from __future__ import absolute_import, division, print_function import iotbx.pdb import mmtbx.utils import mmtbx.model from libtbx.utils import null_out pdb = """ CRYST1 31.000 18.000 43.000 90.00 90.00 90.00 P 2 21 21 HETATM 1 C24 8ZB C 1 -11.000 13.211 10.894 1.00 30.00 C HETATM 2 C28 8ZB C 1 -11.000 11.722 10.295 1.00 30.00 C HETATM 3 C31 8ZB C 1 -10.000 11.074 10.706 1.00 30.00 C HETATM 4 C36 8ZB C 1 -10.000 19.626 10.001 1.00 30.00 C HETATM 5 C38 8ZB C 1 -8.000 18.259 10.474 1.00 30.00 C HETATM 6 C39 8ZB C 1 -8.000 18.457 10.949 1.00 30.00 C HETATM 7 C40 8ZB C 1 -9.000 19.327 10.279 1.00 30.00 C HETATM 8 C49 8ZB C 1 -6.000 19.546 10.455 1.00 30.00 C HETATM 9 C50 8ZB C 1 -6.000 18.069 10.155 1.00 30.00 C HETATM 10 C51 8ZB C 1 -7.000 17.489 10.934 1.00 30.00 C HETATM 11 C53 8ZB C 1 -6.000 15.539 10.000 1.00 30.00 C HETATM 12 C55 8ZB C 1 -5.000 17.242 10.321 1.00 30.00 C HETATM 13 N47 8ZB C 1 -7.000 18.437 10.617 1.00 30.00 N HETATM 14 N48 8ZB C 1 -5.000 19.513 10.551 1.00 30.00 N HETATM 15 N52 8ZB C 1 -7.000 16.248 10.879 1.00 30.00 N HETATM 16 N54 8ZB C 1 -5.000 15.993 10.237 1.00 30.00 N HETATM 17 N57 8ZB C 1 -4.000 17.770 10.517 1.00 30.00 N HETATM 18 O37 8ZB C 1 -9.000 19.010 10.951 1.00 30.00 O HETATM 19 O41 8ZB C 1 -7.000 18.355 10.894 1.00 30.00 O HETATM 20 O42 8ZB C 1 -10.000 18.384 10.923 1.00 30.00 O TER END """ cif = """ data_comp_list # # # # # loop_ _chem_comp.id _chem_comp.three_letter_code _chem_comp.name _chem_comp.group _chem_comp.number_atoms_all _chem_comp.number_atoms_nh _chem_comp.desc_level 8ZB 8ZB '_2__R_,3__R_,4__S_,5__R__-2-_6-aminopurin-9-yl_-5-propyl-oxolane-3,4-diol' non-polymer 37 20 . data_comp_8ZB loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z 8ZB C24 C CH3 -0.065 5.193 -2.668 -0.514 8ZB C28 C CH2 -0.054 4.269 -1.547 -0.941 8ZB C31 C CH2 -0.024 3.677 -0.800 0.239 8ZB C36 C CH1 0.090 2.849 0.415 -0.131 8ZB C38 C CH1 0.167 0.586 0.822 -0.595 8ZB C39 C CH1 0.128 1.070 1.901 0.383 8ZB C40 C CH1 0.111 2.276 1.217 1.029 8ZB C49 C CR16 0.100 -0.400 -1.049 0.802 8ZB C50 C CR6 0.147 -2.470 -0.881 0.363 8ZB C51 C CR6 0.167 -1.837 0.107 -0.374 8ZB C53 C CR16 0.120 -3.743 0.809 -1.235 8ZB C55 C CR6 0.147 -3.871 -0.970 0.239 8ZB N47 N NR6 -0.285 -0.499 -0.007 -0.082 8ZB N48 N NRD6 -0.231 -1.549 -1.607 1.103 8ZB N52 N NRD6 -0.216 -2.419 0.988 -1.196 8ZB N54 N NRD6 -0.219 -4.486 -0.092 -0.584 8ZB N57 N NH2 -0.341 -4.618 -1.871 0.885 8ZB O37 O O2 -0.348 1.695 -0.016 -0.883 8ZB O41 O OH1 -0.385 1.438 3.076 -0.331 8ZB O42 O OH1 -0.387 3.232 2.149 1.524 8ZB H2 H HCH3 0.023 6.163 -2.277 -0.210 8ZB H1 H HCH3 0.023 4.799 -3.242 0.324 8ZB H29 H HCH3 0.023 5.383 -3.375 -1.320 8ZB H28 