from __future__ import absolute_import, division, print_function import mmtbx.model import libtbx.load_env import iotbx.pdb import os import tempfile import time from libtbx.utils import null_out from cctbx import crystal, adptbx from six.moves import range from libtbx.test_utils import approx_equal from scitbx.array_family import flex pdb_str_1 = """ CRYST1 79.110 79.110 37.465 90.00 90.00 90.00 P 43 21 2 ATOM 1 N GLY A 67 11.351 9.426 29.699 1.00 16.57 A N ATOM 2 CA GLY A 67 12.344 8.654 30.419 1.00 16.65 A C ATOM 3 C GLY A 67 13.703 9.318 30.525 1.00 17.27 A C ATOM 4 O GLY A 67 14.613 8.754 31.138 1.00 18.12 A O ATOM 5 HA2 GLY A 67 11.164 8.290 32.128 1.00 16.65 A H ATOM 6 HA3 GLY A 67 12.899 8.562 30.893 1.00 16.65 A H ATOM 7 N ARG A 68 13.850 10.509 29.946 1.00 17.04 A N ATOM 8 CA ARG A 68 15.122 11.232 30.010 1.00 18.21 A C ATOM 9 C ARG A 68 14.955 12.712 30.337 1.00 19.28 A C ATOM 10 O ARG A 68 15.856 13.506 30.060 1.00 18.39 A O ATOM 11 CB ARG A 68 15.888 11.102 28.683 1.00 17.72 A C ATOM 12 CG ARG A 68 15.297 11.878 27.495 1.00 17.98 A C ATOM 13 CD ARG A 68 16.259 11.919 26.349 1.00 18.60 A C ATOM 14 NE ARG A 68 15.794 12.838 25.306 1.00 17.24 A N ATOM 15 CZ ARG A 68 16.143 12.775 24.023 1.00 19.10 A C ATOM 16 NH1 ARG A 68 16.951 11.815 23.586 1.00 18.15 A N ATOM 17 NH2 ARG A 68 15.667 13.670 23.169 1.00 19.17 A N ATOM 18 HA ARG A 68 15.977 11.764 31.624 1.00 18.21 A H ATOM 19 HB2 ARG A 68 17.228 11.790 28.507 1.00 17.72 A H ATOM 20 HB3 ARG A 68 16.065 9.301 28.834 1.00 17.72 A H ATOM 21 HG2 ARG A 68 14.632 11.422 26.483 1.00 17.98 A H ATOM 22 HG3 ARG A 68 15.102 11.944 27.956 1.00 17.98 A H ATOM 23 HD2 ARG A 68 17.713 11.903 27.452 1.00 18.60 A H ATOM 24 HD3 ARG A 68 17.031 10.479 25.184 1.00 18.60 A H ATOM 25 H AARG A 68 13.747 10.274 28.969 0.50 17.04 A H ATOM 26 HE AARG A 68 14.652 14.091 26.079 0.50 17.24 A H ATOM 27 HH11AARG A 68 16.935 11.771 24.831 0.50 18.15 A H ATOM 28 HH12AARG A 68 17.117 12.550 21.627 0.50 18.15 A H ATOM 29 HH21AARG A 68 14.846 14.096 22.818 0.50 19.17 A H ATOM 30 HH22AARG A 68 15.127 14.548 23.046 0.50 19.17 A H ATOM 31 D BARG A 68 12.950 10.336 30.200 0.50 17.04 A D ATOM 32 DE BARG A 68 14.587 13.771 24.772 0.50 17.24 A D ATOM 33 DH11BARG A 68 16.347 11.268 24.478 0.50 18.15 A D ATOM 34 DH12BARG A 68 16.772 11.748 23.372 0.50 18.15 A D ATOM 35 DH21BARG A 68 14.983 15.028 23.897 0.50 19.17 A D ATOM 36 DH22BARG A 68 15.963 14.351 21.579 0.50 19.17 A D ATOM 37 N THR A 69 13.811 13.085 30.907 1.00 18.60 A N ATOM 38 CA THR A 69 13.578 14.468 31.314 1.00 21.27 A C ATOM 39 C THR A 69 13.418 14.522 32.825 1.00 