from __future__ import absolute_import, division, print_function import sys from six.moves import cStringIO as StringIO from libtbx import easy_run preamble='apply_cif_restraints' files = {"%s.pdb" % preamble : ''' HETATM 1 C01 LIG A 1 -1.100 0.000 -0.436 1.00 20.00 A C HETATM 2 C02 LIG A 1 0.428 0.000 -0.436 1.00 20.00 A C HETATM 3 C03 LIG A 1 1.007 0.000 0.977 1.00 20.00 A C HETATM 4 O04 LIG A 1 1.245 -1.090 1.560 1.00 20.00 A O HETATM 5 O07 LIG A 1 1.245 1.090 1.560 1.00 20.00 A O-1 HETATM 6 H011 LIG A 1 -1.461 -0.885 0.075 1.00 20.00 A H HETATM 7 H012 LIG A 1 -1.461 0.885 0.075 1.00 20.00 A H HETATM 8 H013 LIG A 1 -1.461 0.000 -1.457 1.00 20.00 A H HETATM 9 H021 LIG A 1 0.778 0.881 -0.959 1.00 20.00 A H HETATM 10 H022 LIG A 1 0.778 -0.881 -0.959 1.00 20.00 A H HETATM 1 C01 LIG B 1 9.290 -0.103 -0.646 1.00 20.00 A C HETATM 2 C02 LIG B 1 10.237 -0.103 -0.646 1.00 20.00 A C HETATM 3 C03 LIG B 1 10.816 -0.103 0.767 1.00 20.00 A C HETATM 4 O04 LIG B 1 10.767 -1.086 1.427 1.00 20.00 A O HETATM 5 O05 LIG B 1 11.405 1.058 1.282 1.00 20.00 A O HETATM 6 H011 LIG B 1 9.652 -1.043 -0.246 1.00 20.00 A H HETATM 7 H012 LIG B 1 9.652 0.713 -0.032 1.00 20.00 A H HETATM 8 H013 LIG B 1 9.652 0.020 -1.660 1.00 20.00 A H HETATM 9 H021 LIG B 1 10.588 0.778 -1.169 1.00 20.00 A H HETATM 10 H022 LIG B 1 10.588 -0.985 -1.169 1.00 20.00 A H HETATM 11 H051 LIG B 1 11.846 0.855 2.091 1.00 20.00 A H ''', '%s_01.cif' % preamble : ''' 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 LIG LIG 'Unknown ' ligand 10 5 . # data_comp_LIG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z LIG C01 C CH3 0 . -1.0996 0.0000 -0.4358 LIG C02 C CH2 0 . 0.4275 0.0000 -0.4358 LIG C03 C C 0 . 1.0067 0.0000 0.9772 LIG O04 O O 0 . 1.2453 -1.0903 1.5597 LIG O07 O OC -1 . 1.2454 1.0903 1.5597 LIG H011 H HCH3 0 . -1.4607 -0.8845 0.0748 LIG H012 H HCH3 0 . -1.4607 0.8845 0.0749 LIG H013 H HCH3 0 . -1.4607 0.0000 -1.4572 LIG H021 H HCH2 0 . 0.7784 0.8815 -0.9588 LIG H022 H HCH2 0 . 0.7784 -0.8815 -0.9588 # 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 _chem_comp_bond.value_dist_neutron LIG C02 C01 single 1.527 0.020 1.527 LIG C03 C02 single 1.527 0.020 1.527 LIG O04 C03 deloc 1.259 0.020 1.259 LIG O07 C03 deloc 1.259 0.020 1.259 LIG H011 C01 single 0.970 0.020 1.090 LIG H012 C01 single 0.970 0.020 1.090 LIG H013 C01 single 0.970 0.020 1.090 LIG H021 C02 single 0.970 0.020 1.090 LIG H022 C02 single 0.970 0.020 1.090 # 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 LIG H013 C01 H012 109.47 3.000 LIG H013 C01 H011 109.47 3.000 LIG H012 C01 H011 109.47 3.000 LIG H013 C01 C02 109.47 3.000 LIG H012 C01 C02 109.47 3.000 LIG H011 C01 C02 109.47 3.000 LIG H022 C02 H021 108.92 3.000 LIG H022 C02 C03 108.90 3.000 LIG H021 C02 C03 108.90 3.000 LIG H022 C02 C01 108.90 3.000 LIG H021 C02 C01 108.90 3.000 LIG C03 C02 C01 112.29 3.000 LIG O07 C03 O04 120.00 3.000 LIG O07 C03 C02 120.00 3.000 LIG O04 C03 C02 120.00 3.000 # 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 