from __future__ import absolute_import, division, print_function #import libtbx.load_env import sys, os, math from cctbx.array_family import flex from libtbx.utils import remove_files from mmtbx import utils from libtbx.test_utils import approx_equal, not_approx_equal, run_command, \ show_diff import iotbx.pdb from scitbx.array_family import flex from cctbx import adptbx import mmtbx.model from six.moves import cStringIO as StringIO, zip from libtbx import easy_run full_params = mmtbx.model.manager.get_default_pdb_interpretation_params() full_params.pdb_interpretation.flip_symmetric_amino_acids=False class xray_structure_plus(object): def __init__(self, file_name): log = StringIO() pdb_inp = iotbx.pdb.input(file_name=file_name) self.model = mmtbx.model.manager(model_input = pdb_inp, log = log) self.model.process(pdb_interpretation_params = full_params) self.xray_structure = self.model.get_xray_structure() uc = self.model.get_xray_structure().unit_cell() self.occ = self.xray_structure.scatterers().extract_occupancies() self.u_iso = self.xray_structure.scatterers().extract_u_iso() self.u_cart = self.xray_structure.scatterers().extract_u_cart(uc) self.sites_cart = self.xray_structure.sites_cart() self.use_u_iso = self.xray_structure.use_u_iso() self.use_u_aniso = self.xray_structure.use_u_aniso() self.u_iso_used = self.u_iso.select(self.use_u_iso) self.u_cart_used = self.u_cart.select(self.use_u_aniso) self.u_iso_not_used = self.u_iso.select(~self.use_u_iso) self.u_cart_not_used = self.u_cart.select(~self.use_u_aniso) def selection(self, selection_strings): return utils.get_atom_selections(iselection = False, model = self.model, selection_strings= selection_strings)[0] def exercise_basic(): pdb_str = """ CRYST1 12.000 11.000 13.000 80.00 70.00 100.00 P 1 1 ATOM 1 CB PHE A 1 7.767 5.853 7.671 1.00 17.45 C ANISOU 1 CB PHE A 1 1090 2307 3233 1244 1260 2218 C ATOM 2 CG PHE A 1 6.935 5.032 8.622 1.00 17.61 C ANISOU 2 CG PHE A 1 1258 2172 3262 1259 1261 2264 C ATOM 3 CD1 PHE A 1 5.918 4.176 8.140 1.00 17.66 C ANISOU 3 CD1 PHE A 1 1321 2083 3304 1237 1214 2356 C ATOM 4 CD2 PHE A 1 7.161 5.107 10.012 1.00 17.82 C ANISOU 4 CD2 PHE A 1 1374 2150 3248 1279 1308 2217 C ATOM 5 CE1 PHE A 1 5.126 3.395 9.038 1.00 17.96 C ANISOU 5 CE1 PHE A 1 1508 1983 3333 1224 1216 2398 C ATOM 6 CE2 PHE A 1 6.382 4.336 10.930 1.00 18.17 C ANISOU 6 CE2 PHE A 1 1573 2056 3276 1258 1310 2261 C ATOM 7 CZ PHE A 1 5.360 3.476 10.439 1.00 18.27 C ANISOU 7 CZ PHE A 1 1645 1979 3318 1226 1265 2351 C ATOM 8 C PHE A 1 7.956 7.811 6.133 1.00 17.21 C ANISOU 8 C PHE A 1 816 2415 3307 1079 1332 2287 C ATOM 9 O PHE A 1 8.506 7.237 5.169 1.00 17.39 O ANISOU 9 O PHE A 1 818 2555 3234 1097 1244 2232 O ATOM 10 OXT PHE A 1 8.143 9.010 6.428 1.00 17.15 O ANISOU 10 OXT PHE A 1 737 2422 3356 1020 1411 2296 O ATOM 13 N PHE A 1 5.875 6.461 6.183 1.00 17.13 N ANISOU 13 N PHE A 1 934 2156 3419 1076 1303 2452 N ATOM 15 CA PHE A 1 7.000 7.000 7.000 1.00 17.18 C ANISOU 15 CA PHE A 1 931 2249 3347 1119 1342 2337 C ATOM 13 CB PHE B 2 11.715 4.672 7.185 1.00 34.89 C ATOM 14 CG PHE B 2 10.876 4.117 8.301 1.00 35.22 C ATOM 15 CD2 PHE B 2 10.127 2.966 8.118 1.00 35.30 C ATOM 16 CD1 PHE B 2 10.836 4.746 9.534 1.00 35.63 C ATOM 17 CE2 PHE B 2 9.355 2.454 9.143 1.00 35.88 C ATOM 18 CE1 PHE B 2 10.066 4.239 10.563 1.00 36.30 C ATOM 19 CZ PHE B 2 9.324 3.091 10.367 1.00 36.47 C ATOM 20 C PHE B 2 11.961 6.316 5.313 1.00 34.38 C ATOM 21 O PHE B 2 11.902 5.976 4.132 1.00 34.72 O ATOM 22 OXT PHE B 2 12.817 7.140 5.635 1.00 34.24 O ATOM 23 N PHE B 2 9.817 5.175 5.710 1.00 34.25 N ATOM 24 CA PHE B 2 11.002 5.735 6.347 1.00 34.35 C ATOM 1 CB PHE C 3 10.767 8.853 7.671 1.00 52.27 C ANISOU 1 CB PHE C 3 3279 6815 9766 3688 3821 6736 C ATOM 2 CG PHE C 3 9.935 8.032 8.622 1.00 52.60 C ANISOU 2 CG PHE C 3 3617 6545 9825 3719 3822 6829 C ATOM 3 CD1 PHE C 3 8.918 7.176 8.140 1.00 52.70 C ANISOU 3 CD1 PHE C 3 3745 6367 9912 3673 3727 7011 C ATOM 4 CD2 PHE C 3 10.161 8.107 10.012 1.00 53.03 C ANISOU 4 CD2 PHE C 3 3850 6502 9797 3761 3917 6735 C ATOM 5 CE1 PHE C 3 8.126 6.395 9.038 1.00 53.33 C ANISOU 5 CE1 PHE C 3 4119 6169 9973 3647 3734 7098 C ATOM 6 CE2 PHE C 3 9.382 7.336 10.930 1.00 53.74 C ANISOU 6 CE2 PHE C 3 4248 6315 9853 3723 3923 6823 C ATOM 7 CZ PHE C 3 8.360 6.476 10.439 1.00 53.93 C ANISOU 7 CZ PHE C 3 4391 6159 9943 3655 3834 7005 C ATOM 8 C PHE C 3 10.956 10.811 6.133 1.00 51.80 C ANISOU 8 C PHE C 3 2733 7032 9917 3360 3966 6875 C ATOM 9 O PHE C 3 11.506 10.237 5.169 1.00 52.17 O ANISOU 9 O PHE C 3 2737 7311 9773 3399 3791 6767 O ATOM 10 OXT PHE C 3 11.143 12.010 6.428 1.00 51.70 O ANISOU 10 OXT PHE C 3 2580 7045 10018 3240 4125 6894 O ATOM 13 N PHE C 3 8.875 9.461 6.183 1.00 51.64 N ANISOU 13 N PHE C 3 2968 6515 10138 3352 3906 7205 N ATOM 15 CA PHE C 3 10.000 10.000 7.000 1.00 51.73 C ANISOU 15 CA PHE C 3 2963 6697 9995 3440 3985 6975 C END """ verbose=False file_name = "exercise_basic_pdbtools.pdb" pi = iotbx.pdb.input(source_info=None, lines=pdb_str) pi.write_pdb_file(file_name=file_name) output = "exercise_basic_pdbtools_mod.pdb" xrsp_init = xray_structure_plus(file_name = file_name) assert file_name.find('"') < 0 base = \ 'phenix.pdbtools "%s" suffix=none output.prefix=%s '%(file_name, output.replace(".pdb","")) for selection_str in [None, "chain A or chain C"]: selection = xrsp_init.selection(selection_strings = selection_str) if(selection_str is None): assert selection.size() == selection.count(True) else: assert selection.size() == 36 and selection.count(True) == 