23.37 A C ATOM 40 O THR A 69 12.315 14.330 33.336 1.00 22.36 A O ATOM 41 CB THR A 69 12.332 15.076 30.647 1.00 18.85 A C ATOM 42 OG1 THR A 69 12.366 14.826 29.239 1.00 16.82 A O ATOM 43 CG2 THR A 69 12.281 16.578 30.889 1.00 22.56 A C ATOM 44 HA THR A 69 14.647 15.056 30.363 1.00 21.27 A H ATOM 45 HB THR A 69 11.388 15.356 31.910 1.00 18.85 A H ATOM 46 HG21 THR A 69 11.173 17.433 30.334 1.00 22.56 A H ATOM 47 HG22 THR A 69 12.747 16.477 32.550 1.00 22.56 A H ATOM 48 HG23 THR A 69 12.759 16.559 30.395 1.00 22.56 A H ATOM 49 H ATHR A 69 13.914 11.773 30.712 0.50 18.60 A H ATOM 50 HG1ATHR A 69 10.933 14.249 27.986 0.50 16.82 A H ATOM 51 D BTHR A 69 13.543 11.891 30.715 0.50 18.60 A D ATOM 52 DG1BTHR A 69 12.128 14.870 28.337 0.50 16.82 A D TER END """ pdb_str_2 = """ CRYST1 34.238 35.096 43.858 90.00 90.00 90.00 P 21 21 21 0 ATOM 1 N LYS A 45 6.154 2.754 1.212 1.00 12.39 N ATOM 2 C LYS A 45 7.533 2.537 -0.815 1.00 8.18 C ATOM 3 O LYS A 45 8.546 2.217 -1.437 1.00 8.18 O ATOM 4 CA ALYS A 45 7.469 2.388 0.702 0.18 8.95 C ATOM 5 CB ALYS A 45 7.820 0.954 1.105 0.18 15.56 C ATOM 6 CG ALYS A 45 7.880 0.729 2.607 0.18 7.12 C ATOM 7 CD ALYS A 45 8.227 -0.714 2.935 0.18 22.74 C ATOM 8 CE ALYS A 45 8.402 -0.914 4.432 0.18 43.83 C ATOM 9 NZ ALYS A 45 7.134 -0.676 5.175 0.18 58.88 N ATOM 23 CA BLYS A 45 7.396 2.217 0.670 0.82 9.42 C ATOM 24 CB BLYS A 45 7.467 0.704 0.891 0.82 15.14 C ATOM 25 CG BLYS A 45 7.428 0.288 2.352 0.82 9.76 C ATOM 26 CD BLYS A 45 7.539 -1.221 2.500 0.82 22.13 C ATOM 27 CE BLYS A 45 6.396 -1.931 1.793 0.82 22.20 C ATOM 28 NZ BLYS A 45 6.495 -3.411 1.927 0.82 22.09 N ATOM 0 HA ALYS A 45 8.198 3.068 1.142 0.18 9.42 H new ATOM 0 HA BLYS A 45 8.223 2.691 1.198 0.82 9.42 H new ATOM 0 HB2ALYS A 45 7.082 0.276 0.676 0.18 15.14 H new ATOM 0 HB2BLYS A 45 6.636 0.232 0.368 0.82 15.14 H new ATOM 0 HB3ALYS A 45 8.784 0.691 0.670 0.18 15.14 H new ATOM 0 HB3BLYS A 45 8.384 0.324 0.441 0.82 15.14 H new ATOM 0 HG2ALYS A 45 8.624 1.393 3.047 0.18 9.76 H new ATOM 0 HG2BLYS A 45 8.244 0.769 2.891 0.82 9.76 H new ATOM 0 HG3ALYS A 45 6.919 0.985 3.054 0.18 9.76 H new ATOM 0 HG3BLYS A 45 6.499 0.633 2.806 0.82 9.76 H new ATOM 0 HD2ALYS A 45 7.439 -1.372 2.568 0.18 22.13 H new ATOM 0 HD2BLYS A 45 8.490 -1.560 2.089 0.82 22.13 H new ATOM 0 HD3ALYS A 45 9.145 -0.996 2.419 0.18 22.13 H new ATOM 0 HD3BLYS A 45 7.536 -1.486 3.557 0.82 22.13 H new ATOM 0 HE2ALYS A 45 8.751 -1.929 4.625 0.18 22.20 H new ATOM 0 HE2BLYS A 45 5.446 -1.592 2.207 0.82 22.20 H new ATOM 0 HE3ALYS A 45 9.172 -0.237 4.801 0.18 22.20 H new ATOM 0 HE3BLYS A 45 6.398 -1.661 0.737 0.82 22.20 H new