The conformer generation algorithm in ROSHAMBO allows for an optional energy calculation, with the choice of including local minimization as mentioned before. If the energies are available, it calculates the relative energy in comparison to the lowest energy conformer within the same dataset molecule. The algorithm then employs an energy cutoff distance (energy cutoff), which is optionally provided as input by the user, retaining only conformers whose relative energy falls below this threshold. Additionally, the algorithm provides a conformer alignment option. By using the first conformer of each dataset molecule as a reference, it aligns subsequent conformers. Following that, it calculates the Root Mean Square (RMS) matrix for the dataset molecule conformers and then clusters them based on the computed distance matrix. The user can specify the clustering threshold through an optional RMS cutoff value (rms cutoff). Post-clustering, the algorithm selects the centroid of each cluster, representing the most central conformer in each group. Whether employing the energy or RMS cutoff, these features aim to streamline the conformer selection process.