from __future__ import absolute_import, division, print_function import libtbx.load_env from libtbx import easy_run from libtbx.test_utils import assert_lines_in_file pdb_str = """\ ATOM 1 N SER 1 71 10.595 29.158 114.534 1.00300.00 N ATOM 2 CA SER 1 71 10.156 30.582 114.477 1.00300.00 C ATOM 3 C SER 1 71 11.003 31.474 115.392 1.00300.00 C ATOM 4 O SER 1 71 10.892 31.400 116.622 1.00300.00 O """ # ------------------------------------------------------------------------------ cif_str = """\ data_default loop_ _atom_site.group_PDB _atom_site.id _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.auth_asym_id _atom_site.auth_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.type_symbol _atom_site.pdbx_formal_charge _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_model_num ATOM 1 N . PRO H 14 ? 5.39400 6.71500 9.04100 1.000 20.43000 N ? A ? 1 1 ATOM 2 CA . PRO H 14 ? 6.20600 7.23200 10.14700 1.000 20.01000 C ? A ? 1 1 ATOM 3 C . PRO H 14 ? 7.24800 8.27800 9.73800 1.000 20.76000 C ? A ? 1 1 ATOM 4 O . PRO H 14 ? 7.79100 8.23500 8.63500 1.000 16.34000 O ? A ? 1 1 """ # ------------------------------------------------------------------------------ def exercise(prefix="tst_pdb_box_around_mol"): # test pdb format with open("%s.pdb" % prefix, 'w') as f: f.write(pdb_str) assert not easy_run.call("iotbx.pdb.box_around_molecule %s.pdb" % ( prefix)) assert_lines_in_file(file_name="%s_box_000.pdb" % prefix, lines="""\ CRYST1 10.847 12.316 12.145 90.00 90.00 90.00 P 1 SCALE1 0.092191 0.000000 0.000000 0.00000 SCALE2 0.000000 0.081195 0.000000 0.00000 SCALE3 0.000000 0.000000 0.082338 0.00000 ATOM 1 N SER 1 71 5.439 5.000 5.057 1.00300.00 N ATOM 2 CA SER 1 71 5.000 6.424 5.000 1.00300.00 C ATOM 3 C SER 1 71 5.847 7.316 5.915 1.00300.00 C ATOM 4 O SER 1 71 5.736 7.242 7.145 1.00300.00 O TER""") # test mmcif format if libtbx.env.find_in_repositories(relative_path='chem_data') is not None: with open("%s.cif" % prefix, 'w') as f: f.write(cif_str) assert not easy_run.call("iotbx.pdb.box_around_molecule %s.cif" % ( prefix)) # XXX temp fix for python3 failure # XXX changes in python 3 because _cell.length_a and other order differs # Python 3 behavior looks better. # Reason for this discrepancy is that starting from Python 3.7 # "the insertion-order preservation nature of dict objects has been # declared to be an official part of the Python language spec." # https://docs.python.org/3/whatsnew/3.7.html # Basically, dict.keys() in Py3 preserves the order in which keys were added # to the dict. # # Sorting of mmCIF keys here # cctbx_project/iotbx/cif/__init__.py, def category_sort_function() # should be improved to address such issues universally (sorting within # category), note the diference in _space_group and _symmetry categories # as well. import sys if sys.version_info.major == 3: assert_lines_in_file(file_name="%s_box_000.cif" % prefix, lines="""\ data_default _cell.length_a 12.397 _cell.length_b 11.563 _cell.length_c 11.512 _cell.angle_alpha 90.000 _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.volume 1650.205 _space_group.crystal_system triclinic _space_group.IT_number 1 _space_group.name_H-M_alt 'P 1' _space_group.name_Hall ' P 1' _symmetry.space_group_name_H-M 'P 1' _symmetry.space_group_name_Hall ' P 1' _symmetry.Int_Tables_number 1 loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z""") else: # version 2.7 assert_lines_in_file(file_name="%s_box_000.cif" % prefix, lines="""\ data_default _cell.angle_beta 90.000 _cell.angle_gamma 90.000 _cell.length_b 11.563 _cell.length_c 11.512 _cell.angle_alpha 90.000 _cell.volume 1650.205 _cell.length_a 12.397 _space_group.crystal_system triclinic _space_group.name_H-M_alt 'P 1' _space_group.IT_number 1 _space_group.name_Hall ' P 1' _symmetry.space_group_name_H-M 'P 1' _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ' P 1' loop_ _space_group_symop.id _space_group_symop.operation_xyz 1 x,y,z""") else: print('chem_data is not available, skipping') print("OK") # ------------------------------------------------------------------------------ if __name__=="__main__": exercise()