ATOM 0 HZ1ALYS A 45 7.263 -0.936 6.174 0.18 22.09 H new ATOM 0 HZ1BLYS A 45 5.698 -3.859 1.432 0.82 22.09 H new ATOM 0 HZ2ALYS A 45 6.877 0.330 5.110 0.18 22.09 H new ATOM 0 HZ2BLYS A 45 7.390 -3.738 1.510 0.82 22.09 H new ATOM 0 HZ3ALYS A 45 6.375 -1.255 4.761 0.18 22.09 H new ATOM 0 HZ3BLYS A 45 6.467 -3.671 2.934 0.82 22.09 H new TER END """ def run(): if (not libtbx.env.has_module("reduce")): print("Reduce not installed, needed for model.idealize_h_minimization(). skipping") return for pdb_str in [pdb_str_1, pdb_str_2]: for use_neutron_distances in [True, False]: print("use_neutron_distances:", use_neutron_distances, "*"*30) params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.use_neutron_distances = use_neutron_distances inp = iotbx.pdb.input(lines=pdb_str, source_info=None) m = mmtbx.model.manager( model_input = inp, log = null_out()) m.process(pdb_interpretation_params=params, make_restraints=True) r1 = m.geometry_statistics() #m.setup_riding_h_manager() m.idealize_h_minimization(show=False) r2 = m.geometry_statistics() print("%6.3f %6.3f %6.3f %6.3f"%( r1.angle().mean,r1.bond().mean, r2.angle().mean,r2.bond().mean)) assert r2.angle().mean < 1.0, "assertion %f < 1.0" % r2.angle().mean assert r2.bond().mean < 0.01, "assertion %f < 0.01" % r2.bond().mean def exercise_2(): inp = iotbx.pdb.input(lines=pdb_str_1, source_info=None) model = mmtbx.model.manager( model_input = inp) model.setup_scattering_dictionaries(scattering_table="wk1995") g_stat = model.geometry_statistics() def exercise_3(): """ Make sure model can do deep_copy() straight away. """ inp = iotbx.pdb.input(lines=pdb_str_1, source_info=None) model = mmtbx.model.manager( model_input = inp) new_model = model.deep_copy() pdb_str_3 = """CRYST1 20.000 20.000 20.000 90.00 90.00 90.00 P 1 SCALE1 0.050000 0.000000 0.000000 0.00000 SCALE2 0.000000 0.050000 0.000000 0.00000 SCALE3 0.000000 0.000000 0.050000 0.00000 ATOM 1 CA GLY A 1 0.000 0.000 0.000 1.00 30.00 C ATOM 2 CA GLY A 2 1.000 1.000 1.000 1.00 30.00 C ATOM 3 CA GLY A 3 2.000 2.000 2.000 1.00 30.00 C ATOM 4 CA GLY A 4 3.000 3.000 3.000 1.00 30.00 C ATOM 5 CA GLY A 5 4.000 4.000 4.000 1.00 30.00 C ATOM 6 CA GLY A 6 5.000 5.000 5.000 1.00 30.00 C ATOM 7 CA GLY A 7 6.000 6.000 6.000 1.00 30.00 C ATOM 8 CA GLY A 8 7.000 7.000 7.000 1.00 30.00 C ATOM 9 CA GLY A 9 8.000 8.000 8.000 1.00 30.00 C ATOM 10 CA GLY A 10 9.000 9.000 9.000 1.00 30.00 C TER END """ def exercise_convert_to_isotropic(): pdb_str = """ ATOM 104 N SER A 8 14.526 19.060 18.223 1.00 5.10 N ANISOU 104 N SER A 8 500 632 808 -107 58 104 N ATOM 105 CA SER A 8 