comparison BioPDB_align_and_rmsd.py @ 1:a40867ca69fe draft default tip

planemo upload for repository https://github.com/galaxycomputationalchemistry/galaxy-tools-compchem/ commit e9345f76e3f953eea14bad2287cbc5a9c1ff882e

0:6352d6dd74e2

    super_imposer.set_atoms(ref_atoms, sample_atoms)
    super_imposer.apply(sample_model.get_atoms())

    # Save RMSD into an output file:
    with open(args.rmsd, 'w') as rmsd_out:
        rmsd_out.write(str(super_imposer.rms))

    # Save aligned coordinates of the model:
    io = Bio.PDB.PDBIO()
    io.set_structure(sample_structure)
    io.save(args.aligned_structure)

1:a40867ca69fe

    super_imposer.set_atoms(ref_atoms, sample_atoms)
    super_imposer.apply(sample_model.get_atoms())

    # Save RMSD into an output file:
    with open(args.rmsd, 'w') as rmsd_out:
        rmsd_out.write("{}\n".format(super_imposer.rms))

    # Save aligned coordinates of the model:
    io = Bio.PDB.PDBIO()
    io.set_structure(sample_structure)
    io.save(args.aligned_structure)