24 # cmd = base + 'adp.randomize=true modify.selection="%s"'%str(selection_str) print(cmd) check_adp_rand( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base + 'adp.set_b_iso=10.0 modify.selection="%s"'%str(selection_str) print(cmd) check_adp_set_b_iso( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base + 'adp.shift_b_iso=20.0 modify.selection="%s"'%str(selection_str) print(cmd) check_adp_rand( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base + 'adp.scale_adp=2.0 modify.selection="%s"'%str(selection_str) print(cmd) check_adp_rand( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base + 'adp.convert_to_iso=true modify.selection="%s"'%str(selection_str) print(cmd) check_adp_to_iso( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base + 'adp.convert_to_aniso=true modify.selection="%s"'%str(selection_str) print(cmd) check_adp_to_aniso( cmd, xrsp_init, output, selection, selection_str, verbose) # shake = 1.5 cmd = base+'sites.shake=%s modify.selection="%s"'%(str(shake), str(selection_str)) print(cmd) check_sites_shake( cmd, xrsp_init, output, selection, selection_str, shake, verbose) # cmd = base+'sites.rotate="1,2,3" sites.translate="4,5,6" modify.selection="%s"'%( str(selection_str)) print(cmd) check_sites_rt( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base+'occupancies.randomize=true modify.selection="%s"'%(str(selection_str)) print(cmd) check_occ_randomize( cmd, xrsp_init, output, selection, selection_str, verbose) # cmd = base+'occupancies.set=0.75 modify.selection="%s"'%(str(selection_str)) print(cmd) check_occ_set( cmd, xrsp_init, output, selection, selection_str, verbose) # remove_selection_str = "element C" cmd = base+'remove="%s" modify.selection="%s"'%( str(remove_selection_str), str(selection_str)) print(cmd) check_remove_selection( cmd, xrsp_init, output, selection, selection_str, remove_selection_str, verbose) # keep_selection_str = "element C" cmd = base+'keep="%s" modify.selection="%s"'%( str(keep_selection_str), str(selection_str)) print(cmd) check_keep_selection( cmd, xrsp_init, output, selection, selection_str, keep_selection_str, verbose) # # cmd = base print(cmd) check_all_none(cmd, xrsp_init, output, verbose) # cmd = base check_keep_remove_conflict(cmd, output, verbose) def check_adp_rand( cmd, xrsp_init, output, selection, selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance) assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,tolerance) assert approx_equal(xrsp.u_cart_not_used,xrsp_init.u_cart_not_used,tolerance) if(selection_str is None): assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,tolerance) assert not_approx_equal(xrsp.u_cart_used, xrsp_init.u_cart_used,tolerance) else: arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso)) arg2 = xrsp_init.u_iso_used.select(selection.select(xrsp_init.use_u_iso)) if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance) arg1 =xrsp.u_cart_used.select(selection.select(xrsp.use_u_aniso)) arg2 =xrsp_init.u_cart_used.select(selection.select(xrsp_init.use_u_aniso)) if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance) def check_adp_set_b_iso( cmd, xrsp_init, output, selection, selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance) assert approx_equal(xrsp.u_iso_not_used, xrsp_init.u_iso_not_used,tolerance) assert approx_equal(xrsp.u_cart_not_used,xrsp_init.u_cart_not_used,tolerance) if(selection_str is None): assert not_approx_equal(xrsp.u_iso_used, xrsp_init.u_iso_used,tolerance) for ucart in xrsp.u_cart: b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart)) if b_iso > 0: assert approx_equal(b_iso, 10, 0.005) else: assert approx_equal(b_iso, -78.956, 0.005) else: arg1 = xrsp.u_iso_used.select(selection.select(xrsp.use_u_iso)) arg2 = xrsp_init.u_iso_used.select(selection.select(xrsp_init.use_u_iso)) if(arg1.size() > 0): assert not_approx_equal(arg1, arg2,tolerance) for ucart in xrsp.u_cart: b_iso = adptbx.u_as_b(adptbx.u_cart_as_u_iso(ucart)) if b_iso > 0: assert approx_equal(b_iso, 10, 0.005) else: assert approx_equal(b_iso, -78.956, 0.005) def check_adp_to_iso( cmd, xrsp_init, output, selection, selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert not_approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance) assert xrsp.u_iso_not_used.size() == 0 assert xrsp_init.u_iso_not_used.size() > 0 assert xrsp.u_cart_used.size() == 0 assert xrsp_init.u_cart_used.size() > 0 def check_adp_to_aniso( cmd, xrsp_init, output, selection, selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) if(selection_str is None): assert not_approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert not_approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance) assert xrsp.u_iso_used.size() == 0 assert xrsp_init.u_iso_used.size() > 0 assert xrsp.u_cart_not_used.size() == 0 assert xrsp_init.u_cart_not_used.size() > 0 else: assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso,xrsp_init.use_u_aniso,tolerance) def check_sites_shake( cmd, xrsp_init, output, selection, selection_str, shake, verbose, tolerance=1.e-2): remove_files(output) print(cmd) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance) if(selection_str is None): diff = xrsp.sites_cart - xrsp_init.sites_cart assert approx_equal( math.sqrt(flex.mean(diff.dot())), shake, 1.e-3,tolerance) else: diff = xrsp.sites_cart - xrsp_init.sites_cart assert approx_equal( math.sqrt(flex.mean(diff.select(selection).dot())), shake, 1.e-3) assert approx_equal( math.sqrt(flex.mean(diff.select(~selection).dot())),0.,tolerance) def