from __future__ import absolute_import, division, print_function from mmtbx.building import extend_sidechains import mmtbx.monomer_library from scitbx.array_family import flex import iotbx.pdb from libtbx.test_utils import approx_equal mon_lib_srv = mmtbx.monomer_library.server.server() ### pdb_str0_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N ATOM 0 HA LYS A 7 5.646 6.153 2.918 1.00 18.23 H new remark ATOM 0 HB2 LYS A 7 3.514 5.375 1.233 1.00 23.56 H new remark ATOM 0 HB3 LYS A 7 3.315 6.378 2.411 1.00 23.56 H new remark ATOM 0 HG2 LYS A 7 4.599 7.982 1.386 1.00 33.58 H new remark ATOM 0 HG3 LYS A 7 5.161 6.961 0.350 1.00 33.58 H new remark ATOM 0 HD2 LYS A 7 2.426 7.717 0.393 1.00 41.39 H new remark ATOM 0 HD3 LYS A 7 3.456 8.385 -0.570 1.00 41.39 H new remark ATOM 0 HE2 LYS A 7 3.826 6.296 -1.622 1.00 48.81 H new remark ATOM 0 HE3 LYS A 7 2.797 5.628 -0.660 1.00 48.81 H new remark ATOM 0 HZ1 LYS A 7 1.802 6.117 -2.648 1.00 48.81 H new remark ATOM 0 HZ2 LYS A 7 1.154 6.908 -1.616 1.00 48.81 H new remark ATOM 0 HZ3 LYS A 7 2.113 7.530 -2.513 1.00 48.81 H new """ pdb_str0_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N ATOM 0 HA LYS A 7 5.646 6.153 2.918 1.00 18.23 H new ATOM 0 HB2 LYS A 7 3.514 5.375 1.233 1.00 23.56 H new ATOM 0 HB3 LYS A 7 3.315 6.378 2.411 1.00 23.56 H new ATOM 0 HG2 LYS A 7 4.599 7.982 1.386 1.00 33.58 H new ATOM 0 HG3 LYS A 7 5.161 6.961 0.350 1.00 33.58 H new ATOM 0 HD2 LYS A 7 2.426 7.717 0.393 1.00 41.39 H new ATOM 0 HD3 LYS A 7 3.456 8.385 -0.570 1.00 41.39 H new ATOM 0 HE2 LYS A 7 3.826 6.296 -1.622 1.00 48.81 H new ATOM 0 HE3 LYS A 7 2.797 5.628 -0.660 1.00 48.81 H new ATOM 0 HZ1 LYS A 7 1.802 6.117 -2.648 1.00 48.81 H new ATOM 0 HZ2 LYS A 7 1.154 6.908 -1.616 1.00 48.81 H new ATOM 0 HZ3 LYS A 7 2.113 7.530 -2.513 1.00 48.81 H new """ ### pdb_str1_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C remark ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N ATOM 0 HA LYS A 7 5.646 6.153 2.918 1.00 18.23 H new ATOM 0 HB2 LYS A 7 3.514 5.375 1.233 1.00 23.56 H new ATOM 0 HB3 LYS A 7 3.315 6.378 2.411 1.00 23.56 H new ATOM 0 HG2 LYS A 7 4.599 7.982 1.386 1.00 33.58 H new ATOM 0 HG3 LYS A 7 5.161 6.961 0.350 1.00 33.58 H new ATOM 0 HD2 LYS A 7 2.426 7.717 0.393 1.00 41.39 H new ATOM 0 HD3 LYS A 7 3.456 8.385 -0.570 1.00 41.39 H new ATOM 0 HE2 LYS A 7 3.826 6.296 -1.622 1.00 48.81 H new ATOM 0 HE3 LYS A 7 2.797 5.628 -0.660 1.00 48.81 H new ATOM 0 HZ1 LYS A 7 1.802 6.117 -2.648 1.00 48.81 H new ATOM 0 HZ2 LYS A 7 1.154 6.908 -1.616 1.00 48.81 H new ATOM 0 HZ3 LYS A 7 2.113 7.530 -2.513 1.00 48.81 H new """ pdb_str1_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N ATOM 0 HA LYS A 7 5.646 6.153 2.918 1.00 18.23 H new ATOM 0 HB2 LYS A 7 3.514 5.375 1.233 1.00 23.56 H new ATOM 0 HB3 LYS A 7 3.315 6.378 