from __future__ import absolute_import, division, print_function from libtbx import easy_run import libtbx.load_env from six.moves import cStringIO as StringIO l1r_pdb = """ HETATM 3890 C1 AL1R A1247 21.777 10.761 29.793 0.50 4.10 C HETATM 3891 C2 AL1R A1247 21.624 12.183 29.278 0.50 23.99 C HETATM 3892 C3 AL1R A1247 20.238 12.698 29.622 0.50 30.37 C HETATM 3893 O4 AL1R A1247 22.518 13.081 29.986 0.50 26.04 O HETATM 3894 C5 AL1R A1247 23.787 12.666 30.304 0.50 24.33 C HETATM 3895 C6 AL1R A1247 24.205 13.396 31.411 0.50 20.37 C HETATM 3896 C7 AL1R A1247 25.448 13.174 31.967 0.50 22.78 C HETATM 3897 C8 AL1R A1247 26.303 12.246 31.406 0.50 24.56 C HETATM 3898 C9 AL1R A1247 25.914 11.515 30.291 0.50 23.51 C HETATM 3899 N10AL1R A1247 26.803 10.567 29.731 0.50 19.01 N HETATM 3900 C11AL1R A1247 27.021 10.367 28.421 0.50 17.27 C HETATM 3901 O12AL1R A1247 26.512 11.039 27.552 0.50 19.42 O HETATM 3902 C13AL1R A1247 27.975 9.276 28.052 0.50 8.77 C HETATM 3903 C14AL1R A1247 28.790 9.523 26.954 0.50 9.85 C HETATM 3904 C15AL1R A1247 29.707 8.574 26.543 0.50 8.72 C HETATM 3905 CL1 AL1R A1247 30.719 8.896 25.168 0.50 15.30 CL HETATM 3906 C17AL1R A1247 29.805 7.356 27.241 0.50 12.61 C HETATM 3907 O18AL1R A1247 30.698 6.376 26.912 0.50 12.55 O HETATM 3908 C19AL1R A1247 31.814 6.192 27.805 0.50 17.96 C HETATM 3909 C20AL1R A1247 32.392 4.807 27.590 0.50 16.10 C HETATM 3910 N21AL1R A1247 33.124 4.698 26.299 0.50 10.39 N HETATM 3911 C22AL1R A1247 28.996 7.117 28.347 0.50 14.87 C HETATM 3912 CL2 AL1R A1247 29.141 5.627 29.220 0.50 17.63 CL HETATM 3913 C24AL1R A1247 28.081 8.079 28.757 0.50 6.06 C HETATM 3914 C25AL1R A1247 24.657 11.738 29.738 0.50 26.75 C HETATM 3915 H1C1AL1R A1247 23.622 13.862 34.406 0.50 4.10 H HETATM 3916 H1C2AL1R A1247 23.741 15.372 34.937 0.50 4.10 H HETATM 3917 H1C3AL1R A1247 24.624 14.213 35.610 0.50 4.10 H HETATM 3918 H2 AL1R A1247 24.984 15.262 32.978 0.50 23.99 H HETATM 3919 H3C1AL1R A1247 26.894 15.122 35.102 0.50 30.37 H HETATM 3920 H3C2AL1R A1247 27.151 15.812 33.676 0.50 30.37 H HETATM 3921 H3C3AL1R A1247 26.119 16.472 34.712 0.50 30.37 H HETATM 3922 H6 AL1R A1247 24.037 14.353 31.774 0.50 20.37 H HETATM 3923 H7 AL1R A1247 23.526 13.546 29.621 0.50 22.78 H HETATM 3924 H25AL1R A1247 27.038 11.581 32.111 0.50 26.75 H HETATM 3925 H8 AL1R A1247 24.760 11.752 28.709 0.50 24.56 H HETATM 3926 H10AL1R A1247 26.981 9.745 30.294 0.50 19.01 H HETATM 3927 H14AL1R A1247 29.071 10.449 26.709 0.50 9.85 H