check_sites_rt( cmd, xrsp_init, output, selection, selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance) if(selection_str is None): diff = xrsp.sites_cart - xrsp_init.sites_cart assert math.sqrt(flex.mean(diff.dot())) > 1.0 else: diff = xrsp.sites_cart - xrsp_init.sites_cart assert math.sqrt(flex.mean(diff.select(selection).dot())) > 1.0 assert approx_equal( math.sqrt(flex.mean(diff.select(~selection).dot())),0.,tolerance) def check_occ_randomize( cmd, xrsp_init, output, selection,selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.sites_cart,xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance) if(selection_str is None): diff = flex.abs(xrsp.occ - xrsp_init.occ) assert flex.mean(diff) > 0.0 assert flex.max(diff) > 0.0 else: diff = flex.abs(xrsp.occ - xrsp_init.occ) assert flex.mean(diff) > 0.0 assert flex.max(diff) > 0.0 assert approx_equal(flex.mean(diff.select(~selection)),0.,tolerance) def check_occ_set( cmd, xrsp_init, output, selection,selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.sites_cart,xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance) if(selection_str is None): diff = flex.abs(xrsp.occ - xrsp_init.occ) assert flex.mean(diff) > 0.0 assert flex.max(diff) > 0.0 else: occ_init = xrsp_init.occ occ_mod = xrsp.occ assert occ_init.all_eq(1.0) assert occ_mod.select(~selection).all_eq(1.0) assert occ_mod.select(selection).all_eq(0.75) def check_remove_selection( cmd, xrsp_init, output, selection, selection_str, remove_selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) remove_selection = ~xrsp_init.selection( selection_strings = remove_selection_str) assert remove_selection.size() > remove_selection.count(True) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart.select(remove_selection),tolerance) assert approx_equal( xrsp.occ, xrsp_init.occ.select(remove_selection),tolerance) assert approx_equal( xrsp.u_iso, xrsp_init.u_iso.select(remove_selection),tolerance) assert approx_equal( xrsp.u_cart, xrsp_init.u_cart.select(remove_selection),tolerance) sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types() assert sct1.count("C") > 0 sct2 = xrsp.xray_structure.scatterers().extract_scattering_types() assert sct2.count("C") == 0 assert sct2.size() == remove_selection.count(True) assert sct1.size() > sct2.size() def check_keep_selection( cmd, xrsp_init, output, selection, selection_str, keep_selection_str, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) keep_selection = xrsp_init.selection(selection_strings = keep_selection_str) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart.select(keep_selection),tolerance) assert approx_equal(xrsp.occ, xrsp_init.occ.select(keep_selection),tolerance) assert approx_equal( xrsp.u_iso, xrsp_init.u_iso.select(keep_selection),tolerance) assert approx_equal( xrsp.u_cart, xrsp_init.u_cart.select(keep_selection),tolerance) sct1 = xrsp_init.xray_structure.scatterers().extract_scattering_types() assert sct1.count("C") > 0 and sct1.size() > sct1.count("C") sct2 = xrsp.xray_structure.scatterers().extract_scattering_types() assert sct2.count("C") == sct2.size() assert sct1.size() > keep_selection.count(True) assert sct1.size() > sct2.size() def check_all_none(cmd, xrsp_init, output, verbose, tolerance=1.e-3): remove_files(output) run_command(command=cmd, verbose=verbose) xrsp = xray_structure_plus(file_name = output) assert approx_equal(xrsp.occ, xrsp_init.occ,tolerance) assert approx_equal(xrsp.sites_cart, xrsp_init.sites_cart,tolerance) assert approx_equal(xrsp.use_u_iso, xrsp_init.use_u_iso,tolerance) assert approx_equal(xrsp.use_u_aniso, xrsp_init.use_u_aniso,tolerance) assert approx_equal(xrsp.u_iso, xrsp_init.u_iso,tolerance) assert approx_equal(xrsp.u_cart, xrsp_init.u_cart,tolerance) def check_keep_remove_conflict(cmd, output, verbose): cmd += " keep=all remove=all " print(cmd) r = easy_run.go(cmd) assert r.stdout_lines[-1]==\ "Sorry: 'keep' and 'remove' keywords cannot be used simultaneously." def exercise_multiple(): pdb_str = """\ ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O ATOM 2 CA LYS B 32 10.574 8.177 11.768 1.00 11.49 C ATOM 3 CB LYS B 32 9.193 8.732 12.170 1.00 12.23 C ATOM 4 CA VAL C 33 11.708 5.617 14.332 1.00 11.42 C ATOM 5 CB VAL C 33 11.101 4.227 14.591 1.00 11.47 C ATOM 6 O HOH C 3 1.132 5.963 7.065 1.00 15.00 O ATOM 7 O HOH C 4 4.132 9.963 7.800 1.00 15.00 O TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="exercise_multiple.pdb") params = """\ modify{ adp { atom_selection = chain A randomize = True } adp { atom_selection = chain B shift_b_iso = 10 } sites { atom_selection = chain B shake = 1.5 } sites { atom_selection = chain A or chain C translate = 1 2 3 rotate = 4 5 6 } occupancies { atom_selection = chain A randomize = True } occupancies { atom_selection = chain C set = 0.1 } } """ with open("params", "w") as f: f.write(params) cmd = 'phenix.pdbtools exercise_multiple.pdb params' print(cmd) result = run_command(command=cmd, verbose=False) lines = [l.strip() for l in result.stdout_lines] expected_lines = [ "Randomizing ADP: selected atoms: 1 of 7", "Adding shift = 10.00 to all ADP: selected atoms: 2 of 7", "Shaking sites (RMS = 1.500): selected atoms: 2 of 7", "Rigid body shift: selected atoms: 5 of 7", "Randomizing occupancies: selected atoms: 1 of 7", "Setting occupancies to: 0.100: selected atoms: 4 of 7" ] for line in expected_lines: assert line in lines def exercise_no_cryst1(): pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="exercise_no_cryst1.pdb") cmd = 'phenix.pdbtools exercise_no_cryst1.pdb sites.rotate="0 0 0"' print(cmd) run_command(command=cmd, verbose=False) lines1 = [] with open("exercise_no_cryst1.pdb","r") as f: lines = f.readlines() for line in lines: line = line.strip() assert line.count("CRYST1") == 0 if(line.startswith("ATOM") or line.startswith("HETATM")): lines1.append(line) lines2 = [] with open("exercise_no_cryst1_modified.pdb","r") as f: lines = f.readlines() for line in lines: line = line.strip() assert line.count("CRYST1") == 0 if(line.startswith("ATOM") or line.startswith("HETATM")): lines2.append(line) assert len(lines1) == len(lines2) for l1,l2 in zip(lines1, lines2): assert l1[11:70].strip() == l2[11:70].strip() def exercise_truncate_to_polyala(): pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="exercise_exercise_truncate_to_polyala.pdb") cmd = 'phenix.pdbtools exercise_exercise_truncate_to_polyala.pdb truncate_to_polyala=true' print(cmd) run_command(command=cmd) gly_atom_names = [" N ", " CA ", " C ", " O ", " CB "] pdb_inp = iotbx.pdb.input( file_name="exercise_exercise_truncate_to_polyala_modified.pdb") for a in pdb_inp.construct_hierarchy().atoms_with_labels(): assert a.name in gly_atom_names def exercise_set_charge(): input_pdb = """ ATOM 1 CL CL X 1 0.000 0.000 0.000 1.00 20.00 CL END """ with open("tmp_cl.pdb", "w") as f: f.write(input_pdb) cmd='phenix.pdbtools tmp_cl.pdb charge_selection="element Cl" charge=-1' print(cmd) run_command(command=cmd, verbose=False) pdb_in = iotbx.pdb.input("tmp_cl_modified.pdb") hierarchy = pdb_in.construct_hierarchy() xrs = pdb_in.xray_structure_simple() assert (xrs.scatterers()[0].scattering_type == 'Cl1-') assert (hierarchy.atoms()[0].charge == '1-') def exercise_renumber_residues(): input_pdb = """ ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 O ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 O ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 O TER ATOM 4 O SER B 4 0.297 0.843 7.226 1.00 7.65 O ATOM 5 OG ASER B 4 -2.625 1.057 4.064 0.50 5.46 O ATOM 6 OG BSER B 4 -0.885 0.189 3.843 0.50 11.74 O ATOM 7 O LEU B 8 3.613 4.307 6.646 1.00 5.39 O ATOM 8 O PRO B -1 4.398 6.723 8.658 1.00 6.65 O ATOM 9 O TYR B 7 7.294 7.360 6.923 1.00 8.75 O ATOM 10 O CYS B 0 5.256 8.262 4.185 1.00 6.08 O ATOM 11 O ALA B 9 3.028 10.447 5.584 1.00 7.39 O TER ATOM 12 O LEU C 0 5.613 12.448 6.864 1.00 7.32 O TER END """ expected_output_pdb = """ATOM 1 O GLY A 1 1.434 1.460 2.496 1.00 6.04 O ATOM 2 O CYS A 2 2.196 4.467 3.911 1.00 4.51 O ATOM 3 O CYS A 3 -1.433 4.734 5.405 1.00 7.85 O TER ATOM 4 O SER B 1 0.297 0.843 7.226 1.00 7.65 O ATOM 5 OG ASER B 1 -2.625 1.057 4.064 0.50 5.46 O ATOM 6 OG BSER B 1 -0.885 0.189 3.843 0.50 11.74 O ATOM 7 O LEU B 2 3.613 4.307 6.646 1.00 5.39 O ATOM 8 O PRO B 3 4.398 6.723 8.658 1.00 6.65 O ATOM 9 O TYR B 4 7.294 7.360 6.923 1.00 8.75 O ATOM 10 O CYS B 5 5.256 8.262 4.185 1.00 6.08 O ATOM 11 O ALA B 6 3.028 10.447 5.584 1.00 7.39 O TER ATOM 12 O LEU C 1 5.613 12.448 6.864 1.00 7.32 O TER """ ifn = "exercise_renumber_residues.pdb" with open(ifn,"w") as f: f.write(input_pdb) cmd = 'phenix.pdbtools "%s" renumber_residues=true'%ifn print(cmd) run_command(command=cmd, verbose=False) with open("exercise_renumber_residues_modified.pdb") as f: lines = f.readlines() for line1, line2 in zip(lines, expected_output_pdb.splitlines()): line1 = line1.strip() line2 = line2.strip() assert line1 == line2,[line1, line2] # now only a selected chain expected_output_pdb_2 = """\ ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 O ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 O ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 O TER ATOM 4 O SER B 1 0.297 0.843 7.226 1.00 7.65 O ATOM 5 OG ASER B 1 -2.625 1.057 4.064 0.50 5.46 O ATOM 6 OG BSER B 1 -0.885 0.189 3.843 0.50 11.74 O ATOM 7 O LEU B 2 3.613 4.307 6.646 1.00 5.39 O ATOM 8 O PRO B 3 4.398 6.723 8.658 1.00 6.65 O ATOM 9 O TYR B 4 7.294 7.360 6.923 1.00 8.75 O ATOM 10 O CYS B 5 5.256 8.262 4.185 1.00 6.08 O ATOM 11 O ALA B 6 3.028 10.447 5.584 1.00 7.39 O TER ATOM 12 O LEU C 0 5.613 12.448 6.864 1.00 7.32 O TER """ cmd = "phenix.pdbtools \"%s\" renumber_residues=true modify.selection=\"chain B\"" % ifn print(cmd) run_command(command=cmd, verbose=False) with open("exercise_renumber_residues_modified.pdb") as f: for line1, line2 in zip(f.readlines(), expected_output_pdb_2.splitlines()): assert (line1.strip() == line2.strip()) cmd="phenix.pdbtools \"%s\" increment_resseq=10 modify.selection=\"chain B\"" % ifn print(cmd) run_command(command=cmd, verbose=False) with open("exercise_renumber_residues_modified.pdb") as f: pdb_new = f.read() expected_output_pdb_3 = """\ ATOM 1 O GLY A 3 1.434 1.460 2.496 1.00 6.04 O ATOM 2 O CYS A 7 2.196 4.467 3.911 1.00 4.51 O ATOM 3 O CYS A 1 -1.433 4.734 5.405 1.00 7.85 O TER ATOM 4 O SER B 14 0.297 0.843 7.226 1.00 7.65 O ATOM 5 OG ASER B 14 -2.625 1.057 4.064 0.50 5.46 O ATOM 6 OG BSER B 14 -0.885 0.189 3.843 0.50 11.74 O ATOM 7 O LEU B 18 3.613 4.307 6.646 1.00 5.39 O ATOM 8 O PRO B 9 4.398 6.723 8.658 1.00 6.65 O ATOM 9 O TYR B 17 7.294 7.360 6.923 1.00 8.75 O ATOM 10 O CYS B 10 5.256 8.262 4.185 1.00 6.08 O ATOM 11 O ALA B 19 3.028 10.447 5.584 1.00 7.39 O TER ATOM 12 O LEU C 0 5.613 12.448 6.864 1.00 7.32 O TER END """ assert not show_diff(pdb_new, expected_output_pdb_3) def exercise_neutralize_scatterers(): input_pdb = """ATOM 1 N TYR 22 -0.813 -2.199 1.423 1.00 0.00 N ATOM 2 CA TYR 22 0.612 -2.082 1.127 1.00 0.00 C ATOM 3 C TYR 22 1.441 -2.790 