from __future__ import absolute_import, division, print_function from mmtbx.monomer_library import pdb_interpretation from mmtbx.refinement.occupancies import occupancy_selections from mmtbx.command_line import fmodel import mmtbx.model from iotbx import file_reader import iotbx.pdb import iotbx.phil from libtbx.test_utils import approx_equal, Exception_expected from libtbx.utils import format_cpu_times, null_out, Sorry import libtbx.load_env from six.moves import cStringIO as StringIO import os import sys from six.moves import zip def extract_serials(atoms, occ_groups): r = [] # for atom in atoms: # assert atom.serial == atom.i_seq, "%s %d" % (atom.serial, atom.i_seq) for i in occ_groups: ri = [] for j in i: ri.append([int(atoms[k].serial) for k in j]) r.append(ri) return r def make_up_other_constrained_groups_obj(selections): result = [] class foo: def __init__(self, selection): self.selection=selection for sel in selections: result.append( foo(selection = sel) ) return result def get_model(file_name, log): pdb_interpretation_params = iotbx.phil.parse( input_string=pdb_interpretation.grand_master_phil_str, process_includes=True).extract() pdb_interpretation_params.pdb_interpretation.sort_atoms=False pdb_inp = iotbx.pdb.input(file_name=file_name) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = False, log=log) model.process(pdb_interpretation_params=pdb_interpretation_params) return model def get_model_str(strings, log): pdb_interpretation_params = iotbx.phil.parse( input_string=pdb_interpretation.grand_master_phil_str, process_includes=True).extract() pdb_interpretation_params.pdb_interpretation.sort_atoms=False pdb_inp = iotbx.pdb.input(lines=strings, source_info=None) model = mmtbx.model.manager( model_input = pdb_inp, stop_for_unknowns = False, log=log) model.process(pdb_interpretation_params=pdb_interpretation_params) return model def exercise_00(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) base = [ [[2],[3]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[24,25,26,27],[28,29,30,31]] ] # default res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) target = base[:] target.insert(3, [[21]]) target.insert(4, [[23]]) assert approx_equal(res, target) # default + add water res = occupancy_selections( model = model, add_water = True, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) base_21_23 = target[:] target.extend([[[18]], [[19]], [[20]], [[22]]]) assert approx_equal(res, target) # 1 res = occupancy_selections( model = model, as_flex_arrays = False, other_individual_selection_strings = ['resseq 0 and not (altloc A or altloc B)']) res = extract_serials(model.get_atoms(), res) target = base_21_23[:] target.extend([[[0]], [[1]], [[4]], [[5]]]) assert approx_equal(res, target) res = occupancy_selections( model = model, add_water = True, as_flex_arrays = False, other_individual_selection_strings = ['resseq 0 and not (altloc A or altloc B)']) res = extract_serials(model.get_atoms(), res) target.extend([[[18]], [[19]], [[20]], [[22]]]) assert approx_equal(res, target) # 2 other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0 and (name S or name O1)'], ['resseq 0 and (name O3 or name O4)'] ]) res = occupancy_selections( model = model, as_flex_arrays = False, other_constrained_groups = other_constrained_groups) res = extract_serials(model.get_atoms(), res) target = base_21_23[:] target.extend([[[0, 1]], [[4, 5]]]) assert approx_equal(res, target) other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0 and (name S or name O1)'], ['resseq 0 and (name O3 or name O4)'] ]) res = occupancy_selections( model = model, add_water = True, as_flex_arrays = False, other_constrained_groups = other_constrained_groups) res = extract_serials(model.get_atoms(), res) target.extend([[[18]], [[19]], [[20]], [[22]]]) assert approx_equal(res, target) # 3 other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0 and (name O3 or name O4)'] ]) res = occupancy_selections( model = model, as_flex_arrays = False, other_individual_selection_strings = ['resseq 0 and (name S or name O1)'], other_constrained_groups = other_constrained_groups) res = extract_serials(model.get_atoms(), res) target = base_21_23[:] target.extend([[[0]], [[1]], [[4, 5]]]) assert approx_equal(res, target) def exercise_01(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_h.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [ [[0,1,2,3,4,10,12,14,16,18,20,22], [5,6,7,8,9,11,13,15,17,19,21,23]] ] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_02(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/occ_mix1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [ [[0,1,2,3,4,5,6,7,8,9,10,11,12,13], [14,15,16,17,18,19,20,21,22,23,24,25,26,27]] ] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_03(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_hd.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [ [[7]], [[8]], [[9],[12]], [[10],[13]], [[11],[14]] ] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_05(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ala_lys_arg_ser_tyr_neutron_hd.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [ [[9],[12]], [[10],[13]], [[11],[14]], [[33],[37]], [[34],[38]], [[35],[39]], [[36],[40]], [[59],[65]], [[60],[66]], [[61],[67]], [[62],[68]], [[63],[69]], [[64],[70]], [[80],[82]], [[81],[83]], [[103],[105]], [[104],[106]]] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_06(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/NAD_594_HD.