from __future__ import absolute_import, division, print_function import sys from libtbx import easy_run from libtbx.test_utils import assert_lines_in_file from iotbx.pdb import pdb_input from mmtbx.hydrogens.specialised_hydrogen_atoms import add_side_chain_acid_hydrogens from mmtbx.hydrogens.specialised_hydrogen_atoms import add_disulfur_hydrogen_atoms pdb_strings = {'ASP' :''' CRYST1 112.354 50.667 75.061 90.00 127.09 90.00 C 1 2 1 SCALE1 0.008900 0.000000 0.006729 0.00000 SCALE2 0.000000 0.019737 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016701 0.00000 ATOM 1 OE1 GLU A 249 23.084 -14.146 55.991 1.00 28.06 O ATOM 2 OD2 ASP A 258 20.555 -12.607 61.969 1.00 37.35 O ATOM 3 CA ASN A 269 25.385 -16.651 56.738 1.00 15.81 C ATOM 4 C ASN A 269 24.892 -16.548 58.188 1.00 15.44 C ATOM 5 O ASN A 269 25.355 -17.281 59.072 1.00 15.27 O ATOM 6 ND2 ASN A 269 23.311 -19.122 57.209 1.00 18.88 N ATOM 7 N ASP A 270 23.952 -15.610 58.412 1.00 18.53 N ATOM 8 CA ASP A 270 23.251 -15.460 59.662 1.00 19.81 C ATOM 9 C ASP A 270 22.320 -16.673 59.865 1.00 17.50 C ATOM 10 O ASP A 270 21.839 -17.297 58.893 1.00 18.62 O ATOM 11 CB ASP A 270 22.308 -14.226 59.624 1.00 25.44 C ATOM 12 CG ASP A 270 22.950 -13.023 59.939 1.00 30.80 C ATOM 13 OD1 ASP A 270 24.170 -12.930 59.713 1.00 37.22 O ATOM 14 OD2 ASP A 270 22.211 -12.121 60.434 1.00 33.61 O ATOM 15 N ALA A 271 22.030 -16.956 61.120 1.00 15.85 N ATOM 16 CA ALA A 271 21.096 -17.989 61.489 1.00 16.38 C ''', 'GLU' : ''' CRYST1 39.183 52.539 207.533 90.00 90.00 90.00 P 21 21 21 SCALE1 0.025521 0.000000 0.000000 0.00000 SCALE2 0.000000 0.019033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004819 0.00000 ATOM 3 N TRP A 194 -7.810 10.259 62.633 1.00 9.35 N ATOM 4 CA TRP A 194 -8.280 11.585 62.268 1.00 8.84 C ATOM 5 C TRP A 194 -9.778 11.593 61.945 1.00 8.77 C ATOM 6 O TRP A 194 -10.269 10.714 61.243 1.00 8.79 O ATOM 7 CB TRP A 194 -7.513 12.112 61.045 1.00 9.05 C ATOM 8 CG TRP A 194 -6.007 12.290 61.215 1.00 8.60 C ATOM 9 N GLU A 195 -10.509 12.592 62.436 1.00 8.58 N ATOM 10 CA GLU A 195 -11.870 12.816 61.951 1.00 8.31 C ATOM 11 C GLU A 195 -11.832 13.095 60.469 1.00 7.49 C ATOM 12 O GLU A 195 -12.710 12.683 59.735 1.00 7.68 O ATOM 13 CB GLU A 195 -12.550 13.986 62.659 1.00 8.68 C ATOM 14 CG GLU A 195 -12.799 13.775 64.152 1.00 11.46 C ATOM 15 CD GLU A 195 -14.045 14.499 64.657 1.00 12.48 C ATOM 16 OE1 GLU A 195 -14.622 15.293 63.883 1.00 11.73 O ATOM 17 OE2 GLU A 195 -14.441 14.257 65.826 1.00 12.64 O ATOM 18 N ARG A 196 -10.811 13.811 60.021 1.00 7.15 N ATOM 19 CA ARG A 196 -10.703 14.129 58.605 1.00 6.38 C ATOM 20 C ARG A 196 -9.350 13.639 58.107 1.00 6.27 C ATOM 21 O ARG A 196 -8.343 14.350 58.179 1.00 6.00 O ATOM 22 CB ARG A 196 -10.981 15.619 58.367 1.00 6.18 C ATOM 23 CG ARG