2.171 1.00 0.00 C ATOM 4 O TYR 22 0.927 -3.375 3.128 1.00 0.00 O ATOM 5 CB TYR 22 1.052 -0.589 1.096 1.00 0.00 C ATOM 6 CG TYR 22 0.390 0.302 0.038 1.00 0.00 C ATOM 7 CD1 TYR 22 0.807 0.254 -1.296 1.00 0.00 C ATOM 8 CD2 TYR 22 -0.647 1.164 0.406 1.00 0.00 C ATOM 9 CE1 TYR 22 0.188 1.057 -2.250 1.00 0.00 C ATOM 10 CE2 TYR 22 -1.264 1.966 -0.549 1.00 0.00 C ATOM 11 CZ TYR 22 -0.846 1.912 -1.877 1.00 0.00 C ATOM 12 OH TYR 22 -1.452 2.696 -2.817 1.00 0.00 O1- """ expected_output_pdb = """ATOM 1 N TYR 22 -0.813 -2.199 1.423 1.00 10.00 N ATOM 2 CA TYR 22 0.612 -2.082 1.127 1.00 10.00 C ATOM 3 C TYR 22 1.441 -2.790 2.171 1.00 10.00 C ATOM 4 O TYR 22 0.927 -3.375 3.128 1.00 10.00 O ATOM 5 CB TYR 22 1.052 -0.589 1.096 1.00 10.00 C ATOM 6 CG TYR 22 0.390 0.302 0.038 1.00 10.00 C ATOM 7 CD1 TYR 22 0.807 0.254 -1.296 1.00 10.00 C ATOM 8 CD2 TYR 22 -0.647 1.164 0.406 1.00 10.00 C ATOM 9 CE1 TYR 22 0.188 1.057 -2.250 1.00 10.00 C ATOM 10 CE2 TYR 22 -1.264 1.966 -0.549 1.00 10.00 C ATOM 11 CZ TYR 22 -0.846 1.912 -1.877 1.00 10.00 C ATOM 12 OH TYR 22 -1.452 2.696 -2.817 1.00 10.00 O """ ifn = "exercise_neutralize_scatterers.pdb" with open(ifn,"w") as f: f.write(input_pdb) cmd = 'phenix.pdbtools "%s" neutralize_scatterers=true adp.set_b_iso=10'%ifn print(cmd) run_command(command=cmd, verbose=False) with open(ifn.replace(".pdb","_modified.pdb")) as f: lines = f.readlines() for line1, line2 in zip(lines, expected_output_pdb.splitlines()): line1 = line1.strip() line2 = line2.strip() assert line1 == line2 def exercise_remove_atoms(): import random random.seed(1) flex.set_random_seed(1) pdb_str = """ ATOM 1 N AMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 37 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N AMET B 38 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 38 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 38 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 38 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 38 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 38 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 38 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 38 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 38 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 38 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 38 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 38 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 38 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 38 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 38 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 38 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N AMET B 39 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA AMET B 39 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C AMET B 39 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O AMET B 39 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB AMET B 39 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG AMET B 39 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD AMET B 39 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE AMET B 39 8.775 5.000 10.645 1.00 10.00 C ATOM 1 N BMET B 39 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA BMET B 39 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C BMET B 39 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O BMET B 39 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB BMET B 39 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG BMET B 39 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD BMET B 39 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE BMET B 39 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str) ph_in = pi.construct_hierarchy() s1 = ph_in.atoms_size() pi.write_pdb_file(file_name="exercise_remove_atoms.pdb") cmd = " ".join([ "phenix.pdbtools", "exercise_remove_atoms.pdb", "remove_fraction=0.1"]) print(cmd) run_command(command=cmd, verbose=False) pi = iotbx.pdb.input(file_name="exercise_remove_atoms_modified.pdb") ph_in = pi.construct_hierarchy() s2 = ph_in.atoms_size() f = s2*100./s1 # # UNSTABLE 3x # assert f>77 and f<100, f # was getting 79.16, 70.8333 on anaconda t96, def exercise_change_of_basis(): with open("tmp_pdbtools_cb_op.pdb", "w") as f: f.write("""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 1 N GLY A 1 -9.009 4.612 6.102 1.00 16.77 N ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 3 C GLY A 1 -8.015 3.140 4.419 1.00 16.16 C ATOM 4 O GLY A 1 -7.523 2.521 5.381 1.00 16.78 O """) cmd = "phenix.pdbtools tmp_pdbtools_cb_op.pdb change_of_basis='a,c,b'" run_command(command=cmd, verbose=False) with open("tmp_pdbtools_cb_op_modified.pdb") as f: lines = f.readlines() for line in lines: if line.startswith("CRYST1"): assert (line.strip() == """CRYST1 21.937 23.477 4.866 90.00 90.00 107.08 P 1 1 21""") break def exercise_mmcif_support(): from libtbx.test_utils import open_tmp_file f = open_tmp_file(suffix="pdbtools.cif") f.write("""\ data_phenix _space_group.name_H-M_alt 'C 1 2 1' _space_group.name_Hall ' C 2y' _cell.length_a 46.053 _cell.length_b 9.561 _cell.length_c 20.871 _cell.angle_alpha 90.0 _cell.angle_beta 97.43 _cell.angle_gamma 90.0 _cell.volume 9112.60599144 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 2 CA . LYS A 1 ? 7.49733 -0.62028 4.35289 1.000 10.25989 C ? A ? 1 1 ATOM 11 CA . LEU A 2 ? 3.72032 -0.19320 3.89326 1.000 7.80433 C ? A ? 2 1 ATOM 19 CA . VAL A 3 ? 0.78668 -0.39555 6.35234 1.000 5.03864 C ? A ? 3 1 ATOM 26 CA . PHE A 4 ? -2.75438 -0.21383 5.02429 1.000 8.93080 C ? A ? 