14.099 17.792 18.758 1.00 5.95 C """ cs = crystal.symmetry((5.01, 5.01, 5.47, 90, 90, 120), "P 62 2 2") pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) model = mmtbx.model.manager( model_input = pdb_inp, crystal_symmetry = cs) # m = model.deep_copy() m.convert_to_isotropic() assert approx_equal( m.get_hierarchy().atoms().extract_b(), [5.105875, 5.95]) assert approx_equal( m.get_hierarchy().atoms().extract_uij(), [(-1.0, -1.0, -1.0, -1.0, -1.0, -1.0), (-1.0, -1.0, -1.0, -1.0, -1.0, -1.0)]) # m = model.deep_copy() m.convert_to_isotropic(selection=flex.bool([False, True])) assert approx_equal( m.get_hierarchy().atoms().extract_b(), model.get_hierarchy().atoms().extract_b()) assert approx_equal( m.get_hierarchy().atoms().extract_uij(), model.get_hierarchy().atoms().extract_uij()) # m1 = model.deep_copy() m2 = model.deep_copy() m1.convert_to_isotropic(selection=flex.bool([True, False])) m2.convert_to_isotropic() assert approx_equal( m1.get_hierarchy().atoms().extract_b(), m2.get_hierarchy().atoms().extract_b()) assert approx_equal( m1.get_hierarchy().atoms().extract_uij(), m2.get_hierarchy().atoms().extract_uij()) def exercise_set_b_iso(): pdb_str = """ ATOM 104 N SER A 8 14.526 19.060 18.223 1.00 5.10 N ANISOU 104 N SER A 8 500 632 808 -107 58 104 N ATOM 105 CA SER A 8 14.099 17.792 18.758 1.00 5.95 C """ cs = crystal.symmetry((5.01, 5.01, 5.47, 90, 90, 120), "P 62 2 2") uc = cs.unit_cell() pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) model = mmtbx.model.manager( model_input = pdb_inp, crystal_symmetry = cs) # m = model.deep_copy() bs = flex.double([10,20]) m.set_b_iso(values = bs) assert approx_equal(m.get_hierarchy().atoms().extract_b(), [-1.0, 20.0]) us = m.get_hierarchy().atoms().extract_uij() assert approx_equal(us[0], model.get_hierarchy().atoms().extract_uij()[0]) assert approx_equal(us[1], (-1.0, -1.0, -1.0, -1.0, -1.0, -1.0)) u_iso_1 = m.get_xray_structure().scatterers().extract_u_iso() b_iso_2 = m.get_hierarchy().atoms().extract_b() assert approx_equal(u_iso_1[0], -1) assert approx_equal(b_iso_2[0], -1) assert approx_equal(adptbx.u_as_b(u_iso_1[1]), 20) assert approx_equal(b_iso_2[1], 20) # m = model.deep_copy() m.convert_to_isotropic() bs = flex.double([10,20]) sel = flex.bool([True, False]) m.set_b_iso(values=bs, selection=sel) assert approx_equal(m.get_b_iso(), [10, 5.95]) def exercise_from_sites_cart(): from cctbx import crystal from scitbx.matrix import col from scitbx.array_family import flex sites_cart=flex.vec3_double() crystal_symmetry=crystal.symmetry( unit_cell=(20,20,20,90,90,90), space_group_symbol="P 1") for