HETATM 3928 H24AL1R A1247 27.305 7.828 29.328 0.50 6.06 H HETATM 3929 H191AL1R A1247 32.651 6.813 27.086 0.50 17.96 H HETATM 3930 H192AL1R A1247 31.921 6.649 28.507 0.50 17.96 H HETATM 3931 H201AL1R A1247 31.734 4.274 27.962 0.50 16.10 H HETATM 3932 H202AL1R A1247 33.194 4.782 28.360 0.50 16.10 H HETATM 3933 H211AL1R A1247 33.935 4.283 26.431 0.50 10.39 H HETATM 3934 H212AL1R A1247 32.687 3.476 26.242 0.50 10.39 H HETATM 3935 C1 BL1R A1247 24.235 14.539 34.768 0.50 24.67 C HETATM 3936 C2 BL1R A1247 25.347 14.803 33.765 0.50 20.23 C HETATM 3937 C3 BL1R A1247 26.478 15.625 34.367 0.50 10.96 C HETATM 3938 O4 BL1R A1247 25.904 13.526 33.376 0.50 18.91 O HETATM 3939 C5 BL1R A1247 25.578 13.036 32.139 0.50 15.56 C HETATM 3940 C6 BL1R A1247 24.554 13.612 31.397 0.50 15.71 C HETATM 3941 C7 BL1R A1247 24.251 13.135 30.140 0.50 13.06 C HETATM 3942 C8 BL1R A1247 24.978 12.089 29.604 0.50 11.07 C HETATM 3943 C9 BL1R A1247 26.005 11.502 30.330 0.50 14.33 C HETATM 3944 N10BL1R A1247 26.744 10.445 29.752 0.50 18.41 N HETATM 3945 C11BL1R A1247 27.125 10.393 28.461 0.50 22.57 C HETATM 3946 O12BL1R A1247 26.764 11.204 27.639 0.50 21.58 O HETATM 3947 C13BL1R A1247 28.054 9.286 28.075 0.50 23.49 C HETATM 3948 C14BL1R A1247 29.022 9.556 27.113 0.50 24.22 C HETATM 3949 C15BL1R A1247 29.919 8.573 26.720 0.50 22.20 C HETATM 3950 CL1 BL1R A1247 31.123 8.934 25.520 0.50 22.46 CL HETATM 3951 C17BL1R A1247 29.846 7.299 27.295 0.50 21.60 C HETATM 3952 O18BL1R A1247 30.717 6.303 26.941 0.50 17.30 O HETATM 3953 C19BL1R A1247 32.007 6.279 27.601 0.50 18.57 C HETATM 3954 C20BL1R A1247 32.486 4.840 27.681 0.50 17.56 C HETATM 3955 N21BL1R A1247 33.019 4.318 26.392 0.50 14.88 N HETATM 3956 C22BL1R A1247 28.877 7.029 28.259 0.50 22.09 C HETATM 3957 CL2 BL1R A1247 28.784 5.457 28.974 0.50 17.57 CL HETATM 3958 C24BL1R A1247 27.986 8.021 28.649 0.50 22.43 C HETATM 3959 C25BL1R A1247 26.313 11.991 31.592 0.50 14.30 C HETATM 3960 H1C1BL1R A1247 23.622 13.862 34.406 0.50 24.67 H HETATM 3961 H1C2BL1R A1247 23.741 15.372 34.937 0.50 24.67 H HETATM 3962 H1C3BL1R A1247 24.624 14.213 35.610 0.50 24.67 H HETATM 3963 H2 BL1R A1247 24.984 15.262 32.978 0.50 20.23 H HETATM 3964 H3C1BL1R A1247 26.894 15.122 35.102 0.50 10.96 H HETATM 3965 H3C2BL1R A1247 27.151 15.812 33.676 0.50 10.96 H HETATM 3966 H3C3BL1R A1247 26.119 16.472 34.712 0.50 10.96 H HETATM 3967 H6 BL1R A1247 24.037 14.353 31.774 0.50 15.71 H HETATM 3968 H7 BL1R A1247 23.526 13.546 29.621 