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [ [[62]], [[113]], [[65],[77]], [[66],[78]], [[67],[79]], [[68],[80]], [[69],[81]], [[70],[82]], [[71],[83]], [[72],[84]], [[73],[85]], [[74],[86]], [[75],[87]], [[76],[88]], [[124],[127]],[[125],[128]],[[126],[129]]] res = occupancy_selections( model = model, as_flex_arrays = False) assert approx_equal(res, base) def exercise_07(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[0, 1, 2, 3, 4]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0'] ]) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_08(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_2.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answers = [ [ [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[0,1,2,3,4,5]] ], [ [[4],[5]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[6,7,8,9,10,11,12,13,14,15]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[16,17]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[18,19,20]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[23]], [[24,25,26,27],[28,29,30,31]], [[21]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[22]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23,24,25,26,27,28,29,30,31]] ], [ [[0,1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31]] ] ] group_selections = ['resseq 0', 'resseq 1', 'resseq 2', 'resseq 3', 'resseq 4', 'resseq 5', 'resseq 6', 'resseq 0:6'] for group_selection, answer in zip(group_selections, answers): other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ [group_selection] ]) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_09(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_2.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answers = [ [ [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[0]], [[1]], [[2]], [[3]], [[4]], [[5]] ], [ [[4],[5]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[6]], [[7]], [[8]], [[9]], [[10]], [[11]], [[12]], [[13]], [[14]], [[15]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[16]], [[17]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[18]], [[19]], [[20]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[23]], [[24,25,26,27],[28,29,30,31]], [[21]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24,25,26,27],[28,29,30,31]], [[22]] ], [ [[4],[5]], [[6,7,8,9,10],[11,12,13,14,15]], [[16],[17]], [[21]], [[23]], [[24]], [[25]], [[26]], [[27]], [[28]], [[29]], [[30]], [[31]] ] ] individual_selections = ['resseq 0', 'resseq 1', 'resseq 2', 'resseq 3', 'resseq 4', 'resseq 5', 'resseq 6', 'resseq 0:6'] for individual_selection, answer in zip(individual_selections, answers): result = occupancy_selections( model = model, other_individual_selection_strings = [individual_selection], as_flex_arrays = False) assert approx_equal(result, answer) def exercise_10(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) e = None try: other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0'] ]) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, other_individual_selection_strings = ['resseq 0'], as_flex_arrays = False) except Exception as e: assert str(e) == "Duplicate selection: same atoms selected for individual and group occupancy refinement." def exercise_11(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) e = None try: result = occupancy_selections( model = model, remove_selection = ['resseq 0'], other_individual_selection_strings = ['resseq 0'], as_flex_arrays = False) except Exception as e: assert str(e) == "Duplicate selection: occupancies of same atoms selected to be fixed and to be refined." e = None try: other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 0'] ]) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, remove_selection = ['resseq 0'], as_flex_arrays = False) except Exception as e: assert str(e) == "Duplicate selection: occupancies of same atoms selected to be fixed and to be refined." def exercise_12(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_2.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[4],[5]], [[16],[17]], [[21]], [[23,24,25,26,27,28,29,30,31]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['resseq 6'] ]) result = occupancy_selections( model = model, remove_selection = ['resseq 1'], other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) # answer = [ [[4],[5]], [[16],[17]], [[21]], [[23]], [[24]], [[25]], [[26]], [[27]], [[28]], [[29]], [[30]], [[31]] ] result = occupancy_selections( model = model, remove_selection = ['resseq 1'], other_individual_selection_strings = ['resseq 6'], as_flex_arrays = False) assert approx_equal(result, answer) def exercise_13(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9]], [[10]], [[0],[1]], [[2],[3]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and name N','chain A and resseq 1 and name CA'], ['chain A and resseq 1 and name C','chain A and resseq 1 and name O'] ] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_14(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9]], [[10]], [[0,1,2],[3,4]], [[5],[6]], [[7]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and (name N or name CA or name C)', 'chain A and resseq 1 and (name O or name CB)'], ['chain