energetics.py 文件源码

def calculate_unrestricted_toehold_characteristics(self):
        import stickydesign as sd
        ends = sd.easyends('TD',
                           self.length,
                           alphabet=self.alphabet,
                           adjs=self.adjs,
                           energetics=self)
        n_ends = len(ends)
        e_array = sd.energy_array_uniform(ends, self)
        e_array = e_array[n_ends:, :n_ends]
        for i in range(n_ends):
            e_array[i,i] = 0
        e_spr = e_array.max()/self.targetdG
        e_vec_ext = self.th_external_dG(ends)
        e_vec_int = self.th_internal_dG(ends)
        e_vec_all = np.concatenate( (e_vec_int, e_vec_ext))
        e_avg = e_vec_all.mean()
        e_dev = np.max(np.abs(e_vec_all - self.targetdG))
        return e_avg, e_dev, e_spr, n_ends