0.50 13.06 H HETATM 3969 H25BL1R A1247 27.038 11.581 32.111 0.50 14.30 H HETATM 3970 H8 BL1R A1247 24.760 11.752 28.709 0.50 11.07 H HETATM 3971 H10BL1R A1247 26.981 9.745 30.294 0.50 18.41 H HETATM 3972 H14BL1R A1247 29.071 10.449 26.709 0.50 24.22 H HETATM 3973 H24BL1R A1247 27.305 7.828 29.328 0.50 22.43 H HETATM 3974 H191BL1R A1247 32.651 6.813 27.086 0.50 18.57 H HETATM 3975 H192BL1R A1247 31.921 6.649 28.507 0.50 18.57 H HETATM 3976 H201BL1R A1247 31.734 4.274 27.962 0.50 17.56 H HETATM 3977 H202BL1R A1247 33.194 4.782 28.360 0.50 17.56 H HETATM 3978 H211BL1R A1247 33.935 4.283 26.431 0.50 14.88 H HETATM 3979 H212BL1R A1247 32.687 3.476 26.242 0.50 14.88 H """ l1r_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 L1R L1R 'Unknown ' ligand 45 25 . # data_comp_L1R # 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 L1R C1 C CH3 . 2.8974 3.5183 -6.1638 L1R C2 C CH1 . 2.8051 2.8353 -4.8033 L1R C3 C CH3 . 3.0983 3.8453 -3.7109 L1R O4 O O2 . 1.4865 2.3109 -4.6215 L1R C5 C CR6 . 1.4498 1.0843 -3.9638 L1R C6 C CR16 . 1.9122 -0.0757 -4.6162 L1R C7 C CR16 . 1.8001 -1.3045 -4.0047 L1R C8 C CR16 . 1.2312 -1.4031 -2.7447 L1R C9 C CR6 . 0.7688 -0.2476 -2.0911 L1R N10 N NH1 . 0.0935 -0.3502 -0.8144 L1R C11 C C . 0.2928 -1.4890 0.0136 L1R O12 O O . 1.0040 -2.3511 -0.3340 L1R C13 C CR6 . -0.4260 -1.5883 1.3457 L1R C14 C CR16 . -1.4607 -2.5265 1.5148 L1R C15 C CR6 . -2.0425 -2.6929 2.7524 L1R CL1 CL CL . -3.3279 -3.8717 2.9672 L1R C17 C CR6 . -1.6068 -1.9326 3.8358 L1R O18 O O2 . -2.1493 -2.1530 5.1031 L1R C19 C CH2 . -3.2986 -1.3409 5.3928 L1R C20 C CH2 . -3.8899 -1.7593 6.7556 L1R N21 N NH2 . -4.0324 -0.5996 7.5943 L1R C22 C CR6 . -0.5745 -0.9968 3.6662 L1R CL2 CL CL . 0.0312 -0.0872 5.0466 L1R C24 C CR16 . 0.0084 -0.8313 2.4222 L1R C25 C CR16 . 0.8832 0.9906 -2.7102 L1R H1C1 H HCH3 . 3.7452 3.3549 -6.5396 L1R H1C2 H HCH3 . 2.7708 4.4782 -6.0540 L1R H1C3 H HCH3 . 2.1773 3.1498 -6.7790 L1R H2 H HCH1 . 3.4506 2.1144 -4.7592 L1R H3C1 H HCH3 . 2.2868 4.1686 -3.3576 L1R H3C2 H HCH3 . 3.6009 4.5753 -4.0769 L1R H3C3 H HCH3 . 3.6107 3.4212 -3.0058 L1R H6 H HCR6 . 2.2983 -0.0118 -5.4727 L1R H7 H HCR6 . 2.1289 -2.1229 -4.4694 L1R H25 H HCR6 . 0.5581 1.8029 -2.2527 L1R H8 H HCR6 . 1.1516 -2.2771 -2.3119 L1R H10 H HNH1 . -0.5730 0.3075 -0.5714 L1R H14 H HCR6 . -1.6952 -3.1409 0.7736 L1R H24 H HCR6 . 