/home/msneddon/eclipse/galileoSR1_cpp/workspace/NFsim/src/NFreactions/transformations/speciesCreator.hh

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#ifndef SPECIESCREATOR_HH_
#define SPECIESCREATOR_HH_


#include "../NFreactions.hh"

using namespace std;

namespace NFcore
{
        class MoleculeType;
        class TemplateMolecule;

        class SpeciesCreator
        {
                public:
                        SpeciesCreator(
                                        vector <MoleculeType *> &productMoleculeTypes,
                                        vector < vector <int> > &stateInformation,
                                        vector < vector <int> > &bindingSiteInformation);
                        SpeciesCreator(vector <TemplateMolecule *> &templates);
                        ~SpeciesCreator();
                        
                        void create();
                
                protected:
                        
                        unsigned int n_molecules;
                        MoleculeType ** moleculeTypes;
                        
                        Molecule **newMoleculeCreations;
                        
                        
                        //Save the configuration of states we have to set
                        //nd prefix stands for non-default 
                        unsigned int n_ndStates;
                        int *ndStateMolecule;
                        int *ndStateIndex;
                        int *ndStateValue;
                        
                        
                        //Save the bonds that we have to create
                        unsigned int n_bonds;
                        int *bMolecule1;
                        int *bMolecule2;
                        int *bSite1;
                        int *bSite2;
        };




}
























#endif /*SPECIESCREATOR_HH_*/

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