A 196 -12.144 16.088 59.223 1.00 4.12 C ATOM 24 CD ARG A 196 -12.782 17.328 58.735 1.00 3.90 C ATOM 25 N PRO A 197 -9.326 12.382 57.633 1.00 6.31 N ATOM 26 CG PRO A 197 -10.015 10.265 56.861 1.00 5.41 C ATOM 27 CD PRO A 197 -10.537 11.559 57.405 1.00 5.91 C TER HETATM 49 O5 CIT A 500 -11.052 16.238 62.773 0.75 26.13 O HETATM 52 O HOH A 512 -14.767 12.104 68.190 1.00 29.69 O ''', 'CYS_1' : ''' CRYST1 61.314 37.470 44.915 90.00 94.55 90.00 P 1 21 1 SCALE1 0.016309 0.000000 0.001298 0.00000 SCALE2 0.000000 0.026688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022335 0.00000 ATOM 8 N CYS A 26 21.129 -6.109 34.429 1.00 4.21 N ATOM 9 CA CYS A 26 20.061 -5.459 33.689 1.00 4.17 C ATOM 10 C CYS A 26 18.827 -6.331 33.559 1.00 4.48 C ATOM 11 O CYS A 26 17.694 -5.822 33.620 1.00 4.91 O ATOM 12 CB CYS A 26 20.554 -5.076 32.290 1.00 4.37 C ATOM 13 SG CYS A 26 21.811 -3.780 32.291 1.00 4.75 S ATOM 14 H CYS A 26 21.889 -6.315 34.036 1.00 5.05 H ATOM 15 HA CYS A 26 19.806 -4.622 34.173 1.00 5.01 H ATOM 16 HB2 CYS A 26 20.927 -5.881 31.852 1.00 5.24 H ATOM 17 HB3 CYS A 26 19.782 -4.771 31.752 1.00 5.24 H ATOM 18 N ASN A 27 19.008 -7.633 33.365 1.00 4.35 N ATOM 19 CA ASN A 27 17.845 -8.529 33.284 1.00 4.69 C ATOM 20 C ASN A 27 16.993 -8.399 34.537 1.00 5.07 C ATOM 28 CB CYS A 84 20.151 -1.930 30.554 1.00 5.45 C ATOM 29 SG CYS A 84 20.664 -2.084 32.297 1.00 5.40 S ''', 'CYS_2' : ''' CRYST1 61.314 37.470 44.915 90.00 94.55 90.00 P 1 21 1 SCALE1 0.016309 0.000000 0.001298 0.00000 SCALE2 0.000000 0.026688 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022335 0.00000 ATOM 8 N CYS A 26 21.129 -6.109 34.429 1.00 4.21 N ATOM 9 CA CYS A 26 20.061 -5.459 33.689 1.00 4.17 C ATOM 10 C CYS A 26 18.827 -6.331 33.559 1.00 4.48 C ATOM 11 O CYS A 26 17.694 -5.822 33.620 1.00 4.91 O ATOM 12 CB CYS A 26 20.554 -5.076 32.290 1.00 4.37 C ATOM 13 SG CYS A 26 21.811 -3.780 32.291 1.00 4.75 S ATOM 14 H CYS A 26 21.889 -6.315 34.036 1.00 5.05 H ATOM 15 HA CYS A 26 19.806 -4.622 34.173 1.00 5.01 H ATOM 16 HB2 CYS A 26 20.927 -5.881 31.852 1.00 5.24 H ATOM 17 HB3 CYS A 26 19.782 -4.771 31.752 1.00 5.24 H ''', } for key, item in list(pdb_strings.items()): pdb_strings[key+'_D'] = item geo_strings = {'ASP' : {0 : '''nonbonded pdb=" OD2 ASP A 258 " pdb=" HD2 ASP A 270 " model vdw 1.612 1.970''', 1 : '''nonbonded pdb=" OD2 ASP A 258 " pdb=" HD2 ASP A 270 " model vdw 2.750 1.970''', 2 : '''nonbonded pdb=" N ASP A 270 " pdb=" HD2 ASP A 270 " model vdw 2.262 2.650''', 3 : '''nonbonded pdb=" OD1 ASP A 270 " pdb=" HD2 ASP A 270 " model vdw 2.475 2.056''', }, 'ASP_D' : { 0 : '''nonbonded pdb=" OD2 ASP A 258 " pdb=" DD2 ASP A 270 " model vdw 1.583 1.970''', 1 : '''nonbonded pdb=" OD2 ASP A 258 " pdb=" OD2 ASP A 270 " model vdw 2.310 3.040''', 2 : '''nonbonded