H HCH2 0.026 4.777 -0.858 -1.614 8ZB H33 H HCH2 0.026 3.458 -1.960 -1.539 8ZB H35 H HCH2 0.029 3.085 -1.495 0.832 8ZB H31 H HCH2 0.029 4.465 -0.458 0.907 8ZB H61 H HCH1 0.062 3.420 1.059 -0.799 8ZB H62 H HCH1 0.087 0.266 1.231 -1.553 8ZB H44 H HCH1 0.067 0.317 2.156 1.128 8ZB H43 H HCH1 0.065 1.967 0.592 1.865 8ZB H58 H HCR 0.103 0.549 -1.387 1.216 8ZB H56 H HCR 0.105 -4.305 1.478 -1.885 8ZB H60 H HNH2 0.144 -4.185 -2.546 1.507 8ZB H59 H HNH2 0.144 -5.627 -1.913 0.779 8ZB H46 H HOH1 0.210 0.856 3.798 0.026 8ZB H45 H HOH1 0.210 2.872 2.596 2.335 loop_ _chem_comp_bond.comp_id _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.type _chem_comp_bond.value_dist _chem_comp_bond.value_dist_esd 8ZB C24 C28 single 1.513 0.038 8ZB C24 H1 single 1.089 0.010 8ZB C24 H2 single 1.089 0.010 8ZB C24 H29 single 1.089 0.010 8ZB C28 C31 single 1.516 0.024 8ZB C28 H28 single 1.089 0.010 8ZB C28 H33 single 1.089 0.010 8ZB C31 C36 single 1.516 0.013 8ZB C31 H31 single 1.089 0.010 8ZB C31 H35 single 1.089 0.010 8ZB C36 C40 single 1.526 0.013 8ZB C36 H61 single 1.089 0.010 8ZB C36 O37 single 1.444 0.011 8ZB C38 C39 single 1.531 0.014 8ZB C38 H62 single 1.089 0.010 8ZB C38 N47 single 1.459 0.012 8ZB C38 O37 single 1.416 0.011 8ZB C39 C40 single 1.531 0.013 8ZB C39 H44 single 1.089 0.010 8ZB C39 O41 single 1.423 0.012 8ZB C40 H43 single 1.089 0.010 8ZB C40 O42 single 1.423 0.012 8ZB C49 H58 single 1.089 0.010 8ZB C49 N47 aromatic 1.370 0.008 8ZB C49 N48 aromatic 1.311 0.008 8ZB C50 C51 aromatic 1.388 0.011 8ZB C50 C55 aromatic 1.409 0.010 8ZB C50 N48 aromatic 1.387 0.007 8ZB C51 N47 aromatic 1.374 0.008 8ZB C51 N52 aromatic 1.338 0.012 8ZB C53 H56 single 1.089 0.010 8ZB C53 N52 aromatic 1.334 0.011 8ZB C53 N54 aromatic 1.334 0.011 8ZB C55 N54 aromatic 1.350 0.010 8ZB C55 N57 single 1.337 0.014 8ZB N57 H59 single 1.015 0.010 8ZB N57 H60 single 1.015 0.010 8ZB O41 H46 single 0.993 0.010 8ZB O42 H45 single 0.993 0.010 loop_ _chem_comp_angle.comp_id _chem_comp_angle.atom_id_1 _chem_comp_angle.atom_id_2 _chem_comp_angle.atom_id_3 _chem_comp_angle.value_angle _chem_comp_angle.value_angle_esd 8ZB C28 C24 H1 112.7 3.0 8ZB C28 C24 H2 110.9 3.0 8ZB H1 C24 H2 107.3 3.0 8ZB C28 C24 H29 112.1 3.0 8ZB H1 C24 H29 106.8 3.0 8ZB H2 C24 H29 106.6 3.0 8ZB C24 C28 C31 112.7 1.9 8ZB C24 C28 H28 110.8 3.0 8ZB C31 C28 H28 110.5 3.0 8ZB C24 C28 H33 109.3 3.0 8ZB C31 C28 H33 109.0 3.0 8ZB H28 C28 H33 104.4 3.0 8ZB C28 C31 C36 114.6 1.8 8ZB C28 C31 H31 110.5 3.0 8ZB C36 C31 H31 107.1 3.0 8ZB C28 C31 H35 108.9 3.0 8ZB C36 C31 H35 110.4 3.0 8ZB H31 C31 H35 105.2 3.0 8ZB C31 C36 C40 116.2 1.2 8ZB C31 C36 H61 109.6 3.0 8ZB C40 C36 H61 110.7 3.0 8ZB C31 C36 