2.411 1.00 23.56 H new ATOM 0 HG2 LYS A 7 4.599 7.982 1.386 1.00 33.58 H new ATOM 0 HG3 LYS A 7 5.161 6.961 0.350 1.00 33.58 H new ATOM 0 HD2 LYS A 7 2.426 7.717 0.393 1.00 41.39 H new ATOM 0 HD3 LYS A 7 3.456 8.385 -0.570 1.00 41.39 H new ATOM 0 HE2 LYS A 7 3.826 6.296 -1.622 1.00 48.81 H new ATOM 0 HE3 LYS A 7 2.797 5.628 -0.660 1.00 48.81 H new ATOM 0 HZ1 LYS A 7 1.802 6.117 -2.648 1.00 48.81 H new ATOM 0 HZ2 LYS A 7 1.154 6.908 -1.616 1.00 48.81 H new ATOM 0 HZ3 LYS A 7 2.113 7.530 -2.513 1.00 48.81 H new """ ### pdb_str2_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C remark ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ pdb_str2_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ ### pdb_str3_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C remark ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ pdb_str3_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ ### pdb_str4_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C remark ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ pdb_str4_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ ### pdb_str5_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N remark ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ pdb_str5_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ ### pdb_str6_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O remark ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N TER """ pdb_str6_good="""\ ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N TER """ ### pdb_str7_good=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N ATOM 0 HA LYS A 7 5.646 6.153 2.918 1.00 18.23 H new ATOM 0 HB2 LYS A 7 3.514 5.375 1.233 1.00 23.56 H new ATOM 0 HB3 LYS A 7 3.315 6.378 2.411 1.00 23.56 H new ATOM 0 HG2 LYS A 7 4.599 7.982 1.386 1.00 33.58 H new ATOM 0 HG3 LYS A 7 5.161 6.961 0.350 1.00 33.58 H new ATOM 0 HD2 LYS A 7 2.426 7.717 0.393 1.00 41.39 H new ATOM 0 HD3 LYS A 7 3.456 8.385 -0.570 1.00 41.39 H new ATOM 0 HE2 LYS A 7 3.826 6.296 -1.622 1.00 48.81 H new ATOM 0 HE3 LYS A 7 2.797 5.628 -0.660 1.00 48.81 H new ATOM 0 HZ1 LYS A 7 1.802 6.117 -2.648 1.00 48.81 H new ATOM 0 HZ2 LYS A 7 1.154 6.908 -1.616 1.00 48.81 H new ATOM 0 HZ3 LYS A 7 2.113 7.530 -2.513 1.00 48.81 H new """ pdb_str7_bad=""" ATOM 1 N LYS A 7 6.033 4.704 1.582 1.00 17.49 N ATOM 2 CA LYS A 7 5.159 5.427 2.499 1.00 18.23 C ATOM 3 C LYS A 7 4.673 4.437 3.507 1.00 14.78 C ATOM 4 O LYS A 7 4.777 3.208 3.297 1.00 15.83 O ATOM 5 CB LYS A 7 3.959 6.057 1.760 1.00 23.56 C ATOM 6 CG LYS A 7 4.368 7.206 0.851 1.00 33.58 C remark ATOM 7 CD LYS A 7 3.242 7.559 -0.108 1.00 41.39 C ATOM 8 CE LYS A 7 3.009 6.453 -1.124 1.00 48.81 C ATOM 9 NZ LYS A 7 1.909 6.785 -2.070 1.00 48.81 N """ pdb_str_do_no_move_if_complete=""" ATOM 1 N LYS A 7 6.187 5.271 2.497 1.00 17.49 N ATOM 2 CA