i in range(10): sites_cart.append(col((i,i,i))) model=mmtbx.model.manager.from_sites_cart(sites_cart=sites_cart, crystal_symmetry=crystal_symmetry) # print model.model_as_pdb() for i, a in enumerate(model.get_hierarchy().atoms()): assert a.i_seq == i, "iseqs were not set properly" assert model.model_as_pdb()==pdb_str_3 def exercise_has_hd(): inp = iotbx.pdb.input(lines=pdb_str_1, source_info=None) m = mmtbx.model.manager( model_input = inp, log = null_out()) assert m.has_hd() inp = iotbx.pdb.input(lines=pdb_str_3, source_info=None) m = mmtbx.model.manager( model_input = inp, log = null_out()) assert not m.has_hd() def exercise_ss_creation_crash(): pdb_str = """ CRYST1 145.350 135.090 157.320 90.00 90.00 90.00 P 1 SCALE1 0.006880 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007402 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006356 0.00000 ATOM 1 N ASN A 1 47.095 160.279 31.220 1.00 30.00 N ATOM 2 CA ASN A 1 65.985 120.233 34.727 1.00 30.00 C ATOM 3 C ASN A 1 56.657 138.700 33.374 1.00 30.00 C ATOM 4 O ASN A 1 56.353 138.977 34.561 1.00 30.00 O ATOM 5 CB ASN A 1 65.238 120.133 36.068 1.00 30.00 C ATOM 6 CG ASN A 1 66.087 119.360 37.057 1.00 30.00 C ATOM 7 OD1 ASN A 1 65.746 118.217 37.441 1.00 30.00 O ATOM 8 ND2 ASN A 1 67.240 119.920 37.395 1.00 30.00 N ATOM 9 N ASN A 2 56.939 137.441 33.021 1.00 30.00 N ATOM 10 CA ASN A 2 67.135 117.384 35.354 1.00 30.00 C ATOM 11 C ASN A 2 74.935 104.398 35.546 1.00 30.00 C ATOM 12 O ASN A 2 74.423 104.166 34.444 1.00 30.00 O ATOM 13 CB ASN A 2 65.828 116.703 35.809 1.00 30.00 C ATOM 14 CG ASN A 2 66.092 115.518 36.718 1.00 30.00 C ATOM 15 OD1 ASN A 2 66.641 114.515 36.266 1.00 30.00 O ATOM 16 ND2 ASN A 2 65.744 115.556 38.000 1.00 30.00 N ATOM 17 N ASN A 3 76.102 103.886 35.920 1.00 30.00 N ATOM 18 CA ASN A 3 68.960 115.076 35.163 1.00 30.00 C ATOM 19 C ASN A 3 86.047 90.376 35.591 1.00 30.00 C ATOM 20 O ASN A 3 87.134 90.903 35.535 1.00 30.00 O ATOM 21 CB ASN A 3 70.251 115.882 34.903 1.00 30.00 C ATOM 22 CG ASN A 3 71.023 116.208 36.192 1.00 30.00 C ATOM 23 OD1 ASN A 3 70.637 117.096 36.957 1.00 30.00 O ATOM 24 ND2 ASN A 3 72.106 115.481 36.436 1.00 30.00 N ATOM 25 OXT ASN A 3 85.912 89.104 36.045 1.00 30.00 O TER END """ with open("exercise_ss_creation_crash_model.pdb","w") as fo: fo.write(pdb_str) from iotbx.data_manager import DataManager dm=DataManager() params = mmtbx.model.manager.get_default_pdb_interpretation_params() params.pdb_interpretation.secondary_structure.enabled=True model = dm.get_model('exercise_ss_creation_crash_model.pdb') model.process(make_restraints=True, pdb_interpretation_params=params) def