O37 108.8 1.1 8ZB C40 C36 O37 105.2 1.3 8ZB H61 C36 O37 106.3 3.0 8ZB C39 C38 H62 113.0 3.0 8ZB C39 C38 N47 114.2 1.5 8ZB H62 C38 N47 107.6 3.0 8ZB C39 C38 O37 106.5 1.2 8ZB H62 C38 O37 105.9 3.0 8ZB N47 C38 O37 108.3 1.3 8ZB C38 C39 C40 101.5 1.2 8ZB C38 C39 H44 112.9 3.0 8ZB C40 C39 H44 111.5 3.0 8ZB C38 C39 O41 110.5 2.8 8ZB C40 C39 O41 111.9 2.7 8ZB H44 C39 O41 109.4 3.0 8ZB C36 C40 C39 102.5 1.0 8ZB C36 C40 H43 113.0 3.0 8ZB C39 C40 H43 111.0 3.0 8ZB C36 C40 O42 111.0 2.5 8ZB C39 C40 O42 111.9 2.7 8ZB H43 C40 O42 107.5 3.0 8ZB H58 C49 N47 122.9 3.0 8ZB H58 C49 N48 123.1 3.0 8ZB N47 C49 N48 114.1 0.7 8ZB C51 C50 C55 117.0 0.6 8ZB C51 C50 N48 110.7 0.5 8ZB C55 C50 N48 132.1 1.2 8ZB C50 C51 N47 105.8 0.5 8ZB C50 C51 N52 126.8 0.7 8ZB N47 C51 N52 127.0 1.1 8ZB H56 C53 N52 116.3 3.0 8ZB H56 C53 N54 114.9 3.0 8ZB N52 C53 N54 128.7 0.9 8ZB C50 C55 N54 117.6 1.0 8ZB C50 C55 N57 123.5 1.1 8ZB N54 C55 N57 118.2 1.2 8ZB C38 N47 C49 126.8 1.9 8ZB C38 N47 C51 126.8 1.8 8ZB C49 N47 C51 105.7 0.5 8ZB C49 N48 C50 103.7 0.5 8ZB C51 N52 C53 111.9 2.2 8ZB C53 N54 C55 118.6 1.0 8ZB C55 N57 H59 122.2 3.0 8ZB C55 N57 H60 120.4 3.0 8ZB H59 N57 H60 117.3 3.0 8ZB C36 O37 C38 109.4 1.6 8ZB C39 O41 H46 105.4 3.0 8ZB C40 O42 H45 109.5 3.0 loop_ _chem_comp_chir.comp_id _chem_comp_chir.id _chem_comp_chir.atom_id_centre _chem_comp_chir.atom_id_1 _chem_comp_chir.atom_id_2 _chem_comp_chir.atom_id_3 _chem_comp_chir.volume_sign 8ZB chir_04 C36 O37 C40 C31 negative 8ZB chir_05 C38 O37 N47 C39 negative 8ZB chir_06 C39 O41 C40 C38 positive 8ZB chir_07 C40 O42 C39 C36 negative loop_ _chem_comp_plane_atom.comp_id _chem_comp_plane_atom.plane_id _chem_comp_plane_atom.atom_id _chem_comp_plane_atom.dist_esd 8ZB csd-C50 C50 0.020 8ZB csd-C50 C51 0.020 8ZB csd-C50 C55 0.020 8ZB csd-C50 N48 0.020 8ZB csd-C51 C51 0.020 8ZB csd-C51 C50 0.020 8ZB csd-C51 N47 0.020 8ZB csd-C51 N52 0.020 8ZB csd-C55 C55 0.020 8ZB csd-C55 C50 0.020 8ZB csd-C55 N54 0.020 8ZB csd-C55 N57 0.020 8ZB csd-N47 N47 0.020 8ZB csd-N47 C38 0.020 8ZB csd-N47 C49 0.020 8ZB csd-N47 C51 0.020 8ZB qm-C49 C49 0.020 8ZB qm-C49 N47 0.020 8ZB qm-C49 N48 0.020 8ZB qm-C49 H58 0.020 8ZB qm-C53 C53 0.020 8ZB qm-C53 N52 0.020 8ZB qm-C53 N54 0.020 8ZB qm-C53 H56 0.020 8ZB qm-N57 N57 0.020 8ZB qm-N57 C55 0.020 8ZB qm-N57 H59 0.020 8ZB qm-N57 H60 0.020 8ZB qmf-01 C50 0.020 8ZB qmf-01 C55 0.020 8ZB qmf-01 N57 0.020 8ZB qmf-01 H59 0.020 8ZB ring5A-1 C49 0.020 8ZB ring5A-1 N47 0.020 8ZB ring5A-1 C51 0.020 8ZB ring5A-1 C50 0.020 8ZB ring5A-2 N47 0.020 8ZB ring5A-2 C51 0.020 8ZB ring5A-2 C50 0.020 8ZB ring5A-2 N48 0.020 8ZB ring5A-3 C51 0.020 8ZB ring5A-3 C50 0.020 8ZB ring5A-3 N48 0.020 8ZB ring5A-3 