0.7227 -0.1851 2.3037 L1R H191 H HCH2 . -3.0377 -0.4105 5.4269 L1R H192 H HCH2 . -3.9800 -1.4670 4.6814 L1R H201 H HCH2 . -4.7783 -2.1791 6.6150 L1R H202 H HCH2 . -3.2999 -2.3908 7.1809 L1R H211 H HNH2 . -3.2822 -0.0557 7.5009 L1R H212 H HNH2 . -4.8097 -0.1153 7.3360 # 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 L1R C1 C2 single 1.525 0.020 L1R C2 C3 single 1.516 0.020 L1R C2 O4 single 1.431 0.020 L1R O4 C5 single 1.392 0.020 L1R C5 C6 aromatic 1.409 0.020 L1R C5 C25 aromatic 1.379 0.020 L1R C6 C7 aromatic 1.377 0.020 L1R C7 C8 aromatic 1.386 0.020 L1R C7 H7 single 0.997 0.020 L1R C8 C9 aromatic 1.406 0.020 L1R C9 N10 single 1.448 0.020 L1R C9 C25 aromatic 1.389 0.020 L1R N10 C11 single 1.422 0.020 L1R C11 O12 double 1.170 0.020 L1R C11 C13 single 1.517 0.020 L1R C13 C14 aromatic 1.407 0.020 L1R C13 C24 aromatic 1.386 0.020 L1R C14 C15 aromatic 1.378 0.020 L1R C15 CL1 single 1.757 0.020 L1R C15 C17 aromatic 1.393 0.020 L1R C17 O18 single 1.396 0.020 L1R C17 C22 aromatic 1.404 0.020 L1R O18 C19 single 1.437 0.020 L1R C19 C20 single 1.543 0.020 L1R C20 N21 single 1.438 0.020 L1R C22 CL2 single 1.761 0.020 L1R C22 C24 aromatic 1.384 0.020 L1R C1 H1C1 single 0.942 0.020 L1R C1 H1C2 single 0.974 0.020 L1R C1 H1C3 single 1.016 0.020 L1R C2 H2 single 0.969 0.020 L1R C3 H3C1 single 0.942 0.020 L1R C3 H3C2 single 0.959 0.020 L1R C3 H3C3 single 0.969 0.020 L1R C6 H6 single 0.942 0.020 L1R C25 H25 single 0.987 0.020 L1R C8 H8 single 0.979 0.020 L1R N10 H10 single 0.967 0.020 L1R C14 H14 single 0.991 0.020 L1R C24 H24 single 0.970 0.020 L1R C19 H191 single 0.967 0.020 L1R C19 H192 single 0.993 0.020 L1R C20 H201 single 0.993 0.020 L1R C20 H202 single 0.963 0.020 L1R N21 H211 single 0.931 0.020 L1R N21 H212 single 0.952 0.020 # 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 L1R H1C3 C1 H1C2 109.48 3.000 L1R H1C3 C1 H1C1 109.48 3.000 L1R H1C2 C1 H1C1 109.45 3.000 L1R H1C3 C1 C2 109.55 3.000 L1R H1C2 C1 C2 109.43 3.000 L1R H1C1 C1 C2 109.44 3.000 L1R H2 C2 O4 109.61 3.000 L1R H2 C2 C3 109.52 3.000 L1R O4 C2 C3 109.32 3.000 L1R H2 C2 C1 109.48 3.000 L1R O4 C2 C1 109.47 3.000 L1R C3 C2 C1 109.43 3.000 L1R H3C3 C3 H3C2 109.50 3.000 L1R H3C3 C3 H3C1 109.43 3.000 L1R H3C2 C3 H3C1 109.47 3.000 L1R H3C3 C3 C2 109.56 3.000 L1R H3C2 C3 C2 109.48 3.000 L1R H3C1 C3 C2 109.40 3.000 L1R C5 O4 C2 114.03 3.000 L1R C25 C5 C6 119.99 3.000 L1R C25 C5 O4 120.01 3.000 L1R C6 C5 O4 119.87 3.000 L1R H6 C6 C7 119.86 3.000 L1R H6 C6 C5 119.99 3.000 L1R C7 C6 C5 120.15 3.000 L1R H7 C7 C8 120.05 3.000 L1R H7 C7 C6 119.91 3.000 L1R