jade.rosetta_jade.alignment.align_to_second_pose_save_pdb(pose_name, pose, second_pose, outdir, overhang=0, stem_align=False)[source]
jade.rosetta_jade.alignment.get_map_for_rmsd(pose, second_pose, overhang=3)[source]
jade.rosetta_jade.alignment.get_mask_for_alignment(pose, second_pose, overhang=0)[source]

Get mask assuming they are both the same length!

jade.rosetta_jade.alignment.get_mask_for_stem_alignment(pose, second_pose, stem_size)[source]
jade.rosetta_jade.alignment.get_rmsd(pose, second_pose, overhang=0)[source]

Get RMSD assuming they are both the same length!