A and resseq 1 and name CG','chain A and resseq 1 and name CD'], ['chain A and resseq 1 and name CE'] ] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_15(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9]], [[0,1,2],[10]], [[5,7]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and (name N or name CA or name C)', 'chain S and resseq 1'], ['chain A and resseq 1 and name CG or chain A and resseq 1 and name CE'] ] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_16(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9],[10]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and name NZ and altloc A', 'chain A and resseq 1 and name NZ and altloc B', 'chain S and resseq 1'] ] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_17(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8,9,10]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and name NZ and altloc A or chain A and resseq 1 and name NZ and altloc B or chain S and resseq 1'] ] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_18(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_2.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9],[10]] ] other_constrained_groups = make_up_other_constrained_groups_obj( selections = [ ['chain A and resseq 1 and name NZ and altloc A','chain A and resseq 1 and name NZ and altloc B','chain S and resseq 1 and altloc C']] ) result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_19(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/lys_1.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[8],[9],[10]] ] tmp = "chain A and resseq 1 and name XX and altloc A" other_constrained_groups = make_up_other_constrained_groups_obj( selections = [[ tmp, 'chain A and resseq 1 and name NZ and altloc B', 'chain S and resseq 1']]) try: result = occupancy_selections( model = model, other_constrained_groups = other_constrained_groups, as_flex_arrays = False) except Exception as e: assert str(e) == \ 'Selection string results in empty selection (selects no atoms): "%s"' \ % tmp def exercise_20(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/ile_2conf_h.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) answer = [ [[4,5,6,7,8,9,10,11,12,13,14,15,16,17,18], [19,20,21,22,23,24,25,26,27,28,29,30,31,32,33]] ] result = occupancy_selections( model = model, as_flex_arrays = False) assert approx_equal(result, answer) def exercise_21(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_3.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [[[2], [3]], [[6, 7, 8, 9, 10], [11, 12, 13, 14, 15]], [[16], [17]], [[21]], [[23]], [[24, 25, 26, 27], [28, 29, 30, 31]], [[36]], [[47]], [[48]], [[49]], [[50]], [[51]], [[53]], [[56, 57, 58, 59]], [[60, 61, 62, 63]], [[64, 65, 66, 67, 68]], [[37], [40]], [[38], [41]], [[39], [42]], [[43, 44, 45, 46]]] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_22(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_4.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [[[0, 1, 2, 3, 8, 9, 10, 11, 12], [4, 5, 6, 7, 13, 14, 15, 16, 17]]] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_23(verbose): pdb_file = libtbx.env.find_in_repositories( relative_path="phenix_regression/pdb/gocr_5.pdb", test=os.path.isfile) if (verbose): log = sys.stdout else: log = StringIO() model = get_model(pdb_file, log) # base = [[[1, 2, 3, 4, 5, 6]], [[7, 8, 9, 10, 11], [12, 13, 14, 15, 16]]] res = occupancy_selections( model = model, as_flex_arrays = False) res = extract_serials(model.get_atoms(), res) assert approx_equal(res, base) def exercise_24(verbose): pdb_str1="""\ CRYST1 10.707 11.101 13.552 90.00 90.00 90.00 P 1 ATOM 0 N AALA A 9 3.452 6.807 3.508 0.19 9.33 A N ATOM 1 CA AALA A 9 4.572 6.204 4.211 0.19 9.82 A C ATOM 2 C AALA A 9 4.165 5.990 5.664 0.19 10.34 A C ATOM 3 O AALA A 9 3.000 6.165 6.021 0.19 10.96 A O ATOM 4 CB AALA A 9 5.792 7.098 4.116 0.19 10.31 A C ATOM 5 H AALA A 9 3.466 7.667 3.487 0.19 8.78 A H ATOM 6 HA AALA A 9 4.802 5.351 3.810 0.19 9.23 A H ATOM 7 HB1AALA A 9 6.533 6.686 4.588 0.19 9.91 A H ATOM 8 HB2AALA A 9 6.031 7.221 3.184 0.19 9.91 A H ATOM 9 HB3AALA A 9 5.594 7.960 4.515 0.19 9.91 A H ATOM 10 N BALA A 9 3.348 6.697 3.518 0.28 8.28 A N ATOM 11 CA BALA A 9 4.461 6.052 4.195 0.28 9.14 A C ATOM 12 C BALA A 9 4.138 5.964 5.683 0.28 9.84 A C ATOM 13 O BALA A 9 3.003 6.215 6.089 0.28 10.68 A O ATOM 14 CB BALA A 9 5.726 6.829 3.952 0.28 9.20 A C ATOM 15 H BALA A 9 3.422 7.551 3.454 0.28 8.78 A H ATOM 16 HA BALA A 9 4.597 5.156 3.849 0.28 9.23 A H ATOM 17 HB1BALA A 9 6.465 6.395 4.406 0.28 9.91 A H ATOM 18 HB2BALA A 9 5.907 6.863 3.000 0.28 9.91 A H ATOM 19 HB3BALA A 9 5.623 7.731 4.294 0.28 9.91 A H ATOM 20 N CALA A 9 3.608 6.763 3.402 0.28 8.32 A N ATOM 21 CA CALA A 9 4.617 6.060 4.177 0.28 9.56 A C ATOM 22 C CALA A 9 4.219 6.081 5.651 0.28 10.15 A C ATOM 23 O CALA A 9 3.126 6.528 6.006 0.28 10.64 A O ATOM 24 CB CALA A 9 5.981 6.684 3.973 0.28 10.39 A C ATOM 25 H CALA A 9 3.801 7.579 3.210 0.28 8.78 A H ATOM 26 HA CALA A 9 4.671 5.139 3.876 0.28 9.23 A H ATOM 27 HB1CALA A 9 6.639 6.202 4.497 0.28 9.91 A H ATOM 28 HB2CALA A 9 6.220 6.639 3.034 0.28 9.91 A H ATOM 29 HB3CALA A 9 5.959 7.611 4.257 0.28 9.91 A H ATOM 30 N DALA A 9 3.518 6.930 3.530 0.25 8.78 A N ATOM 31 CA DALA A 9 4.639 6.333 4.232 0.25 9.23 A C ATOM 32 C DALA A 9 4.203 6.093 5.674 0.25 10.10 A C ATOM 