C49 0.020 8ZB ring5A-4 C50 0.020 8ZB ring5A-4 N48 0.020 8ZB ring5A-4 C49 0.020 8ZB ring5A-4 N47 0.020 8ZB ring5A-5 N48 0.020 8ZB ring5A-5 C49 0.020 8ZB ring5A-5 N47 0.020 8ZB ring5A-5 C51 0.020 8ZB ring6A-1 C50 0.020 8ZB ring6A-1 C51 0.020 8ZB ring6A-1 N52 0.020 8ZB ring6A-1 C53 0.020 8ZB ring6A-2 C51 0.020 8ZB ring6A-2 N52 0.020 8ZB ring6A-2 C53 0.020 8ZB ring6A-2 N54 0.020 8ZB ring6A-3 N52 0.020 8ZB ring6A-3 C53 0.020 8ZB ring6A-3 N54 0.020 8ZB ring6A-3 C55 0.020 8ZB ring6A-4 C53 0.020 8ZB ring6A-4 N54 0.020 8ZB ring6A-4 C55 0.020 8ZB ring6A-4 C50 0.020 8ZB ring6A-5 N54 0.020 8ZB ring6A-5 C55 0.020 8ZB ring6A-5 C50 0.020 8ZB ring6A-5 C51 0.020 8ZB ring6A-6 C55 0.020 8ZB ring6A-6 C50 0.020 8ZB ring6A-6 C51 0.020 8ZB ring6A-6 N52 0.020 loop_ _chem_comp_tor.comp_id _chem_comp_tor.id _chem_comp_tor.atom_id_1 _chem_comp_tor.atom_id_2 _chem_comp_tor.atom_id_3 _chem_comp_tor.atom_id_4 _chem_comp_tor.value_angle _chem_comp_tor.value_angle_esd _chem_comp_tor.period 8ZB other-001 H1 C24 C28 C31 0.0 1000000.0 10 8ZB csd-sp3sp3-01 C24 C28 C31 C36 180.0 12.3 3 8ZB csd-sp3sp3-02 C28 C31 C36 C40 180.0 12.3 3 8ZB other-002 C31 C36 C40 C39 0.0 1000000.0 10 8ZB other-003 C31 C36 O37 C38 0.0 1000000.0 10 8ZB other-004 N47 C38 C39 C40 0.0 1000000.0 10 8ZB other-005 C39 C38 N47 C49 0.0 1000000.0 10 8ZB other-006 C39 C38 O37 C36 0.0 1000000.0 10 8ZB other-007 C38 C39 C40 C36 0.0 1000000.0 10 8ZB other-008 C38 C39 O41 H46 0.0 1000000.0 10 8ZB other-009 C36 C40 O42 H45 0.0 1000000.0 10 8ZB CONST_ring5A-5 N48 C49 N47 C51 0.0 1000000.0 0 8ZB CONST_ring5A-4 N47 C49 N48 C50 0.0 1000000.0 0 8ZB CONST_ring6A-6 C55 C50 C51 N52 0.0 1000000.0 0 8ZB CONST_ring6A-5 C51 C50 C55 N54 0.0 1000000.0 0 8ZB CONST_ring5A-3 C51 C50 N48 C49 0.0 1000000.0 0 8ZB CONST_ring5A-1 C50 C51 N47 C49 0.0 1000000.0 0 8ZB CONST_ring6A-1 C50 C51 N52 C53 0.0 1000000.0 0 8ZB CONST_ring6A-2 N54 C53 N52 C51 0.0 1000000.0 0 8ZB CONST_ring6A-3 N52 C53 N54 C55 0.0 1000000.0 0 8ZB CONST_ring6A-4 C50 C55 N54 C53 0.0 1000000.0 0 8ZB qmf-01 C50 C55 N57 H59 180.0 1000000.0 2 # # """ def run(prefix = "tst_model_get_vdw_radii"): fo = open("%s.pdb"%prefix,"w") print(pdb, file=fo) fo.close() fo = open("%s.cif"%prefix,"w") print(cif, file=fo) fo.close() # i = mmtbx.utils.process_command_line_args(args = ["%s.cif"%prefix]) pdb_inp = iotbx.pdb.input(file_name = "%s.pdb"%prefix) model = mmtbx.model.manager( model_input = pdb_inp, restraint_objects = i.cif_objects, log = null_out()) model.process() derived_keys = model.get_vdw_radii() # compare with answer for atom_name in pdb_inp.atoms().extract_name(): assert atom_name.strip() in derived_keys if (__name__ == "__main__"): run()