| atom1_type | PAPRECA::PredefinedReaction | protected |
| atom2_type | PAPRECA::PredefinedReaction | protected |
| bond_dist_sqr | PAPRECA::PredefinedBondForm | protected |
| bond_type | PAPRECA::PredefinedReaction | protected |
| catalyzing_types | PAPRECA::PredefinedReaction | protected |
| delete_atoms | PAPRECA::PredefinedBondForm | protected |
| getAtom1Type() const | PAPRECA::PredefinedReaction | |
| getAtom2Type() const | PAPRECA::PredefinedReaction | |
| getBondDistSqr() const | PAPRECA::PredefinedBondForm | |
| getBondType() const | PAPRECA::PredefinedReaction | |
| getCatalyzingTypes() const | PAPRECA::PredefinedReaction | |
| getLengthEquil() const | PAPRECA::PredefinedReaction | |
| getLimitHighSqr() const | PAPRECA::PredefinedReaction | |
| getLimitLowSqr() const | PAPRECA::PredefinedReaction | |
| getRate() const | PAPRECA::PredefinedReaction | |
| is_form | PAPRECA::PredefinedReaction | protected |
| isDeleteAtoms() const | PAPRECA::PredefinedBondForm | |
| isForm() const | PAPRECA::PredefinedReaction | |
| isLone() const | PAPRECA::PredefinedBondForm | |
| isSameMol() const | PAPRECA::PredefinedBondForm | |
| length_equil | PAPRECA::PredefinedReaction | protected |
| limit_high_sqr | PAPRECA::PredefinedReaction | protected |
| limit_low_sqr | PAPRECA::PredefinedReaction | protected |
| lone_candidates | PAPRECA::PredefinedBondForm | protected |
| PredefinedBondForm(const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const double &bond_dist_sqr_in, const int &delete_atoms_in, const int &lone_candidates_in, const bool &same_mol_in) | PAPRECA::PredefinedBondForm | |
| PredefinedBondForm(const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const double &bond_dist_sqr_in, const int &delete_atoms_in, const int &lone_candidates_in, const bool &same_mol_in, const std::vector< int > &catalyzing_types_in) | PAPRECA::PredefinedBondForm | |
| PredefinedReaction(const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in) | PAPRECA::PredefinedReaction | |
| PredefinedReaction(const int &atom1_type_in, const int &atom2_type_in, const int &bond_type_in, const double &rate_in, const std::vector< int > &catalyzing_types_in) | PAPRECA::PredefinedReaction | |
| rate | PAPRECA::PredefinedReaction | protected |
| same_mol | PAPRECA::PredefinedBondForm | protected |
| setLengthEquil(const double &length_equil_in) | PAPRECA::PredefinedReaction | |
| setLimitHighSqr(const double &limit_high_sqr_in) | PAPRECA::PredefinedReaction | |
| setLimitLowSqr(const double &limit_low_sqr_in) | PAPRECA::PredefinedReaction | |
| setSqrLimits(const double &length_equil_in, const double &length_perc_in) | PAPRECA::PredefinedReaction | |
| ~PredefinedBondForm() | PAPRECA::PredefinedBondForm | |
| ~PredefinedReaction() | PAPRECA::PredefinedReaction | |