pdb=" N ASP A 270 " pdb=" DD2 ASP A 270 " model vdw 2.228 2.650''', 3 : '''nonbonded pdb=" N ASP A 270 " pdb=" DD2 ASP A 270 " model vdw 3.904 2.650''', }, 'GLU' : { 0 : '''nonbonded pdb=" HE2 GLU A 195 " pdb=" O HOH A 512 " model vdw 2.511 1.970''', 1 : '''nonbonded pdb=" HE2 GLU A 195 " pdb=" O HOH A 512 " model vdw 3.316 1.970''', 2 : '''nonbonded pdb=" HE2 GLU A 195 " pdb=" O5 CIT A 500 " model vdw 3.338 1.970''', 3 : '''nonbonded pdb=" HE2 GLU A 195 " pdb=" O5 CIT A 500 " model vdw 4.592 1.970''', }, 'CYS_2' : '''bond pdb=" SG CYS A 26 " pdb=" HG CYS A 26 " ideal model delta sigma weight residual 1.200 1.200 0.000 2.00e-02 2.50e+03 3.33e-04''', 'CYS_2_D' : '''bond pdb=" SG CYS A 26 " pdb=" DG CYS A 26 " ideal model delta sigma weight residual 1.200 1.200 0.000 2.00e-02 2.50e+03 3.33e-04''', } def tst_adding_side_chain_acid_hydrogen_atoms(switch): element='H' if switch.endswith('_D'): element='D' for i in range(4): fn = 'tst_ready_hydrogens_%s_%d.pdb' % (switch, i) with open(fn, 'w') as f: f.write(pdb_strings[switch]) pdb_inp = pdb_input(fn) hierarchy = pdb_inp.construct_hierarchy() add_side_chain_acid_hydrogens(hierarchy, configuration_index=i, element=element) hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb')) cmd='phenix.pdb_interpretation %s flip_sym=0 write_geo=True' % fn.replace('.pdb', '_updated.pdb') print(cmd) easy_run.go(cmd) assert_lines_in_file(file_name='%s.geo' % fn.replace('.pdb', '_updated.pdb'), lines = geo_strings[switch][i]) def tst_adding_disulfur_hydrogen_atoms(switch): element='H' if switch.endswith('_D'): element='D' fn = 'tst_ready_hydrogens_%s.pdb' % (switch) with open(fn, 'w') as f: f.write(pdb_strings[switch]) pdb_inp = pdb_input(fn) hierarchy = pdb_inp.construct_hierarchy() from mmtbx.conformation_dependent_library.testing_utils import get_geometry_restraints_manager grm = get_geometry_restraints_manager(pdb_filename=fn) add_disulfur_hydrogen_atoms(grm, hierarchy, element=element) hierarchy.write_pdb_file(fn.replace('.pdb', '_updated.pdb')) if switch=='CYS_1': with open(fn.replace('.pdb', '_updated.pdb'), 'r') as f: lines = f.read() assert lines.find('HG')==-1 else: cmd='phenix.pdb_interpretation %s write_geo=True' % fn.replace('.pdb', '_updated.pdb') print(cmd) easy_run.go(cmd) assert_lines_in_file(file_name='%s.geo' % fn.replace('.pdb', '_updated.pdb'), lines = geo_strings[switch]) def switcher(switch): if switch in ['ASP', 'GLU', 'ASP_D']: tst_adding_side_chain_acid_hydrogen_atoms(switch) elif switch in ['CYS_1', 'CYS_2', 'CYS_2_D']: tst_adding_disulfur_hydrogen_atoms(switch) def main(switch=None): if switch is None: for switch in ['ASP', 'GLU', 'CYS_1', 'CYS_2', 'ASP_D', 'CYS_2_D']: switcher(switch) else: switcher(switch) if __name__ == '__main__': main(*tuple(sys.argv[1:]))