from __future__ import absolute_import, division, print_function import iotbx.pdb from scitbx.array_family import flex from libtbx.test_utils import assert_lines_in_text def tst_1(): pdb_str = """\ ATOM 3705 N PRO A 839 -72.061 7.475 91.699 1.00 19.22 N ATOM 3706 CA PRO A 839 -71.162 6.864 90.749 1.00 15.72 C ATOM 3707 C PRO A 839 -70.566 7.946 89.845 1.00 19.35 C ATOM 3708 O PRO A 839 -71.127 9.016 89.760 1.00 16.63 O ATOM 3709 CB PRO A 839 -72.065 5.933 89.906 1.00 21.17 C ATOM 3710 CG PRO A 839 -73.211 5.597 90.858 1.00 24.24 C ATOM 3711 CD PRO A 839 -73.429 6.917 91.585 1.00 16.35 C ATOM 3719 N AMET A 840 -69.536 7.589 89.072 0.22 22.15 N ATOM 3720 CA AMET A 840 -68.907 8.564 88.135 0.22 20.67 C ATOM 3721 C AMET A 840 -69.805 8.754 86.915 0.22 19.08 C ATOM 3722 O AMET A 840 -70.492 7.790 86.550 0.22 20.65 O ATOM 3723 CB AMET A 840 -67.538 8.082 87.621 0.22 21.34 C ATOM 3724 CG AMET A 840 -66.422 8.081 88.677 0.22 26.22 C ATOM 3725 SD AMET A 840 -64.849 7.459 88.020 0.22 35.67 S ATOM 3726 CE AMET A 840 -64.456 8.716 86.804 0.22 27.23 C ATOM 3736 N BMET A 840 -69.531 7.591 89.077 0.42 22.17 N ATOM 3737 CA BMET A 840 -68.906 8.565 88.135 0.42 20.62 C ATOM 3738 C BMET A 840 -69.810 8.756 86.920 0.42 18.97 C ATOM 3739 O BMET A 840 -70.488 7.791 86.549 0.42 20.61 O ATOM 3740 CB BMET A 840 -67.543 8.081 87.610 0.42 21.27 C ATOM 3741 CG BMET A 840 -66.418 8.078 88.653 0.42 26.27 C ATOM 3742 SD BMET A 840 -64.866 7.435 87.968 0.42 35.93 S ATOM 3743 CE BMET A 840 -65.243 5.686 87.845 0.42 17.98 C ATOM 3753 N CMET A 840 -69.533 7.590 89.075 0.36 22.17 N ATOM 3754 CA CMET A 840 -68.906 8.564 88.135 0.36 20.64 C ATOM 3755 C CMET A 840 -69.808 8.756 86.919 0.36 19.02 C ATOM 3756 O CMET A 840 -70.489 7.791 86.549 0.36 20.62 O ATOM 3757 CB CMET A 840 -67.542 8.079 87.611 0.36 21.30 C ATOM 3758 CG CMET A 840 -66.426 8.032 88.663 0.36 26.24 C ATOM 3759 SD CMET A 840 -64.891 7.366 87.964 0.36 35.95 S ATOM 3760 CE CMET A 840 -63.880 7.218 89.436 0.36 19.93 C ATOM 3770 N ASP A 841 -69.924 9.986 86.413 1.00 20.11 N ATOM 3771 CA ASP A 841 -70.719 10.250 85.211 1.00 23.77 C ATOM 3772 C ASP A 841 -72.158 9.760 85.347 1.00 26.73 C ATOM 3773 O ASP A 841 -72.719 9.126 84.444 1.00 26.93 O ATOM 3774 CB ASP A 841 -70.043 9.623 83.985 1.00 20.96 C ATOM 3775 CG ASP A 841 -68.601 10.057 83.840 1.00 38.39 C ATOM 3776 OD1 ASP A 841 -68.357 11.284 83.832 1.00 51.85 O ATOM 3777 OD2 ASP A 841 -67.711 9.179 83.749 1.00 53.14 O """ h = iotbx.pdb.input(lines=pdb_str, source_info=None).construct_hierarchy() h_atoms = h.atoms() ogs = h.occupancy_groups_simple() # set occupancy values that will be rounded wrong test_occ = [0.225, 0.225, 0.55] for i, g in enumerate(ogs[0]): h_atoms.select(flex.size_t(g)).set_occ(flex.double([test_occ[i]]*len(g))) # observe wrong rounding wrong_pdb_str = h.as_pdb_string() assert_lines_in_text(wrong_pdb_str, """\ ATOM 8 N AMET A 840 -69.536 7.589 89.072 0.23 22.15 N ATOM 9 CA AMET A 840 -68.907 8.564 88.135 0.23 20.67 C ATOM 10 C AMET A 840 -69.805 8.754 86.915 0.23 19.08 C ATOM 11 O AMET A 840 -70.492 7.790 86.550 0.23 20.65 O ATOM 12 CB AMET A 840 -67.538 8.082 87.621 0.23 21.34 C ATOM 13 CG AMET A 840 -66.422 8.081 88.677 0.23 26.22 C ATOM 14 SD AMET A 840 -64.849 7.459 88.020 0.23 35.67 S ATOM 15 CE AMET A 840 -64.456 8.716 86.804 0.23 27.23 C ATOM 16 N BMET A 840 -69.531 7.591 89.077 0.23 22.17 N ATOM 17 CA BMET A 840 -68.906 8.565 88.135 0.23 20.62 C ATOM 18 C BMET A 840 -69.810 8.756 86.920 0.23 18.97 C ATOM 19 O BMET A 840 -70.488 7.791 86.549 0.23 20.61 O ATOM 20 CB BMET A 840 -67.543 8.081 87.610 0.23 21.27 C ATOM 21 CG BMET A 840 -66.418 8.078 88.653 0.23 26.27 C ATOM 22 SD BMET A 840 -64.866 7.435 87.968 0.23 35.93 S ATOM 23 CE BMET A 840 -65.243 5.686 87.845 0.23 17.98 C ATOM 24 N CMET A 840 -69.533 7.590 89.075 0.55 22.17 N ATOM 25 CA CMET A 840 -68.906 8.564 88.135 0.55 20.64 C ATOM 26 C CMET A 840 -69.808 8.756 86.919 0.55 19.02 C ATOM 27 O CMET A 840 -70.489 7.791 86.549 0.55 20.62 O ATOM 28 CB CMET A 840 -67.542 8.079 87.611 0.55 21.30 C ATOM 29 CG CMET A 840 -66.426 8.032 88.663 0.55 26.24 C ATOM 30 SD CMET A 840 -64.891 7.366 87.964 0.55 35.95 S ATOM 31 CE CMET A 840 -63.880 7.218 89.436 0.55 19.93 C """) h.round_occupancies_in_place(2) correct_pdb_str = h.as_pdb_string() assert_lines_in_text(correct_pdb_str, """\ ATOM 8 N AMET A 840 -69.536 7.589 89.072 0.23 22.15 N ATOM 9 CA AMET A 840 -68.907 8.564 88.135 0.23 20.67 C ATOM 10 C AMET A 840 -69.805 8.754 86.915 0.23 19.08 C ATOM 11 O AMET A 840 -70.492 7.790 86.550 0.23 20.65 O ATOM 12 CB AMET A 840 -67.538 8.082 87.621 0.23 21.34 C ATOM 13 CG AMET A 840 -66.422 8.081 88.677 0.23 26.22 C ATOM 14 SD AMET A 840 -64.849 7.459 88.020 0.23 35.67 S ATOM 15 CE AMET A 840 -64.456 8.716 86.804 0.23 27.23 C ATOM 16 N BMET A 840 -69.531 7.591 89.077 0.22 22.17 N ATOM 17 CA BMET A 840 -68.906 8.565 88.135 0.22 20.62 C ATOM 18 C BMET A 840 -69.810 8.756 86.920 0.22 18.97 C ATOM 19 O BMET A 840 -70.488 7.791 86.549 0.22 20.61 O ATOM 20 CB BMET A 840 -67.543 8.081 87.610 0.22 21.27 C ATOM 21 CG BMET A 840 -66.418 8.078 88.653 0.22 26.27 C ATOM 22 SD BMET A 840 -64.866 7.435 87.968 0.22 35.93 S ATOM 23 CE BMET A 840 -65.243 5.686 87.845 0.22 17.98 C ATOM 24 N CMET A 840 -69.533 7.590 89.075 0.55 22.17 N ATOM 25 CA CMET A 840 -68.906 8.564 88.135 0.55 20.64 C ATOM 26 C CMET A 840 -69.808 8.756 86.919 0.55 19.02 C ATOM 27 O CMET A 840 -70.489 7.791 86.549 0.55 20.62 O ATOM 28 CB CMET A 840 -67.542 8.079 87.611 0.55 21.30 C ATOM 29 CG CMET A 840 -66.426 8.032 88.663 0.55 26.24 C ATOM 30 SD CMET A 840 -64.891 7.366 87.964 0.55 35.95 S ATOM 31 CE CMET A 840 -63.880 7.218 89.436 0.55 19.93 C """) if (__name__ == "__main__"): tst_1() print('OK')