exercise_flip_nqh(): """ Expected flips: C 190 ASN D 212 ASN A 190 ASN B 212 ASN """ pdb_str = """ CRYST1 19.391 14.196 16.627 90.00 90.00 90.00 P 1 SCALE1 0.051570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.070442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.060143 0.00000 ATOM 1 N ASN A 190 14.391 7.875 10.959 1.00 25.08 N ATOM 2 CA ASN A 190 12.965 7.729 10.710 1.00 25.31 C ATOM 3 C ASN A 190 12.031 8.507 11.627 1.00 25.45 C ATOM 4 O ASN A 190 11.129 9.196 11.149 1.00 24.83 O ATOM 5 CB ASN A 190 12.578 6.250 10.760 1.00 29.15 C ATOM 6 CG ASN A 190 11.141 6.007 10.323 1.00 31.49 C ATOM 7 OD1 ASN A 190 10.458 5.135 10.858 1.00 30.98 O ATOM 8 ND2 ASN A 190 10.682 6.773 9.339 1.00 34.25 N TER ATOM 9 N ASN B 212 7.583 7.891 7.004 1.00 63.62 N ATOM 10 CA ASN B 212 6.962 6.727 6.387 1.00 70.84 C ATOM 11 C ASN B 212 5.525 7.117 6.075 1.00 76.13 C ATOM 12 O ASN B 212 5.000 6.819 5.000 1.00 78.13 O ATOM 13 CB ASN B 212 6.978 5.532 7.341 1.00 71.04 C ATOM 14 CG ASN B 212 8.376 5.163 7.790 1.00 72.56 C ATOM 15 OD1 ASN B 212 9.289 5.017 6.974 1.00 70.76 O ATOM 16 ND2 ASN B 212 8.551 5.000 9.096 1.00 73.07 N TER ATOM 1 N ASN C 190 24.391 17.875 20.959 1.00 25.08 N ATOM 2 CA ASN C 190 22.965 17.729 20.710 1.00 25.31 C ATOM 3 C ASN C 190 22.031 18.507 21.627 1.00 25.45 C ATOM 4 O ASN C 190 21.129 19.196 21.149 1.00 24.83 O ATOM 5 CB ASN C 190 22.578 16.250 20.760 1.00 29.15 C ATOM 6 CG ASN C 190 21.141 16.007 20.323 1.00 31.49 C ATOM 7 OD1 ASN C 190 20.458 15.135 20.858 1.00 30.98 O ATOM 8 ND2 ASN C 190 20.682 16.773 19.339 1.00 34.25 N TER ATOM 9 N ASN D 212 17.583 17.891 17.004 1.00 63.62 N ATOM 10 CA ASN D 212 16.962 16.727 16.387 1.00 70.84 C ATOM 11 C ASN D 212 15.525 17.117 16.075 1.00 76.13 C ATOM 12 O ASN D 212 15.000 16.819 15.000 1.00 78.13 O ATOM 13 CB ASN D 212 16.978 15.532 17.341 1.00 71.04 C ATOM 14 CG ASN D 212 18.376 15.163 17.790 1.00 72.56 C ATOM 15 OD1 ASN D 212 19.289 15.017 16.974 1.00 70.76 O ATOM 16 ND2 ASN D 212 18.551 15.000 19.096 1.00 73.07 N END """ pdb_str_answer = """ CRYST1 19.391 14.196 16.627 90.00 90.00 90.00 P 1 SCALE1 0.051570 0.000000 0.000000 0.00000 SCALE2 0.000000 0.070442 0.000000 0.00000 SCALE3 0.000000 0.000000 0.060143 0.00000 ATOM 1 N ASN A 190 14.391 7.875 10.959 1.00 25.08 N ATOM 2 CA ASN A 190 12.965 7.729 10.710 1.00 25.31 C ATOM 3 C ASN A 190 12.031 8.507 11.627 1.00 25.45 C ATOM 4 O ASN A 190 11.129 9.196 11.149 1.00 24.83 O ATOM 5 CB ASN A 190 12.578 6.250 10.760 1.00 29.15 C ATOM 6 CG ASN A 190 11.141 6.007 10.323 1.00 31.49 C ATOM 7 OD1 ASN A 190 10.633 6.678 