LYS A 7 5.198 6.138 3.127 1.00 18.23 C ATOM 3 C LYS A 7 4.507 5.426 4.285 1.00 14.78 C ATOM 4 O LYS A 7 3.859 4.396 4.096 1.00 15.83 O ATOM 5 CB LYS A 7 4.161 6.608 2.104 1.00 23.56 C ATOM 6 CG LYS A 7 4.553 7.868 1.345 1.00 33.58 C ATOM 7 CD LYS A 7 5.574 7.573 0.257 1.00 41.39 C ATOM 8 CE LYS A 7 4.958 6.765 -0.874 1.00 48.81 C ATOM 9 NZ LYS A 7 5.929 6.522 -1.976 1.00 48.81 N TER END """ ### def check(answer, result, bad): a = list(answer.atoms().extract_name()) a.sort() # r = list(result.atoms().extract_name()) r.sort() # b = list(bad.atoms().extract_name()) b.sort() # diff = list(set(r).symmetric_difference(set(a))) assert len(diff) in [0,1], diff if(len(diff)==1): assert diff[0]==' H ', diff assert b!=a # xyz_a = flex.vec3_double() xyz_r = flex.vec3_double() for aa in answer.atoms(): for ar in result.atoms(): if(aa.name == ar.name): xyz_a.append(aa.xyz) xyz_r.append(ar.xyz) print(flex.max(flex.sqrt((xyz_a - xyz_r).dot()))) def exercise_extend_sidechains(pdb_str_bad, pdb_str_good, i, Sorry_msg, add_h): pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_bad) pdb_h = pdb_inp.construct_hierarchy() pdb_h.write_pdb_file(file_name="m_in_%d.pdb"%i) pdb_h_bad = pdb_h.deep_copy() e = None try: extend_sidechains.extend_protein_model( pdb_hierarchy = pdb_h, mon_lib_srv = mon_lib_srv, add_hydrogens = add_h) except Exception as e: if(Sorry_msg is not None): assert str(e).find(Sorry_msg)>-1 return # pdb_h.write_pdb_file(file_name="m_completed_%d.pdb"%i) pdb_h_result = pdb_h.deep_copy() # pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_good) pdb_h_answer = pdb_inp.construct_hierarchy() pdb_h_answer.write_pdb_file(file_name="m_good_%d.pdb"%i) # check(answer=pdb_h_answer, result=pdb_h_result, bad=pdb_h_bad) def exercise_do_not_move_if_complete(): pdb_inp = iotbx.pdb.input(source_info=None, lines=pdb_str_do_no_move_if_complete) pdb_h = pdb_inp.construct_hierarchy() xyz1 = pdb_h.atoms().extract_xyz() pdb_h_completed = pdb_h.deep_copy() extend_sidechains.extend_protein_model( pdb_hierarchy = pdb_h_completed, mon_lib_srv = mon_lib_srv, add_hydrogens = False) xyz2 = pdb_h_completed.atoms().extract_xyz() assert approx_equal(flex.max(flex.sqrt((xyz1 - xyz2).dot())),0.0) if(__name__ == "__main__"): exercise_do_not_move_if_complete() # for i, t in enumerate([ (pdb_str0_bad, pdb_str0_good, None, None), (pdb_str1_bad, pdb_str1_good, None, None), (pdb_str2_bad, pdb_str2_good, None, None), (pdb_str3_bad, pdb_str3_good, None, None), (pdb_str4_bad, pdb_str4_good, "Main chain must be complete.", None), (pdb_str5_bad, pdb_str5_good, "Main chain must be complete.", None), (pdb_str6_bad, pdb_str6_good, None, None), (pdb_str7_bad, pdb_str7_good, None, True), ]): exercise_extend_sidechains( pdb_str_bad=t[0], pdb_str_good=t[1], i=i, Sorry_msg=t[2], add_h=t[3]) print("OK")