LIG Var_01 O04 C03 C02 C01 90.00 30.0 2 LIG Var_02 H011 C01 C02 C03 -60.00 30.0 3 ''', '%s_02.cif' % preamble : ''' 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 LIG LIG 'Unknown ' ligand 11 5 . # data_comp_LIG # loop_ _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.type_symbol _chem_comp_atom.type_energy _chem_comp_atom.charge _chem_comp_atom.partial_charge _chem_comp_atom.x _chem_comp_atom.y _chem_comp_atom.z LIG C01 C CH3 0 . -1.2904 -0.1034 -0.6460 LIG C02 C CH2 0 . 0.2367 -0.1034 -0.6460 LIG C03 C C 0 . 0.8158 -0.1034 0.7671 LIG O04 O O 0 . 0.7666 -1.0857 1.4274 LIG O05 O OH1 0 . 1.4049 1.0580 1.2825 LIG H011 H HCH3 0 . -1.6516 -1.0432 -0.2460 LIG H012 H HCH3 0 . -1.6516 0.7129 -0.0321 LIG H013 H HCH3 0 . -1.6515 0.0201 -1.6598 LIG H021 H HCH2 0 . 0.5875 0.7781 -1.1689 LIG H022 H HCH2 0 . 0.5875 -0.9849 -1.1689 LIG H051 H HOH1 0 . 1.8459 0.8548 2.0907 # 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 _chem_comp_bond.value_dist_neutron LIG C02 C01 single 1.527 0.020 1.527 LIG C03 C02 single 1.527 0.020 1.527 LIG O04 C03 double 1.185 0.020 1.185 LIG O05 C03 single 1.401 0.020 1.401 LIG H011 C01 single 0.970 0.020 1.090 LIG H012 C01 single 0.970 0.020 1.090 LIG H013 C01 single 0.970 0.020 1.090 LIG H021 C02 single 0.970 0.020 1.090 LIG H022 C02 single 0.970 0.020 1.090 LIG H051 O05 single 0.850 0.020 0.980 # 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 LIG H013 C01 H012 109.47 3.000 LIG H013 C01 H011 109.47 3.000 LIG H012 C01 H011 109.47 3.000 LIG H013 C01 C02 109.47 3.000 LIG H012 C01 C02 109.47 3.000 LIG H011 C01 C02 109.47 3.000 LIG H022 C02 H021 108.92 3.000 LIG H022 C02 C03 108.90 3.000 LIG H021 C02 C03 108.90 3.000 LIG H022 C02 C01 108.90 3.000 LIG H021 C02 C01 108.90 3.000 LIG C03 C02 C01 112.29 3.000 LIG O05 C03 O04 120.00 3.000 LIG O05 C03 C02 120.00 3.000 LIG O04 C03 C02 120.00 3.000 LIG H051 O05 C03 109.48 3.000 # 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 LIG CONST_01 H051 O05 C03 C02 -169.90 0.0 0 LIG Var_01 O04 C03 C02 C01 73.23 30.0 2 LIG Var_02 H011 C01 C02 C03 -66.94 30.0 3 # 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 LIG plan-1 C02 0.020 LIG plan-1 C03 0.020 LIG plan-1 O04 0.020 LIG plan-1 O05 0.020 LIG plan-1 H051 0.020 ''', '%s.eff' % preamble : ''' pdb_interpretation { apply_cif_restraints { restraints_file_name=%s_02.cif residue_selection="chain B and resname LIG" } } ''' % preamble, } def run(): for name, text in files.items(): f=open(name, 'w') f.write(text) f.close() cmd = 'phenix.geometry_minimization %(preamble)s.pdb %(preamble)s_01.cif' % {'preamble' : preamble} print(cmd) ero = easy_run.fully_buffered(command=cmd) err = StringIO() ero.show_stderr(out=err) assert err.getvalue() print('ok') cmd += ' %(preamble)s.eff' % {'preamble' : preamble} print(cmd) ero = easy_run.fully_buffered(command=cmd) err = StringIO() ero.show_stderr(out=err) assert not err.getvalue() print('ok') return err.getvalue() if __name__=="__main__": run()#sys.argv[1])