4 1 ATOM 37 CA . PHE A 5 ? -6.05155 -0.46197 6.85390 1.000 9.57417 C ? A ? 5 1 ATOM 48 CA . ALA A 6 ? -9.57646 -0.10942 5.55847 1.000 17.73488 C ? A ? 6 1 ATOM 54 CA . LYS B 1 ? -8.86604 -5.20044 5.46515 1.000 16.15297 C ? B ? 7 1 """) f.close() cmd = " ".join(["phenix.pdbtools", "\"%s\"" % f.name, "rename_chain_id.old_id=A", "rename_chain_id.new_id=C"]) print(cmd) run_command(command=cmd, verbose=False) ofn = f.name[:].replace(".cif","_modified.cif") assert os.path.isfile(ofn) pdb_inp = iotbx.pdb.input(file_name=ofn) assert pdb_inp.file_type() == "mmcif" hierarchy = pdb_inp.construct_hierarchy() assert [chain.id for chain in hierarchy.chains()] == ['C', 'B'] def exercise_mmcif_support_2(prefix="tst_pdbtools_mmcif2"): f = open("%s.pdb" % prefix, 'w') f.write("""\ HELIX 1 1 GLN A 10 GLN A 14 5 5 HELIX 2 2 ARG A 17 ASN A 29 1 13 SHEET 1 A 2 GLN A 33 GLN A 38 0 SHEET 2 A 2 GLN A 51 GLN A 56 1 O VAL A 54 N ILE A 35 SSBOND 1 CYS A 4 CYS A 49 CRYST1 62.654 62.654 45.906 90.00 90.00 90.00 P 43 21 2 SCALE1 0.015961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021784 0.00000 ATOM 1 N GLN A 3 23.762 12.429 1.265 1.00 45.30 N ATOM 2 CA GLN A 3 22.670 12.004 2.148 1.00 39.46 C ATOM 3 C GLN A 3 21.818 10.942 1.458 1.00 42.86 C ATOM 4 O GLN A 3 21.337 11.133 0.339 1.00 44.81 O ATOM 5 CB GLN A 3 21.794 13.195 2.571 1.00 42.53 C ATOM 6 N CYS A 4 21.620 9.817 2.129 1.00 36.33 N ATOM 7 CA CYS A 4 20.902 8.709 1.518 1.00 31.46 C ATOM 8 C CYS A 4 19.419 8.891 1.670 1.00 34.16 C ATOM 9 O CYS A 4 18.979 9.537 2.607 1.00 38.12 O ATOM 10 CB CYS A 4 21.307 7.409 2.205 1.00 31.53 C ATOM 11 SG CYS A 4 23.070 7.194 2.148 1.00 29.88 S ATOM 12 N SER A 5 18.657 8.290 0.760 1.00 33.83 N ATOM 13 CA SER A 5 17.211 8.293 0.854 1.00 38.94 C ATOM 14 C SER A 5 16.676 6.917 1.254 1.00 32.88 C ATOM 15 O SER A 5 17.295 5.879 0.981 1.00 32.57 O ATOM 16 CB SER A 5 16.603 8.683 -0.488 1.00 39.48 C ATOM 17 OG SER A 5 16.893 7.668 -1.432 1.00 47.16 O ATOM 18 N GLY A 6 15.520 6.924 1.901 1.00 31.69 N ATOM 19 CA GLY A 6 14.811 5.694 2.191 1.00 32.41 C ATOM 20 C GLY A 6 15.257 5.112 3.511 1.00 29.00 C ATOM 2 CA GLN A 10 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 11 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 12 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 13 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 14 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 33 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 34 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 35 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 36 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 37 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 38 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 51 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 52 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 53 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 54 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 55 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 56 22.670 12.004 2.148 1.00 39.46 C """) f.close() cmd = " ".join([ "phenix.pdb_as_cif", "%s.pdb" % prefix]) run_command(command=cmd, verbose=False) cmd = " ".join([ "phenix.pdbtools", "%s.cif" % prefix, "suffix=none", "output.prefix=%s" % prefix]) print(cmd) run_command(command=cmd, verbose=False) cif_f = open("%s.cif" % prefix, 'r') cif_l = cif_f.readlines() cif_f.close() for l in ["_cell.angle_alpha 90.000\n", " _struct_conf.pdbx_PDB_helix_id\n", " _struct_sheet.id\n", " _struct_sheet_range.id\n", " _atom_site.label_atom_id\n"]: assert l in cif_l, "%s not in cif file!" % l def exercise_move_waters(): pdb_in = """\ ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O ATOM 19 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H ATOM 20 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H HETATM 2397 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P HETATM 2398 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O HETATM 2399 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O HETATM 2400 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O HETATM 2401 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O ATOM 23 CL CL B 1 6.302 6.419 1.560 0.50 10.00 CL HETATM 6362 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O HETATM 6363 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O HETATM 6364 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O HETATM 6365 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O HETATM 6366 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O """ pdb_out = """\ ATOM 1 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 2 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C ATOM 3 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C TER HETATM 6 O1 PO4 1 -6.610 24.262 38.967 1.00 40.00 O HETATM 7 O2 PO4 1 -6.901 25.919 37.049 1.00 41.07 O HETATM 8 O3 PO4 1 -8.894 24.741 38.097 1.00 45.09 O HETATM 9 O4 PO4 1 -7.722 26.556 39.350 1.00 42.48 O HETATM 10 P PO4 1 -7.520 25.376 38.369 1.00 39.37 P ATOM 11 CL CL B 1 6.302 6.419 1.560 0.50 10.00 Cl ATOM 12 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O ATOM 13 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O ATOM 14 H1 HOH A 3 1.160 5.211 6.437 1.00 15.00 H ATOM 15 H2 HOH A 3 1.122 5.579 7.967 1.00 15.00 H HETATM 16 O HOH B 2 47.616 10.724 150.212 1.00 46.48 B O HETATM 17 O AHOH B 3 46.408 16.672 146.066 0.50 12.81 B O HETATM 18 O HOH B 4 29.343 12.806 185.898 1.00 35.57 B O