33 O DALA A 9 3.051 6.346 6.031 0.25 10.72 A O ATOM 34 CB DALA A 9 5.837 7.255 4.177 0.25 9.91 A C ATOM 35 H DALA A 9 3.490 7.789 3.568 0.25 8.78 A H ATOM 36 HA DALA A 9 4.898 5.494 3.819 0.25 9.23 A H ATOM 37 HB1DALA A 9 6.581 6.848 4.648 0.25 9.91 A H ATOM 38 HB2DALA A 9 6.086 7.408 3.252 0.25 9.91 A H ATOM 39 HB3DALA A 9 5.614 8.101 4.595 0.25 9.91 A H ATOM 40 N VAL A 10 5.119 5.606 6.502 1.00 11.13 A N ATOM 41 CA VAL A 10 4.846 5.470 7.925 1.00 12.50 A C ATOM 42 C VAL A 10 4.347 6.801 8.520 1.00 11.26 A C ATOM 43 O VAL A 10 4.763 7.871 8.095 1.00 11.53 A O ATOM 44 HA VAL A 10 4.118 4.835 8.017 1.00 12.50 A H ATOM 45 CB AVAL A 10 5.994 4.806 8.722 0.21 14.17 A C ATOM 46 CG1AVAL A 10 6.640 3.699 7.889 0.21 14.17 A C ATOM 47 CG2AVAL A 10 7.005 5.815 9.197 0.21 15.20 A C ATOM 48 H AVAL A 10 5.926 5.421 6.269 0.19 11.13 A H ATOM 49 HB AVAL A 10 5.616 4.404 9.520 0.21 14.91 A H ATOM 50 HG11AVAL A 10 7.358 3.289 8.396 0.21 16.29 A H ATOM 51 HG12AVAL A 10 5.975 3.028 7.671 0.21 16.29 A H ATOM 52 HG13AVAL A 10 6.998 4.077 7.070 0.21 16.29 A H ATOM 53 HG21AVAL A 10 7.707 5.363 9.691 0.21 15.63 A H ATOM 54 HG22AVAL A 10 7.391 6.271 8.433 0.21 15.63 A H ATOM 55 HG23AVAL A 10 6.570 6.462 9.774 0.21 15.63 A H ATOM 56 CB BVAL A 10 6.135 4.987 8.645 0.79 14.91 A C ATOM 57 CG1BVAL A 10 6.081 5.228 10.144 0.79 16.28 A C ATOM 58 CG2BVAL A 10 6.351 3.507 8.360 0.79 15.63 A C ATOM 59 H BVAL A 10 5.928 5.441 6.263 0.28 11.13 A H ATOM 60 HB BVAL A 10 6.879 5.504 8.299 0.79 14.91 A H ATOM 61 HG11BVAL A 10 6.902 4.913 10.552 0.79 16.29 A H ATOM 62 HG12BVAL A 10 5.978 6.177 10.316 0.79 16.29 A H ATOM 63 HG13BVAL A 10 5.328 4.748 10.522 0.79 16.29 A H ATOM 64 HG21BVAL A 10 7.156 3.205 8.809 0.79 15.63 A H ATOM 65 HG22BVAL A 10 5.590 3.000 8.685 0.79 15.63 A H ATOM 66 HG23BVAL A 10 6.445 3.372 7.404 0.79 15.63 A H ATOM 67 H CVAL A 10 5.907 5.353 6.270 0.28 11.13 A H ATOM 68 H DVAL A 10 5.903 5.349 6.260 0.25 11.13 A H TER END """ pdb_str2="""\ CRYST1 10.707 11.101 13.552 90.00 90.00 90.00 P 1 ATOM 0 N AALA A 9 3.452 6.807 3.508 0.19 9.33 A N ATOM 1 CA AALA A 9 4.572 6.204 4.211 0.19 9.82 A C ATOM 2 C AALA A 9 4.165 5.990 5.664 0.19 10.34 A C ATOM 3 O AALA A 9 3.000 6.165 6.021 0.19 10.96 A O ATOM 4 CB AALA A 9 5.792 7.098 4.116 0.19 10.31 A C ATOM 5 D AALA A 9 3.466 7.667 3.487 0.19 8.78 A D ATOM 6 DA AALA A 9 4.802 5.351 3.810 0.19 9.23 A D ATOM 7 DB1AALA A 9 6.533 6.686 4.588 0.19 9.91 A D ATOM 8 DB2AALA A 9 6.031 7.221 3.184 0.19 9.91 A D ATOM 9 DB3AALA A 9 5.594 7.960 4.515 0.19 9.91 A D ATOM 10 N BALA A 9 3.348 6.697 3.518 0.28 8.28 A N ATOM 11 CA BALA A 9 4.461 6.052 4.195 0.28 9.14 A C ATOM 12 C BALA A 9 4.138 5.964 5.683 0.28 9.84 A C ATOM 13 O BALA A 9 3.003 6.215 6.089 0.28 10.68 A O ATOM 14 CB BALA A 9 5.726 6.829 3.952 0.28 9.20 A C ATOM 15 D BALA A 9 3.422 7.551 3.454 0.28 8.78 A D ATOM 16 DA BALA A 9 4.597 5.156 3.849 0.28 9.23 A D ATOM 17 DB1BALA A 9 6.465 6.395 4.406 0.28 9.91 A D ATOM 18 DB2BALA A 9 5.907 6.863 3.000 0.28 9.91 A D ATOM 19 DB3BALA A 9 5.623 7.731 4.294 0.28 9.91 A D ATOM 20 N CALA A 9 3.608 6.763 3.402 0.28 8.32 A N ATOM 21 CA CALA A 9 4.617 6.060 4.177 0.28 9.56 A C ATOM 22 C CALA A 9 4.219 6.081 5.651 0.28 10.15 A C ATOM 23 O CALA A 9 3.126 6.528 6.006 0.28 10.64 A O ATOM 24 CB CALA A 9 5.981 6.684 3.973 0.28 10.39 A C ATOM 25 D CALA A 9 3.801 7.579 3.210 0.28 8.78 A D ATOM 26 DA CALA A 9 4.671 5.139 3.876 0.28 9.23 A D ATOM 27 DB1CALA A 9 6.639 6.202 4.497 0.28 9.91 A D ATOM 28 DB2CALA A 9 6.220 6.639 3.034 0.28 9.91 A D ATOM 29 DB3CALA A 9 5.959 7.611 4.257 0.28 9.91 A D ATOM 30 N DALA A 9 3.518 6.930 3.530 0.25 8.78 A N ATOM 31 CA DALA A 9 4.639 6.333 4.232 0.25 9.23 A C ATOM 32 C DALA A 9 4.203 6.093 5.674 0.25 10.10 A C ATOM 33 O DALA A 9 3.051 6.346 6.031 0.25 10.72 A O ATOM 34 CB DALA A 9 5.837 7.255 4.177 0.25 9.91 A C ATOM 35 D DALA A 9 3.490 7.789 3.568 0.25 8.78 A D ATOM 36 DA DALA A 9 4.898 5.494 3.819 0.25 9.23 A D ATOM 37 DB1DALA A 9 6.581 6.848 4.648 0.25 9.91 A D ATOM 38 DB2DALA A 9 6.086 7.408 3.252 0.25 9.91 A D ATOM 39 DB3DALA A 9 5.614 8.101 4.595 0.25 9.91 A D ATOM 40 N VAL A 10 5.119 5.606 6.502 1.00 11.13 A N ATOM 41 CA VAL A 10 4.846 5.470 7.925 1.00 12.50 A C ATOM 42 C VAL A 10 4.347 6.801 8.520 1.00 11.26 A C ATOM 43 O VAL A 10 4.763 7.871 8.095 1.00 11.53 A O ATOM 44 HA VAL A 10 4.118 4.835 8.017 1.00 12.50 A D ATOM 45 CB AVAL A 10 5.994 4.806 8.722 0.21 14.17 A C ATOM 46 CG1AVAL A 10 6.640 3.699 7.889 0.21 14.17 A C ATOM 47 CG2AVAL A 10 7.005 5.815 9.197 0.21 15.20 A C ATOM 48 D AVAL A 10 5.926 5.421 6.269 0.19 11.13 A D ATOM 49 DB AVAL A 10 5.616 4.404 9.520 0.21 14.91 A D ATOM 50 DG11AVAL A 10 7.358 3.289 8.396 0.21 16.29 A D ATOM 51 DG12AVAL A 10 5.975 3.028 7.671 0.21 16.29 A D ATOM 52 DG13AVAL A 10 6.998 4.077 7.070 0.21 16.29 A D ATOM 53 DG21AVAL A 10 7.707 5.363 9.691 0.21 15.63 A D ATOM 54 DG22AVAL A 10 7.391 6.271 8.433 0.21 15.63 A D ATOM 55 DG23AVAL A 10 6.570 6.462 9.774 0.21 15.63 A D ATOM 56 CB BVAL A 10 6.135 4.987 8.645 0.79 14.91 A C ATOM 57 CG1BVAL A 10 6.081 5.228 10.144 0.79 16.28 A C ATOM 58 CG2BVAL A 10 6.351 3.507 8.360 0.79 15.63 A C ATOM 59 D BVAL A 10 5.928 5.441 6.263 0.28 11.13 A D ATOM 60 DB BVAL A 10 6.879 5.504 8.299 0.79 14.91 A D ATOM 61 DG11BVAL A 10 6.902 4.913 10.552 0.79 16.29 A D ATOM 62 DG12BVAL A 10 5.978 6.177 10.316 0.79 16.29 A D ATOM 