C8 C7 C6 120.04 3.000 L1R H8 C8 C9 120.12 3.000 L1R H8 C8 C7 119.93 3.000 L1R C9 C8 C7 119.95 3.000 L1R C25 C9 N10 119.64 3.000 L1R C25 C9 C8 119.89 3.000 L1R N10 C9 C8 120.34 3.000 L1R H10 N10 C11 119.65 3.000 L1R H10 N10 C9 119.65 3.000 L1R C11 N10 C9 120.32 3.000 L1R C13 C11 O12 120.04 3.000 L1R C13 C11 N10 119.82 3.000 L1R O12 C11 N10 120.14 3.000 L1R C24 C13 C14 120.09 3.000 L1R C24 C13 C11 119.86 3.000 L1R C14 C13 C11 119.85 3.000 L1R H14 C14 C15 119.81 3.000 L1R H14 C14 C13 119.84 3.000 L1R C15 C14 C13 119.94 3.000 L1R C17 C15 CL1 119.98 3.000 L1R C17 C15 C14 120.03 3.000 L1R CL1 C15 C14 119.99 3.000 L1R C22 C17 O18 120.05 3.000 L1R C22 C17 C15 119.99 3.000 L1R O18 C17 C15 119.88 3.000 L1R C19 O18 C17 113.87 3.000 L1R H192 C19 H191 109.42 3.000 L1R H192 C19 C20 109.59 3.000 L1R H191 C19 C20 109.46 3.000 L1R H192 C19 O18 109.43 3.000 L1R H191 C19 O18 109.58 3.000 L1R C20 C19 O18 109.35 3.000 L1R H202 C20 H201 109.48 3.000 L1R H202 C20 N21 109.38 3.000 L1R H201 C20 N21 109.56 3.000 L1R H202 C20 C19 109.45 3.000 L1R H201 C20 C19 109.42 3.000 L1R N21 C20 C19 109.53 3.000 L1R H212 N21 H211 109.48 3.000 L1R H212 N21 C20 109.45 3.000 L1R H211 N21 C20 109.43 3.000 L1R C24 C22 CL2 119.88 3.000 L1R C24 C22 C17 119.88 3.000 L1R CL2 C22 C17 120.18 3.000 L1R H24 C24 C22 119.96 3.000 L1R H24 C24 C13 119.97 3.000 L1R C22 C24 C13 120.07 3.000 L1R H25 C25 C9 119.98 3.000 L1R H25 C25 C5 120.05 3.000 L1R C9 C25 C5 119.97 3.000 """ def run(): if (not libtbx.env.has_module("phenix")): print("phenix not configured, skipping") return elif (not libtbx.env.find_in_repositories("chem_data")): print("chem_data not configured, skipping") return f=open("l1r.pdb", "w") f.write(l1r_pdb) f.close() f=open("l1r.cif", "w") f.write(l1r_cif) f.close() cmd = 'phenix.geometry_minimization' cmd += " l1r.pdb l1r.cif use_neutron_distances=False" cmd += ' selection="element H or element D" write_geo_file=False' cmd += ' correct_hydrogens=True' print(cmd) ero = easy_run.fully_buffered(command=cmd) err = StringIO() ero.show_stdout(out=err) cmd = "phenix.fmodel high_res=4.5 format=mtz label=FOBS type=real r_free=0.1 l1r.pdb generate_fake_p1_symmetry=1" easy_run.call(cmd) cmd = 'phenix.refine' cmd += " l1r.pdb l1r.pdb.mtz l1r.cif" cmd += " main.number_of_macro_cycles=1" cmd += ' correct_hydrogens=True' print(cmd) ero = easy_run.fully_buffered(command=cmd) err = StringIO() ero.show_stdout(out=err) print("OK") if __name__=="__main__": run()