HETATM 19 O BHOH B 5 43.786 12.615 147.734 0.50 28.43 B O HETATM 20 O HOH B 6 35.068 19.167 155.349 1.00 15.97 B O END """ with open("tst_pdbtools_move_waters.pdb", "w") as f: f.write(pdb_in) cmd = "phenix.pdbtools tst_pdbtools_move_waters.pdb move_waters_last=True" print(cmd) run_command(command=cmd, verbose=False) with open("tst_pdbtools_move_waters_modified.pdb") as f: pdb_new = f.read() assert pdb_new == pdb_out, pdb_new def exercise_stop_for_unknowns(): pdb_in = """\ HETATM 16 O UNK B 2 47.616 10.724 150.212 1.00 46.48 B O HETATM 17 O UNK B 3 46.408 16.672 146.066 0.50 12.81 B O HETATM 18 O UNK B 4 29.343 12.806 185.898 1.00 35.57 B O HETATM 19 O UNK B 5 43.786 12.615 147.734 0.50 28.43 B O HETATM 20 O UNK B 6 35.068 19.167 155.349 1.00 15.97 B O """ with open("tst_pdbtools_unknown.pdb", "w") as f: f.write(pdb_in) cmd = "phenix.pdbtools tst_pdbtools_unknown.pdb set_b_iso=20" print(cmd) run_command(command=cmd, sorry_expected=True) cmd2 = cmd + " stop_for_unknowns=False" print(cmd2) run_command(command=cmd2) def exercise_remove_alt_confs(): pdb_in = """\ ATOM 16 O AHOH A 2 5.131 5.251 5.823 0.60 10.00 O ATOM 60 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 63 CB ALYS A 32 9.197 8.686 12.246 0.29 14.71 C ATOM 64 CB BLYS A 32 9.193 8.732 12.170 0.71 12.23 C ATOM 74 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 77 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C ATOM 18 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O ATOM 19 O BHOH A 4 4.132 9.963 7.800 0.50 15.00 O """ with open("tst_pdbtools_alt_confs.pdb", "w") as f: f.write(pdb_in) cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True" print(cmd) run_command(command=cmd, verbose=False) with open("tst_pdbtools_alt_confs_modified.pdb") as f: pdb_new = f.read() assert (pdb_new == """\ ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 3 CB LYS A 32 9.197 8.686 12.246 1.00 14.71 C ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O TER END """) cmd = "phenix.pdbtools tst_pdbtools_alt_confs.pdb remove_alt_confs=True " +\ "always_keep_one_conformer=True" run_command(command=cmd, verbose=False) with open("tst_pdbtools_alt_confs_modified.pdb") as f: pdb_new = f.read() assert (pdb_new == """\ ATOM 1 O HOH A 2 5.131 5.251 5.823 1.00 10.00 O ATOM 2 CA LYS A 32 10.574 8.177 11.768 1.00 11.49 C ATOM 3 CB LYS A 32 9.193 8.732 12.170 1.00 12.23 C ATOM 4 CA VAL A 33 11.708 5.617 14.332 1.00 11.42 C ATOM 5 CB VAL A 33 11.101 4.227 14.591 1.00 11.47 C ATOM 6 O HOH A 3 1.132 5.963 7.065 1.00 15.00 O ATOM 7 O HOH A 4 4.132 9.963 7.800 1.00 15.00 O TER END """) def exercise_convert_met_to_semet(): pdb_str_met = """ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str_met) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="exercise_convert_met_to_semet.pdb") cmd = " ".join([ "phenix.pdbtools", "exercise_convert_met_to_semet.pdb", "convert_met_to_semet=true"]) print(cmd) run_command(command=cmd, verbose=False) pi_out = iotbx.pdb.input( file_name="exercise_convert_met_to_semet_modified.pdb" ).construct_hierarchy() for rg in pi_out.residue_groups(): for rn in rg.unique_resnames(): assert rn=="MSE" cmd = " ".join([ "phenix.pdbtools", "exercise_convert_met_to_semet_modified.pdb", "convert_semet_to_met=true"]) run_command(command=cmd, verbose=False) pi_out = iotbx.pdb.input( file_name="exercise_convert_met_to_semet_modified_modified.pdb" ).construct_hierarchy() for rg in pi_out.residue_groups(): for rn in rg.unique_resnames(): assert rn=="MET" def exercise_switch_rotamers(prefix="exercise_switch_rotamers"): pdb_str_met = """ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str_met) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="%s.pdb"%prefix) for o in ["max_distant","min_distant","exact_match","fix_outliers"]: cmd = " ".join([ "phenix.pdbtools", "%s.pdb"%prefix, "switch_rotamers=%s"%o, "suffix=none", "output.prefix=%s_%s"%(o,prefix)]) print(cmd) run_command(command=cmd, verbose=False) def exercise_segid_manipulations(prefix="tst_pdbtools_ex_segid"): pdb_str_met = """ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 A N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 A C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 A C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 A O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 A C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 A C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 A S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 A C TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str_met) ph_met_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="%s.pdb"%prefix) for o in ["clear_seg_id", "set_seg_id_to_chain_id"]: cmd = " ".join([ "phenix.pdbtools", "%s.pdb"%prefix, "%s=True" % o, "suffix=none", "output.prefix=%s_%s"%(o,prefix)]) print(cmd) run_command(command=cmd, verbose=False) with open("%s_%s.pdb"%(o,prefix)) as f: pdb_new = f.read() if o == "clear_seg_id": assert (pdb_new == """\ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 C TER END """), pdb_new else: assert (pdb_new == """\ ATOM 1 N MET B 37 7.525 5.296 6.399 1.00 10.00 B N ATOM 2 CA MET B 37 6.533 6.338 6.634 1.00 10.00 B C ATOM 3 C MET B 37 6.175 7.044 5.330 1.00 10.00 B C ATOM 4 O MET B 37 5.000 7.200 5.000 1.00 10.00 B O ATOM 5 CB MET B 37 7.051 7.351 7.655 1.00 10.00 B C ATOM 6 CG MET B 37 7.377 6.750 9.013 1.00 10.00 B C ATOM 7 SD MET B 37 8.647 5.473 8.922 1.00 10.00 B S ATOM 8 CE MET B 37 8.775 5.000 10.645 1.00 10.00 B C TER END """), pdb_new def