9.426 1.00 30.98 O ATOM 8 ND2 ASN A 190 10.478 5.051 10.966 1.00 34.25 N TER ATOM 9 N ASN B 212 7.583 7.891 7.004 1.00 63.62 N ATOM 10 CA ASN B 212 6.962 6.727 6.387 1.00 70.84 C ATOM 11 C ASN B 212 5.525 7.117 6.075 1.00 76.13 C ATOM 12 O ASN B 212 5.000 6.819 5.000 1.00 78.13 O ATOM 13 CB ASN B 212 6.978 5.532 7.341 1.00 71.04 C ATOM 14 CG ASN B 212 8.376 5.163 7.790 1.00 72.56 C ATOM 15 OD1 ASN B 212 8.639 4.999 8.984 1.00 70.76 O ATOM 16 ND2 ASN B 212 9.288 5.039 6.833 1.00 73.07 N TER ATOM 17 N ASN C 190 24.391 17.875 20.959 1.00 25.08 N ATOM 18 CA ASN C 190 22.965 17.729 20.710 1.00 25.31 C ATOM 19 C ASN C 190 22.031 18.507 21.627 1.00 25.45 C ATOM 20 O ASN C 190 21.129 19.196 21.149 1.00 24.83 O ATOM 21 CB ASN C 190 22.578 16.250 20.760 1.00 29.15 C ATOM 22 CG ASN C 190 21.141 16.007 20.323 1.00 31.49 C ATOM 23 OD1 ASN C 190 20.633 16.678 19.426 1.00 30.98 O ATOM 24 ND2 ASN C 190 20.478 15.051 20.966 1.00 34.25 N TER ATOM 25 N ASN D 212 17.583 17.891 17.004 1.00 63.62 N ATOM 26 CA ASN D 212 16.962 16.727 16.387 1.00 70.84 C ATOM 27 C ASN D 212 15.525 17.117 16.075 1.00 76.13 C ATOM 28 O ASN D 212 15.000 16.819 15.000 1.00 78.13 O ATOM 29 CB ASN D 212 16.978 15.532 17.341 1.00 71.04 C ATOM 30 CG ASN D 212 18.376 15.163 17.790 1.00 72.56 C ATOM 31 OD1 ASN D 212 18.639 14.999 18.984 1.00 70.76 O ATOM 32 ND2 ASN D 212 19.288 15.039 16.833 1.00 73.07 N TER END """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) m = mmtbx.model.manager(model_input = pdb_inp) m.flip_nqh() sc_flipped = m.get_sites_cart() sc_orig = iotbx.pdb.input(source_info=None, lines=pdb_str).atoms().extract_xyz() sc_answer = iotbx.pdb.input(source_info=None, lines=pdb_str_answer).atoms().extract_xyz() assert flex.max(flex.sqrt((sc_flipped - sc_answer).dot())) < 0.001 assert flex.max(flex.sqrt((sc_flipped - sc_orig).dot())) > 2.3 def exercise_macromolecule_plus_hetatms_by_chain_selections(): pdb_str = """ CRYST1 29.071 35.014 35.025 90.00 90.00 90.00 P 1 ATOM 0 N GLN A 595 15.775 6.909 5.000 1.00 77.72 N ATOM 1 CA GLN A 595 15.250 6.223 6.187 1.00 77.72 C ATOM 2 C GLN A 595 14.070 5.304 5.864 1.00 77.72 C ATOM 3 O GLN A 595 13.250 5.000 6.737 1.00 77.72 O ATOM 4 CB GLN A 595 14.885 7.217 7.303 1.00 77.72 C ATOM 5 CG GLN A 595 13.621 8.046 7.104 1.00 77.72 C ATOM 6 CD GLN A 595 13.921 9.467 6.669 1.00 77.72 C ATOM 7 OE1 GLN A 595 15.074 9.827 6.433 1.00 77.72 O ATOM 8 NE2 GLN A 595 12.881 10.285 6.561 1.00 77.72 N TER HETATM 9 MG MG A4002 136.594 129.025 155.295 1.00 76.36 Mg TER HETATM 10 P 64T T 21 9.610 14.398 8.714 1.00 78.87 P HETATM 11 OP1 64T T 21 10.939 13.757 