63 DG13BVAL A 10 5.328 4.748 10.522 0.79 16.29 A D ATOM 64 DG21BVAL A 10 7.156 3.205 8.809 0.79 15.63 A D ATOM 65 DG22BVAL A 10 5.590 3.000 8.685 0.79 15.63 A D ATOM 66 DG23BVAL A 10 6.445 3.372 7.404 0.79 15.63 A D ATOM 67 D CVAL A 10 5.907 5.353 6.270 0.28 11.13 A D ATOM 68 D DVAL A 10 5.903 5.349 6.260 0.25 11.13 A D TER END """ if (verbose): log = sys.stdout else: log = StringIO() for pdb_str in [pdb_str1, pdb_str2]: model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = \ [[[0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 48], [10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 59], [20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 67], [30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 68]], [[45, 46, 47, 49, 50, 51, 52, 53, 54, 55], [56, 57, 58, 60, 61, 62, 63, 64, 65, 66]]] assert approx_equal(res, answer) def exercise_25(verbose): pdb_str="""\ CRYST1 10.707 11.101 13.552 90.00 90.00 90.00 P 1 ATOM 0 N ALA A 9 3.452 6.807 3.508 1.00 9.33 A N ATOM 1 CA ALA A 9 4.572 6.204 4.211 1.00 9.82 A C ATOM 2 C ALA A 9 4.165 5.990 5.664 1.00 10.34 A C ATOM 3 O ALA A 9 3.000 6.165 6.021 1.00 10.96 A O ATOM 4 CB ALA A 9 5.792 7.098 4.116 1.00 10.31 A C ATOM 5 HA ALA A 9 4.802 5.351 3.810 1.00 9.23 A H ATOM 6 HB1 ALA A 9 6.533 6.686 4.588 1.00 9.91 A H ATOM 7 HB2 ALA A 9 6.031 7.221 3.184 1.00 9.91 A H ATOM 8 HB3 ALA A 9 5.594 7.960 4.515 1.00 9.91 A H ATOM 9 H AALA A 9 3.466 7.667 3.487 0.40 8.78 A H ATOM 10 D BALA A 9 3.466 7.667 3.487 0.60 8.78 A D ATOM 11 N VAL A 10 5.119 5.606 6.502 1.00 11.13 A N ATOM 12 CA VAL A 10 4.846 5.470 7.925 1.00 12.50 A C ATOM 13 C VAL A 10 4.347 6.801 8.520 1.00 11.26 A C ATOM 14 O VAL A 10 4.763 7.871 8.095 1.00 11.53 A O ATOM 15 HA VAL A 10 4.118 4.835 8.017 1.00 12.50 A H ATOM 16 CB VAL A 10 5.994 4.806 8.722 1.00 14.17 A C ATOM 17 CG1 VAL A 10 6.640 3.699 7.889 1.00 14.17 A C ATOM 18 CG2 VAL A 10 7.005 5.815 9.197 1.00 15.20 A C ATOM 19 HB VAL A 10 5.616 4.404 9.520 1.00 14.91 A H ATOM 20 HG11 VAL A 10 7.358 3.289 8.396 1.00 16.29 A H ATOM 21 HG12 VAL A 10 5.975 3.028 7.671 1.00 16.29 A H ATOM 22 HG13 VAL A 10 6.998 4.077 7.070 1.00 16.29 A H ATOM 23 HG21 VAL A 10 7.707 5.363 9.691 1.00 15.63 A H ATOM 24 HG22 VAL A 10 7.391 6.271 8.433 1.00 15.63 A H ATOM 25 HG23 VAL A 10 6.570 6.462 9.774 1.00 15.63 A H ATOM 26 H AVAL A 10 5.926 5.421 6.269 0.30 11.13 A H ATOM 27 D BVAL A 10 5.926 5.421 6.269 0.70 11.13 A D TER END """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [ [[9],[10]], [[26],[27]] ] assert approx_equal(res, answer) def exercise_26(verbose): pdb_str="""\ CRYST1 71.040 72.017 72.362 90.00 100.48 90.00 C 1 2 1 ATOM 96 N PRO L 5 2.689 13.877 15.387 1.00 13.65 N ATOM 97 CA PRO L 5 1.824 14.762 14.572 1.00 17.31 C ATOM 98 C PRO L 5 0.338 14.432 14.641 1.00 20.79 C ATOM 99 O PRO L 5 -0.466 15.376 14.642 1.00 20.37 O ATOM 100 CB PRO L 5 2.330 14.534 13.143 1.00 20.71 C ATOM 101 CG PRO L 5 3.772 14.184 13.326 1.00 20.25 C ATOM 102 CD PRO L 5 3.871 13.403 14.633 1.00 16.57 C ATOM 103 HA PRO L 5 1.981 15.805 14.846 1.00 17.31 H ATOM 104 HB2 PRO L 5 1.780 13.709 12.691 1.00 20.71 H ATOM 105 HB3 PRO L 5 2.220 15.447 12.558 1.00 20.71 H ATOM 106 HG2 PRO L 5 4.103 13.567 12.492 1.00 20.25 H ATOM 107 HG3 PRO L 5 4.363 15.098 13.382 1.00 20.25 H ATOM 108 HD2 PRO L 5 3.805 12.331 14.446 1.00 16.57 H ATOM 109 HD3 PRO L 5 4.791 13.666 15.154 1.00 16.57 H ATOM 110 N LEU L 6 -0.052 13.175 14.677 1.00 13.93 N ATOM 111 CA LEU L 6 -1.446 12.769 14.667 1.00 15.53 C ATOM 112 C LEU L 6 -2.079 12.634 16.029 1.00 17.57 C ATOM 113 O LEU L 6 -3.268 12.311 16.111 1.00 18.17 O ATOM 114 CB LEU L 6 -1.648 11.435 13.889 1.00 17.76 C ATOM 115 CG LEU L 6 -1.291 11.544 12.396 1.00 18.22 C ATOM 116 CD1 LEU L 6 -1.474 10.257 11.651 1.00 18.93 C ATOM 117 CD2 LEU L 6 -2.125 12.629 11.689 1.00 22.55 C ATOM 118 HA LEU L 6 -2.017 13.534 14.144 1.00 15.53 H ATOM 119 HB2 LEU L 6 -1.011 10.669 14.331 1.00 17.76 H ATOM 120 HB3 LEU L 6 -2.693 11.135 13.959 1.00 17.76 H ATOM 121 HG LEU L 6 -0.242 11.827 12.310 1.00 18.22 H ATOM 122 HD11 LEU L 6 -0.750 10.210 10.838 1.00 18.93 H ATOM 123 HD12 LEU L 6 -1.319 9.426 12.338 1.00 18.93 H ATOM 124 HD13 LEU L 6 -2.488 10.221 11.252 1.00 18.93 H ATOM 125 HD21 LEU L 6 -2.084 12.462 10.613 1.00 22.55 H ATOM 126 HD22 LEU L 6 -3.156 12.565 12.037 1.00 22.55 H ATOM 127 HD23 LEU L 6 -1.712 13.609 11.929 1.00 22.55 H ATOM 128 H ALEU L 6 0.595 12.387 14.715 0.50 13.93 H ATOM 129 D BLEU L 6 0.595 12.387 14.715 0.50 13.93 D """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [ [[32], [33]] ] assert approx_equal(res, answer) def exercise_27(verbose): pdb_str="""\ CRYST1 64.714 39.225 38.645 90.00 117.38 90.00 C 1 2 1 ATOM 0 N SER A -1 20.605 9.913 24.660 1.00 32.98 N ATOM 1 CA SER A -1 21.415 10.057 23.431 1.00 25.22 C ATOM 2 C SER A -1 20.514 10.247 22.233 1.00 25.05 C ATOM 3 O SER A -1 19.332 9.926 22.266 1.00 28.08 O ATOM 4 CB SER A -1 22.253 8.810 23.194 1.00 28.97 C ATOM 5 OG SER A -1 21.417 7.708 22.900 1.00 37.21 O ATOM 6 H1 SER A -1 19.896 10.449 24.612 1.00 38.17 H ATOM 7 H2 SER A -1 20.335 9.069 24.737 1.00 27.38 H ATOM 8 H3 SER A -1 21.098 10.134 25.368 1.00 38.75 H ATOM 9 HA SER A -1 21.997 10.829 23.514 1.00 12.22 H ATOM 10 HB2 SER A -1 22.844 8.970 22.440 1.00 22.78 H ATOM 11 HB3 SER A -1 22.771 8.614 23.990 1.00 30.47 H ATOM 12 HG SER A -1 21.872 