exercise_flip_symmetric_amino_acids( prefix="exercise_flip_symmetric_amino_acids"): pdb_str_in = """ ATOM 3356 N ARG H 228 20.811-103.620 24.514 1.00 56.77 N ATOM 3357 CA ARG H 228 21.863-104.460 23.967 1.00 64.89 C ATOM 3358 C ARG H 228 21.258-105.679 23.284 1.00 69.98 C ATOM 3359 O ARG H 228 20.179-106.141 23.657 1.00 70.23 O ATOM 3360 CB ARG H 228 22.810-104.925 25.075 1.00 63.55 C ATOM 3361 CG ARG H 228 23.354-103.810 25.936 1.00 64.01 C ATOM 3362 CD ARG H 228 24.570-104.271 26.712 1.00 65.11 C ATOM 3363 NE ARG H 228 25.126-103.194 27.523 1.00 68.09 N ATOM 3364 CZ ARG H 228 26.373-103.169 27.982 1.00 66.49 C ATOM 3365 NH1 ARG H 228 26.790-102.145 28.717 1.00 64.08 N ATOM 3366 NH2 ARG H 228 27.205-104.163 27.694 1.00 65.11 N TER END """ pdb_str_out = """ ATOM 3355 N ARG H 228 20.811-103.620 24.514 1.00 56.77 N ATOM 3356 CA ARG H 228 21.863-104.460 23.967 1.00 64.89 C ATOM 3357 C ARG H 228 21.258-105.679 23.284 1.00 69.98 C ATOM 3358 O ARG H 228 20.179-106.141 23.657 1.00 70.23 O ATOM 3359 CB ARG H 228 22.810-104.925 25.075 1.00 63.55 C ATOM 3360 CG ARG H 228 23.354-103.810 25.936 1.00 64.01 C ATOM 3361 CD ARG H 228 24.570-104.271 26.712 1.00 65.11 C ATOM 3362 NE ARG H 228 25.126-103.194 27.523 1.00 68.09 N ATOM 3363 CZ ARG H 228 26.373-103.169 27.982 1.00 66.49 C ATOM 3364 NH1 ARG H 228 27.205-104.163 27.694 1.00 65.11 N ATOM 3365 NH2 ARG H 228 26.790-102.145 28.717 1.00 64.08 N TER END """ pi = iotbx.pdb.input(source_info=None, lines=pdb_str_in) ph_in = pi.construct_hierarchy() pi.write_pdb_file(file_name="%s.pdb"%prefix) cmd = " ".join([ "phenix.pdbtools", "%s.pdb"%prefix, "flip_symmetric_amino_acids=True", "output.prefix=%s"%prefix]) print(cmd) run_command(command=cmd, verbose=False) h1 = iotbx.pdb.input(source_info=None, lines=pdb_str_out).construct_hierarchy() h2 = iotbx.pdb.input(file_name= "exercise_flip_symmetric_amino_acids_modified.pdb").construct_hierarchy() assert h1.is_similar_hierarchy(h2) ph_in.flip_symmetric_amino_acids() assert h1.is_similar_hierarchy(ph_in) def exercise_result_is_empty(prefix='exercise_result_is_empty'): pdb_str = """ HELIX 1 1 GLN A 10 GLN A 14 5 5 HELIX 2 2 ARG A 17 ASN A 29 1 13 SHEET 1 A 2 GLN A 33 GLN A 38 0 SHEET 2 A 2 GLN A 51 GLN A 56 1 O VAL A 54 N ILE A 35 SSBOND 1 CYS A 4 CYS A 49 CRYST1 62.654 62.654 45.906 90.00 90.00 90.00 P 43 21 2 SCALE1 0.015961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021784 0.00000 ATOM 1 N GLN A 3 23.762 12.429 1.265 1.00 45.30 N ATOM 2 CA GLN A 3 22.670 12.004 2.148 1.00 39.46 C ATOM 3 C GLN A 3 21.818 10.942 1.458 1.00 42.86 C ATOM 4 O GLN A 3 21.337 11.133 0.339 1.00 44.81 O ATOM 5 CB GLN A 3 21.794 13.195 2.571 1.00 42.53 C ATOM 6 N CYS A 4 21.620 9.817 2.129 1.00 36.33 N ATOM 7 CA CYS A 4 20.902 8.709 1.518 1.00 31.46 C ATOM 8 C CYS A 4 19.419 8.891 1.670 1.00 34.16 C ATOM 9 O CYS A 4 18.979 9.537 2.607 1.00 38.12 O ATOM 10 CB CYS A 4 21.307 7.409 2.205 1.00 31.53 C ATOM 11 SG CYS A 4 23.070 7.194 2.148 1.00 29.88 S ATOM 12 N SER A 5 18.657 8.290 0.760 1.00 33.83 N ATOM 13 CA SER A 5 17.211 8.293 0.854 1.00 38.94 C ATOM 14 C SER A 5 16.676 6.917 1.254 1.00 32.88 C ATOM 15 O SER A 5 17.295 5.879 0.981 1.00 32.57 O ATOM 16 CB SER A 5 16.603 8.683 -0.488 1.00 39.48 C ATOM 17 OG SER A 5 16.893 7.668 -1.432 1.00 47.16 O ATOM 18 N GLY A 6 15.520 6.924 1.901 1.00 31.69 N ATOM 19 CA GLY A 6 14.811 5.694 2.191 1.00 32.41 C ATOM 20 C GLY A 6 15.257 5.112 3.511 1.00 29.00 C ATOM 2 CA GLN A 10 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 11 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 12 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 13 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 14 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 33 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 34 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 35 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 36 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 37 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 38 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 51 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 52 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 53 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 54 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 55 22.670 12.004 2.148 1.00 39.46 C ATOM 2 CA GLN A 56 22.670 12.004 2.148 1.00 39.46 C """ with open("%s.pdb"%prefix, 'w') as f: f.write(pdb_str) cmd = " ".join([ "phenix.pdbtools", "%s.pdb"%prefix, "keep='resname ALA'", "output.prefix=out_%s"%(prefix)]) print(cmd) run_command(command=cmd, verbose=False) # assert os.path.isfile("out_%s_modified.pdb"%(prefix)) with open("out_%s_modified.pdb"%(prefix), 'r') as f: pdb_new = f.read() assert pdb_new == """\ CRYST1 62.654 62.654 45.906 90.00 90.00 90.00 P 43 21 2 SCALE1 0.015961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.015961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021784 0.00000 END """ def exercise(args): exercise_flip_symmetric_amino_acids() exercise_switch_rotamers() exercise_mmcif_support_2() exercise_basic() exercise_multiple() exercise_no_cryst1() exercise_renumber_residues() exercise_change_of_basis() exercise_move_waters() exercise_remove_alt_confs() exercise_truncate_to_polyala() exercise_convert_met_to_semet() exercise_set_charge() exercise_neutralize_scatterers() exercise_remove_atoms() exercise_mmcif_support() exercise_segid_manipulations() exercise_result_is_empty() if (__name__ == "__main__"): exercise(sys.argv[1:])