| 133 | } |
| 134 | |
| 135 | EmpiricalFormula NASequence::getFormula(NASFragmentType type, Int charge) const |
| 136 | { |
| 137 | static const EmpiricalFormula H_form = EmpiricalFormula::hydrogen(); |
| 138 | static const EmpiricalFormula phosphate_form = EmpiricalFormula("HPO3"); |
| 139 | static const EmpiricalFormula thiophosphate_form = EmpiricalFormula("HPO2S1"); |
| 140 | static const EmpiricalFormula internal_to_full = EmpiricalFormula::water(); |
| 141 | // static const EmpiricalFormula five_prime_to_full = EmpiricalFormula("HPO3"); |
| 142 | // static const EmpiricalFormula three_prime_to_full = EmpiricalFormula(""); |
| 143 | static const EmpiricalFormula a_ion_to_full = EmpiricalFormula::water(-1); |
| 144 | static const EmpiricalFormula b_ion_to_full = EmpiricalFormula(); |
| 145 | static const EmpiricalFormula c_ion_to_full = EmpiricalFormula("H-1PO2"); |
| 146 | static const EmpiricalFormula d_ion_to_full = phosphate_form; |
| 147 | static const EmpiricalFormula w_ion_to_full = d_ion_to_full; |
| 148 | static const EmpiricalFormula x_ion_to_full = c_ion_to_full; |
| 149 | static const EmpiricalFormula y_ion_to_full = b_ion_to_full; |
| 150 | static const EmpiricalFormula z_ion_to_full = a_ion_to_full; |
| 151 | static const EmpiricalFormula aminusB_ion_to_full = EmpiricalFormula::water(-2); |
| 152 | // static const EmpiricalFormula abasicform_RNA = EmpiricalFormula("C5H8O4"); |
| 153 | // static const EmpiricalFormula abasicform_DNA = EmpiricalFormula("C5H7O5P"); |
| 154 | |
| 155 | if (seq_.empty()) |
| 156 | return EmpiricalFormula(); |
| 157 | |
| 158 | EmpiricalFormula our_form; |
| 159 | // Add all the ribonucleotide masses |
| 160 | for (const auto& i : seq_) |
| 161 | { |
| 162 | our_form += i->getFormula(); |
| 163 | // Add the phosphate (of thiophosphate) per linkage |
| 164 | if (&i != &seq_.back()) // no linkage at last base |
| 165 | { |
| 166 | if (i->getCode().back() == '*') |
| 167 | { |
| 168 | our_form += (thiophosphate_form - internal_to_full); |
| 169 | } |
| 170 | else |
| 171 | { |
| 172 | our_form += (phosphate_form - internal_to_full); |
| 173 | } |
| 174 | } |
| 175 | } |
| 176 | |
| 177 | EmpiricalFormula local_three_prime, local_five_prime; |
| 178 | |
| 179 | // Make local copies of the formulas for the terminal mods so we don't get into trouble dereferencing null ptrs |
| 180 | if (three_prime_ != nullptr) |
| 181 | { |
| 182 | local_three_prime = three_prime_->getFormula() - H_form; |
| 183 | } |
| 184 | if (five_prime_ != nullptr) |
| 185 | { |
| 186 | local_five_prime = five_prime_->getFormula() - H_form; |
| 187 | } |
| 188 | |
| 189 | switch (type) |
| 190 | { |
| 191 | case Full: |
| 192 | return our_form + (H_form * charge) + local_five_prime + local_three_prime; |
nothing calls this directly
no test coverage detected