7.007 22.826 1.00 42.35 H ATOM 13 N AMET A 0 21.097 10.723 21.147 0.49 20.67 N ATOM 14 CA AMET A 0 20.340 10.870 19.929 0.49 21.49 C ATOM 15 C AMET A 0 21.236 10.795 18.720 0.49 18.70 C ATOM 16 O AMET A 0 22.394 11.216 18.750 0.49 19.47 O ATOM 17 CB AMET A 0 19.569 12.183 19.945 0.49 22.62 C ATOM 18 CG AMET A 0 20.423 13.414 20.138 0.49 24.87 C ATOM 19 SD AMET A 0 19.580 14.932 19.650 0.49 29.00 S ATOM 20 CE AMET A 0 17.946 14.760 20.377 0.49 36.23 C ATOM 21 H AMET A 0 21.920 10.964 21.095 0.49 28.25 H ATOM 22 HA AMET A 0 19.697 10.146 19.870 0.49 7.25 H ATOM 23 HB2AMET A 0 19.093 12.280 19.105 0.49 13.51 H ATOM 24 HB3AMET A 0 18.941 12.141 20.681 0.49 7.62 H ATOM 25 HG2AMET A 0 20.671 13.490 21.072 0.49 26.02 H ATOM 26 HG3AMET A 0 21.219 13.333 19.589 0.49 30.87 H ATOM 27 HE1AMET A 0 17.284 14.819 19.669 0.49 20.79 H ATOM 28 HE2AMET A 0 17.863 13.908 20.829 0.49 8.45 H ATOM 29 HE3AMET A 0 17.812 15.481 21.012 0.49 30.25 H ATOM 30 N BMET A 0 21.082 10.809 21.171 0.51 21.19 N ATOM 31 CA BMET A 0 20.368 11.023 19.923 0.51 23.13 C ATOM 32 C BMET A 0 21.273 10.654 18.766 0.51 21.10 C ATOM 33 O BMET A 0 22.496 10.703 18.893 0.51 19.93 O ATOM 34 CB BMET A 0 19.961 12.488 19.782 0.51 27.15 C ATOM 35 CG BMET A 0 19.070 12.993 20.889 0.51 29.67 C ATOM 36 SD BMET A 0 18.685 14.739 20.684 0.51 41.63 S ATOM 37 CE BMET A 0 17.734 15.043 22.171 0.51 35.23 C ATOM 38 HA BMET A 0 19.568 10.476 19.897 0.51 36.28 H ATOM 39 HB2BMET A 0 20.762 13.035 19.778 0.51 8.59 H ATOM 40 HB3BMET A 0 19.485 12.602 18.945 0.51 27.25 H ATOM 41 HG2BMET A 0 18.236 12.497 20.877 0.51 21.33 H ATOM 42 HG3BMET A 0 19.519 12.877 21.741 0.51 34.36 H ATOM 43 HE1BMET A 0 17.141 15.795 22.018 0.51 42.08 H ATOM 44 HE2BMET A 0 17.217 14.249 22.380 0.51 22.21 H ATOM 45 HE3BMET A 0 18.343 15.241 22.899 0.51 40.99 H """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [[[13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29], [30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45]]] assert approx_equal(res, answer) def exercise_28(verbose): pdb_str="""\ CRYST1 64.360 64.360 46.038 90.00 90.00 120.00 P 63 ATOM 0 N ASP A 48 8.896 25.394 -7.791 1.00 8.05 N ATOM 1 CA ASP A 48 8.495 26.452 -6.936 1.00 8.42 C ATOM 2 C ASP A 48 8.287 26.047 -5.477 1.00 8.20 C ATOM 3 O ASP A 48 8.309 26.881 -4.579 1.00 10.68 O ATOM 4 CB ASP A 48 7.216 27.151 -7.426 1.00 9.40 C ATOM 5 CG ASP A 48 7.457 27.744 -8.791 1.00 10.91 C ATOM 6 OD1 ASP A 48 8.234 28.729 -8.836 1.00 16.64 O ATOM 7 OD2 ASP A 48 6.845 27.293 -9.764 1.00 12.53 O ATOM 8 HA ASP A 48 9.193 27.122 -6.935 1.00 8.42 H ATOM 9 HB2 ASP A 48 6.494 26.507 -7.490 1.00 9.40 H ATOM 10 HB3 ASP A 48 6.981 27.867 -6.815 1.00 9.40 H ATOM 11 H AASP A 48 8.303 25.156 -8.367 0.50 8.04 H ATOM 12 H BASP A 48 8.242 25.041 -8.223 0.50 8.04 H ATOM 13 N ALEU A 49 8.083 24.740 -5.245 0.79 7.34 N ATOM 14 CA ALEU A 49 7.817 24.239 -3.906 0.79 6.67 C ATOM 15 C ALEU A 49 8.124 22.738 -3.941 0.79 5.81 C ATOM 16 O ALEU A 49 7.880 22.074 -4.958 0.79 6.71 O ATOM 17 CB ALEU A 49 6.385 24.559 -3.494 0.79 7.19 C ATOM 18 CG ALEU A 49 5.914 24.092 -2.111 0.79 7.07 C ATOM 19 CD1ALEU A 49 4.885 25.059 -1.536 0.79 8.84 C ATOM 20 CD2ALEU A 49 5.323 22.713 -2.192 0.79 7.46 C ATOM 21 H ALEU A 49 8.095 24.131 -5.852 0.79 7.25 H ATOM 22 HA ALEU A 49 8.421 24.661 -3.275 0.79 7.14 H ATOM 23 HB2ALEU A 49 6.277 25.523 -3.518 0.79 9.16 H ATOM 24 HB3ALEU A 49 5.791 24.158 -4.147 0.79 9.16 H ATOM 25 HG ALEU A 49 6.673 24.062 -1.508 0.79 6.91 H ATOM 26 HD11ALEU A 49 4.592 24.730 -0.672 0.79 9.95 H ATOM 27 HD12ALEU A 49 5.294 25.933 -1.437 0.79 9.95 H ATOM 28 HD13ALEU A 49 4.130 25.113 -2.143 0.79 9.95 H ATOM 29 HD21ALEU A 49 4.960 22.476 -1.324 0.79 8.29 H ATOM 30 HD22ALEU A 49 4.616 22.710 -2.856 0.79 8.29 H ATOM 31 HD23ALEU A 49 6.015 22.082 -2.442 0.79 8.29 H ATOM 32 N BLEU A 49 7.975 24.768 -5.242 0.21 7.25 N ATOM 33 CA BLEU A 49 7.654 24.205 -3.941 0.21 7.15 C ATOM 34 C BLEU A 49 8.003 22.716 -3.887 0.21 7.83 C ATOM 35 O BLEU A 49 7.689 22.025 -4.858 0.21 5.06 O ATOM 36 CB BLEU A 49 6.162 24.365 -3.605 0.21 9.16 C ATOM 37 CG BLEU A 49 5.681 23.652 -2.331 0.21 6.91 C ATOM 38 CD1BLEU A 49 6.301 24.276 -1.095 0.21 9.95 C ATOM 39 CD2BLEU A 49 4.156 23.640 -2.248 0.21 8.29 C ATOM 40 H BLEU A 49 7.943 24.178 -5.867 0.21 7.25 H ATOM 41 HA BLEU A 49 8.173 24.662 -3.262 0.21 7.14 H ATOM 42 HB2BLEU A 49 5.975 25.310 -3.494 0.21 9.16 H ATOM 43 HB3BLEU A 49 5.645 24.021 -4.346 0.21 9.16 H ATOM 44 HG BLEU A 49 5.963 22.725 -2.358 0.21 6.91 H ATOM 45 HD11BLEU A 49 6.470 23.579 -0.443 0.21 9.95 H ATOM 46 HD12BLEU A 49 7.132 24.697 -1.346 0.21 9.95 H ATOM 47 HD13BLEU A 49 5.691 24.937 -0.731 0.21 9.95 H ATOM 48 HD21BLEU A 49 3.888 23.174 -1.441 0.21 8.29 H ATOM 49 HD22BLEU A 49 3.834 24.555 -2.225 0.21 8.29 H ATOM 50 HD23BLEU A 49 3.802 23.184 -3.027 0.21 8.29 H ATOM 51 N VAL A 50 8.616 22.239 -2.807 1.00 5.93 N ATOM 52 CA VAL A 50 8.845 20.793 -2.609 1.00 5.53 C ATOM 53 C VAL A 50 7.981 20.307 -1.457 1.00 5.75 C ATOM 54 O VAL A 50 7.971 20.912 -0.389 1.00 6.63 O ATOM 55 CB VAL A 50 10.325 20.527 -2.343 1.00 6.31 C ATOM 56 CG1 VAL A 50 10.556 19.043 -2.072 1.00 7.62 C ATOM 57 CG2 VAL A 50 11.170 20.998 -3.512 1.00 7.52 C ATOM 58 HA VAL A 50 8.593 20.305 -3.404 1.00 5.53 H ATOM 59 HB VAL A 50 10.599 21.022 -1.555 1.00 6.31 H ATOM 60 HG11 VAL A 50 11.507 18.860 -2.118 1.00 7.62 