educts < energy_products
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 | 44 |   };
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 | 45 | 
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 | 46 |   typedef std::vector<StabilityCriterion> stabilities_t;
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 | 47 | 
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 | 48 |   stabilities_t operator()() const;
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 | 49 | 
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 | 50 | private:
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 | 51 |   double getLowestEnergyFromHomologyContainer(const HomologyGraph &nodes_graph) const;
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 | 52 | 
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 | 53 | 
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 | 54 | private:
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 | 55 |   const molecule * mol;
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 | 56 | 
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 | 57 |   const HomologyContainer &container;
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 | 58 | };
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 | 59 | 
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 | 60 | std::ostream& operator<<(std::ostream &ost, const StabilityEvaluator::StabilityCriterion &_stability);
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 | 61 | 
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 | 62 | #endif /* FRAGMENTATION_EVALUATION_STABILITYEVALUATOR_HPP_ */
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