9.035 1.00 78.87 O HETATM 12 OP2 64T T 21 9.433 15.199 7.448 1.00 78.87 O HETATM 13 O5' 64T T 21 8.476 13.255 8.731 1.00 78.87 O HETATM 14 C5' 64T T 21 8.535 12.150 7.834 1.00 78.87 C HETATM 15 C4' 64T T 21 9.475 11.087 8.384 1.00 78.87 C HETATM 16 O4' 64T T 21 9.311 10.945 9.798 1.00 78.87 O HETATM 17 C3' 64T T 21 9.192 9.737 7.756 1.00 78.87 C HETATM 18 O3' 64T T 21 10.364 9.248 7.103 1.00 78.87 O HETATM 19 C2' 64T T 21 8.794 8.819 8.892 1.00 78.87 C HETATM 20 C1' 64T T 21 9.189 9.565 10.156 1.00 78.87 C HETATM 21 N1 64T T 21 8.104 9.357 11.105 1.00 78.87 N HETATM 22 C2 64T T 21 8.020 8.233 11.809 1.00 78.87 C HETATM 23 O2 64T T 21 8.605 7.219 11.466 1.00 78.87 O HETATM 24 N3 64T T 21 7.275 8.245 12.907 1.00 78.87 N HETATM 25 C4 64T T 21 6.769 9.387 13.359 1.00 78.87 C HETATM 26 O4 64T T 21 6.720 9.660 14.546 1.00 78.87 O HETATM 27 C5 64T T 21 6.246 10.366 12.344 1.00 78.87 C HETATM 28 C6 64T T 21 7.210 10.501 11.171 1.00 78.87 C HETATM 29 C5M 64T T 21 6.024 11.715 13.011 1.00 78.87 C HETATM 30 O5 64T T 21 5.000 9.880 11.839 1.00 78.87 O TER END """ pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str) m = mmtbx.model.manager(model_input = pdb_inp) sels = m.macromolecule_plus_hetatms_by_chain_selections() sels = [list(s.iselection()) for s in sels] assert len(sels)==3 assert sels[0] == [0, 1, 2, 3, 4, 5, 6, 7, 8] assert sels[1] == [10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28, 29, 30] assert sels[2] == [9] # sels = m.macromolecule_plus_hetatms_by_chain_selections(max_radius=20) sels = [list(s.iselection()) for s in sels] assert len(sels)==2 assert sels[0] == [0, 1, 2, 3, 4, 5, 6, 7, 8] assert sels[1] == [9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28, 29, 30] def exercise_model_filename(): for suffix in ['.pdb', '.cif']: with tempfile.NamedTemporaryFile(dir=os.getcwd(), suffix=suffix) as f: filename = f.name inp = iotbx.pdb.input(file_name=os.path.basename(filename)) m = mmtbx.model.manager(model_input=inp) assert os.path.abspath(filename) == m.get_source_filename() assert os.path.basename(filename) == m.get_source_filename(full_path=False) inp = iotbx.pdb.input(source_info=None, lines=pdb_str_1) m = mmtbx.model.manager(model_input=inp) assert m.get_source_filename() is None if (__name__ == "__main__"): t0 = time.time() exercise_macromolecule_plus_hetatms_by_chain_selections() exercise_ss_creation_crash() exercise_set_b_iso() exercise_convert_to_isotropic() run() exercise_2() exercise_3() exercise_from_sites_cart() exercise_has_hd() exercise_flip_nqh() exercise_model_filename() print("Time: %6.3f"%(time.time()-t0))