H ATOM 61 HG12 VAL A 50 10.221 18.824 -1.188 1.00 7.62 H ATOM 62 HG13 VAL A 50 10.087 18.523 -2.744 1.00 7.62 H ATOM 63 HG21 VAL A 50 12.097 20.765 -3.345 1.00 7.52 H ATOM 64 HG22 VAL A 50 10.860 20.562 -4.321 1.00 7.52 H ATOM 65 HG23 VAL A 50 11.081 21.960 -3.600 1.00 7.52 H ATOM 66 H AVAL A 50 8.830 22.718 -2.125 0.79 5.93 H ATOM 67 H BVAL A 50 8.914 22.729 -2.166 0.21 5.93 H TER END """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [ [[11],[12]], [[13,14,15,16,17,18,19,20,21,22,23,24,25,26,27,28,29,30,31,66], [32,33,34,35,36,37,38,39,40,41,42,43,44,45,46,47,48,49,50,67]]] assert approx_equal(res, answer) def exercise_29(verbose): pdb_str="""\ CRYST1 148.270 44.010 47.390 90.00 101.57 90.00 C 1 2 1 ATOM 0 N GLY A 285 -41.269 16.430 -4.458 1.00 18.77 N ATOM 1 CA GLY A 285 -41.021 16.772 -5.854 1.00 20.45 C ATOM 2 H GLY A 285 -42.080 16.182 -4.313 1.00 22.53 H ATOM 3 C AGLY A 285 -41.133 18.291 -6.119 0.85 20.52 C ATOM 4 O AGLY A 285 -41.030 18.770 -7.258 0.85 22.89 O ATOM 5 HA2AGLY A 285 -40.130 16.482 -6.104 0.85 24.54 H ATOM 6 HA3AGLY A 285 -41.663 16.314 -6.418 0.85 24.54 H ATOM 7 C BGLY A 285 -40.556 18.155 -6.113 0.15 20.45 C ATOM 8 O BGLY A 285 -39.925 18.445 -7.127 0.15 21.06 O ATOM 9 HA2BGLY A 285 -40.352 16.166 -6.208 0.15 24.54 H ATOM 10 HA3BGLY A 285 -41.839 16.638 -6.357 0.15 24.54 H ATOM 11 N AASN A 286 -41.375 19.070 -5.066 0.75 20.63 N ATOM 12 CA AASN A 286 -41.558 20.524 -5.179 0.75 21.34 C ATOM 13 C AASN A 286 -40.921 21.176 -3.941 0.75 19.76 C ATOM 14 O AASN A 286 -41.136 20.695 -2.825 0.75 18.94 O ATOM 15 CB AASN A 286 -43.061 20.822 -5.246 0.75 23.19 C ATOM 16 CG AASN A 286 -43.390 22.293 -5.087 0.75 24.76 C ATOM 17 OD1AASN A 286 -43.580 22.784 -3.975 0.75 25.15 O ATOM 18 ND2AASN A 286 -43.491 22.996 -6.206 0.75 26.38 N ATOM 19 H AASN A 286 -41.441 18.778 -4.260 0.75 24.76 H ATOM 20 HA AASN A 286 -41.121 20.863 -5.988 0.75 25.61 H ATOM 21 HB2AASN A 286 -43.400 20.532 -6.107 0.75 27.82 H ATOM 22 HB3AASN A 286 -43.509 20.338 -4.535 0.75 27.82 H ATOM 23 HD21AASN A 286 -43.371 22.614 -6.967 0.75 31.65 H ATOM 24 HD22AASN A 286 -43.677 23.835 -6.171 0.75 31.65 H ATOM 25 N BASN A 286 -40.878 19.026 -5.184 0.25 20.30 N ATOM 26 CA BASN A 286 -40.589 20.401 -5.396 0.25 20.20 C ATOM 27 C BASN A 286 -40.224 21.016 -4.085 0.25 18.88 C ATOM 28 O BASN A 286 -40.136 20.364 -3.047 0.25 18.65 O ATOM 29 CB BASN A 286 -41.798 21.088 -6.023 0.25 22.27 C ATOM 30 CG BASN A 286 -42.950 21.238 -5.058 0.25 23.28 C ATOM 31 OD1BASN A 286 -42.781 21.720 -3.938 0.25 23.18 O ATOM 32 ND2BASN A 286 -44.137 20.828 -5.491 0.25 24.35 N ATOM 33 H BASN A 286 -41.259 18.841 -4.435 0.25 24.36 H ATOM 34 HA BASN A 286 -39.828 20.488 -6.007 0.25 24.24 H ATOM 35 HB2BASN A 286 -41.538 21.974 -6.321 0.25 26.72 H ATOM 36 HB3BASN A 286 -42.105 20.561 -6.777 0.25 26.72 H ATOM 37 HD21BASN A 286 -44.216 20.499 -6.282 0.25 29.22 H ATOM 38 HD22BASN A 286 -44.826 20.891 -4.981 0.25 29.22 H ATOM 39 CA GLU A 287 -39.388 22.905 -3.000 1.00 16.67 C ATOM 40 C GLU A 287 -40.376 23.372 -1.952 1.00 15.65 C ATOM 41 O GLU A 287 -40.132 23.201 -0.755 1.00 14.31 O ATOM 42 CB GLU A 287 -38.514 24.074 -3.481 1.00 17.80 C ATOM 43 CG GLU A 287 -37.273 23.645 -4.302 1.00 19.41 C ATOM 44 CD GLU A 287 -36.290 24.789 -4.558 1.00 20.84 C ATOM 45 OE1 GLU A 287 -36.554 25.925 -4.128 1.00 21.26 O ATOM 46 OE2 GLU A 287 -35.220 24.552 -5.185 1.00 22.93 O ATOM 47 HB2 GLU A 287 -39.052 24.654 -4.041 1.00 21.36 H ATOM 48 HB3 GLU A 287 -38.200 24.566 -2.707 1.00 21.36 H ATOM 49 HG2 GLU A 287 -36.801 22.949 -3.818 1.00 23.29 H ATOM 50 HG3 GLU A 287 -37.568 23.308 -5.163 1.00 23.29 H ATOM 51 N AGLU A 287 -40.109 22.235 -4.122 0.02 18.26 N ATOM 52 H AGLU A 287 -39.954 22.592 -4.889 0.02 21.91 H ATOM 53 HA AGLU A 287 -38.796 22.250 -2.576 0.02 20.01 H ATOM 54 N BGLU A 287 -40.017 22.305 -4.119 0.98 18.44 N ATOM 55 H BGLU A 287 -40.228 22.836 -4.762 0.98 22.13 H ATOM 56 HA BGLU A 287 -38.799 22.245 -2.580 0.98 20.01 H TER END """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [ [[3,4,5,6,19], [7,8,9,10,33]], [[11,12,13,14,15,16,17,18,20,21,22,23,24,52], [25,26,27,28,29,30,31,32,34,35,36,37,38,55]], [[51,53], [54,56]]] assert approx_equal(res, answer) def exercise_30(verbose): pdb_str="""\ CRYST1 42.198 121.958 37.277 90.00 90.00 90.00 P 21 21 2 ATOM 0 CG GLU A 115 30.700 22.521 0.401 0.55 25.56 C ATOM 1 CD GLU A 115 31.809 23.320 -0.265 1.00 25.96 C ATOM 2 OE1 GLU A 115 32.842 22.797 -0.723 1.00 24.92 O ATOM 3 OE2 GLU A 115 31.621 24.544 -0.376 1.00 27.30 O ATOM 4 N AGLU A 115 27.819 20.841 -1.012 0.44 19.61 N ATOM 5 CA AGLU A 115 28.757 21.222 -0.004 0.44 20.79 C ATOM 6 C AGLU A 115 28.192 21.930 1.203 0.44 19.50 C ATOM 7 O AGLU A 115 27.475 22.922 1.098 0.44 20.38 O ATOM 8 CB AGLU A 115 29.799 22.079 -0.601 0.44 23.59 C ATOM 9 N BGLU A 115 27.018 20.969 -0.446 0.56 27.49 N ATOM 10 CA BGLU A 115 28.194 21.387 0.311 0.56 26.06 C ATOM 11 C BGLU A 115 27.541 21.859 1.611 0.56 25.00 C ATOM 12 O BGLU A 115 26.660 22.715 1.640 0.56 26.43 O ATOM 13 CB BGLU A 115 29.189 22.459 -0.356 0.56 26.03 C ATOM 14 N AVAL A 116 28.585 21.407 2.363 0.53 19.29 N ATOM 15 CA AVAL A 116 28.181 21.931 3.670 0.53 18.27 C ATOM 16 C AVAL A 116 29.427 21.990 4.589 0.53 17.81 C ATOM 17 O AVAL A 116 30.464 21.420 4.280 0.53 17.67 O ATOM 18 CB AVAL A 116 27.090 21.046 4.342 0.53 20.31 C ATOM 19 CG1AVAL A 116 25.743 21.168 3.633 0.53 22.78 C ATOM 20 CG2AVAL A 116 27.498 19.598 4.395 0.53 20.85 C ATOM 21 H AVAL A 116 29.104 20.724 2.421 0.53 23.15 H ATOM 22 HA AVAL A 116 27.827 22.838 3.564 0.53 21.92 H ATOM 23 HB AVAL A 116 26.967 21.353 5.264 0.53 24.37 H ATOM 24 N BVAL A 116 27.987 21.231 2.690 0.47 21.87 N ATOM 25 CA BVAL A 116 27.614 21.560 4.041 0.47 19.86 C ATOM 26 C BVAL A 116 28.915 21.857 4.746 0.47 19.34 C ATOM 27 O BVAL A 116 29.983 21.603 4.213 0.47 18.81 O ATOM 28 CB BVAL A 116 26.938 20.336 4.707 0.47 19.81 C ATOM 29 CG1BVAL A 116 25.591 20.061 4.058 0.47 21.33 C ATOM 30 CG2BVAL A 116 27.825 19.086 4.627 0.47 19.25 C ATOM 31 H BVAL A 116 28.539 20.573 2.651 0.47 26.24 H ATOM 32 HA BVAL A 116 27.021 22.340 4.070 0.47 23.83 H ATOM 33 HB BVAL A 116 26.782 20.535 5.654 0.47 23.76 H TER END """ if (verbose): log = sys.stdout else: log = StringIO() model = get_model_str(pdb_str, log) res = occupancy_selections( model = model, as_flex_arrays = False) answer = [ [[0]], [[4, 5, 6, 7, 8, 21], [9, 10, 11, 12, 13, 31]], [[14, 15, 16, 17, 18, 19, 20, 22, 23], [24, 25, 26, 27, 28, 29, 30, 32, 33]] ] assert approx_equal(res, answer) def prepare_correlated_occupancy_inputs( prefix="tst_group_correlated_occupancy", create_mtz=False, d_min=1.0): pdb_raw = """\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 SCALE1 0.045585 0.000000 0.014006 0.00000 SCALE2 0.000000 0.205508 0.000000 0.00000 SCALE3 0.000000 0.000000 0.044560 0.00000 ATOM 1 N GLY A 1 -9.056 4.638 6.050 1.00 16.77 N ATOM 2 CA GLY A 1 -9.058 4.194 4.668 1.00 16.57 C ATOM 3 C GLY A 1 -7.993 3.144 4.430 1.00 16.16 C ATOM 4 O GLY A 1 -7.521 2.511 5.374 1.00 16.78 O ATOM 5 N ASN A 2 -7.616 2.953 3.169 1.00 15.02 N ATOM 6 CA ASN A 2 -6.526 2.044 2.840 1.00 14.10 C ATOM 7 C ASN A 2 -5.216 2.527 3.434 1.00 13.13 C ATOM 8 O ASN A 2 -4.943 3.727 3.466 1.00 11.91 O ATOM 9 CB ASN A 2 -6.382 1.888 1.330 1.00 15.38 C ATOM 10 CG ASN A 2 -7.632 1.344 0.685 1.00 14.08 C ATOM 11 OD1 ASN A 2 -8.042 0.216 0.957 1.00 17.46 O ATOM 12 ND2 ASN A 2 -8.247 2.142 -0.178 1.00 11.72 N ATOM 13 N ASN A 3 -4.405 1.583 3.898 1.00 12.26 N ATOM 14 CA ASN A 3 -3.172 1.915 4.595 1.00 11.74 C ATOM 15 C ASN A 3 -1.922 1.362 3.915 1.00 11.10 C ATOM 16 O ASN A 3 -1.816 0.158 3.672 1.00 10.42 O ATOM 17 CB ASN A 3 -3.243 1.409 6.039 1.00 12.15 C ATOM 18 CG ASN A 3 -2.000 1.749 6.841 1.00 12.82 C ATOM 19 OD1 ASN A 3 -1.705 2.920 7.082 1.00 15.05 O ATOM 20 ND2 ASN A 3 -1.272 0.724 7.270 1.00 13.48 N ATOM 21 N GLN A 4 -0.987 2.256 3.598 1.00 10.29 N ATOM 22 CA GLN A 4 0.361 1.860 3.201 1.00 10.53 C ATOM 23 C GLN A 4 1.398 2.605 4.031 1.00 10.24 C ATOM 24 O GLN A 4 1.454 3.834 4.025 1.00 8.86 O ATOM 25 CB GLN A 4 0.626 2.117 1.712 1.00 9.80 C ATOM 26 CG GLN A 4 1.924 1.459 1.221 1.00 10.25 C ATOM 27 CD GLN A 4 2.465 2.050 -0.073 1.00 12.43 C ATOM 28 OE1 GLN A 4 2.674 3.260 -0.178 1.00 14.62 O ATOM 29 NE2 GLN A 4 2.708 1.192 -1.059 1.00 9.05 N ATOM 30 N AGLN A 5 2.202 1.848 4.775 0.62 10.38 N ATOM 31 CA AGLN A 5 3.288 2.419 5.569 0.62 11.39 C ATOM 32 C AGLN A 5 4.638 1.844 5.123 0.62 11.52 C ATOM 33 O AGLN A 5 4.824 0.625 5.095 0.62 12.05 O ATOM 34 CB AGLN A 5 3.046 2.170 7.063 0.62 11.96 C ATOM 35 CG AGLN A 5 1.854 2.946 7.622 0.62 10.81 C ATOM 36 CD AGLN A 5 1.361 2.406 8.951 0.62 13.10 C ATOM 37 OE1AGLN A 5 0.800 1.312 9.019 0.62 10.65 O ATOM 38 NE2AGLN A 5 1.562 3.175 10.016 0.62 12.30 N ATOM 39 N BGLN A 5 2.239 1.858 4.725 0.38 10.38 N ATOM 40 CA BGLN A 5 3.326 2.476 5.450 0.38 11.39 C ATOM 41 C BGLN A 5 4.639 1.850 5.057 0.38 11.52 C ATOM 42 O BGLN A 5 4.814 0.627 5.020 0.38 12.05 O ATOM 43 CB BGLN A 5 3.110 2.331 6.919 0.38 11.96 C ATOM 44 CG BGLN A 5 2.695 0.980 7.141 0.38 10.81 C ATOM 45 CD BGLN A 5 2.882 0.618 8.479 0.38 13.10 C ATOM 46 OE1BGLN A 5 2.538 1.369 9.406 0.38 10.65 O ATOM 47 NE2BGLN A 5 3.380 -0.597 8.664 0.38 12.30 N ATOM 48 N ASN A 6 5.565 2.732 4.753 1.00 11.99 N ATOM 49 CA ASN A 6 6.868 2.339 4.280 1.00 12.30 C ATOM 50 C ASN A 6 7.881 2.785 5.302 1.00 13.40 C ATOM 51 O ASN A 6 8.262 3.954 5.351 1.00 13.92 O ATOM 52 CB ASN A 6 7.133 2.954 2.915 1.00 12.13 C ATOM 53 CG ASN A 6 5.988 2.721 1.955 1.00 12.77 C ATOM 54 OD1 ASN A 6 5.795 1.608 1.466 1.00 14.27 O ATOM 55 ND2 ASN A 6 5.211 3.764 1.690 1.00 10.07 N ATOM 56 N ATYR A 7 8.304 1.849 6.146 0.59 14.70 N ATOM 57 CA ATYR A 7 9.167 2.166 7.280 0.59 15.18 C ATOM 58 C ATYR A 7 10.622 2.326 6.868 0.59 15.91 C ATOM 59 O ATYR A 7 11.054 1.799 5.844 0.59 15.76 O ATOM 60 CB ATYR A 7 9.044 1.086 8.356 0.59 15.35 C ATOM 61 CG ATYR A 7 7.640 0.946 8.887 0.59 14.45 C ATOM 62 CD1ATYR A 7 6.759 0.027 8.335 0.59 15.68 C ATOM 63 CD2ATYR A 7 7.187 1.750 9.924 0.59 14.80 C ATOM 64 CE1ATYR A 7 5.469 -0.098 8.810 0.59 13.46 C ATOM 65 CE2ATYR A 7 5.899 1.633 10.407 0.59 14.33 C ATOM 66 CZ ATYR A 7 5.044 0.707 9.845 0.59 15.09 C ATOM 67 OH ATYR A 7 3.759 0.583 10.319 0.59 14.39 O ATOM 68 OXTATYR A 7 11.394 2.990 7.558 0.59 17.49 O ATOM 70 N BTYR A 7 8.323 1.843 6.116 0.41 14.70 N ATOM 71 CA BTYR A 7 9.149 2.183 7.247 0.41 15.18 C ATOM 72 C BTYR A 7 10.629 2.316 6.861 0.41 15.91 C ATOM 73 O BTYR A 7 11.084 1.756 5.864 0.41 15.76 O ATOM 74 CB BTYR A 7 8.954 1.147 8.348 0.41 15.35 C ATOM 75 CG BTYR A 7 9.942 1.356 9.417 0.41 14.45 C ATOM 76 CD1BTYR A 7 9.807 2.381 10.320 0.41 15.68 C ATOM 77 CD2BTYR A 7 11.054 0.580 9.473 0.41 14.80 C ATOM 78 CE1BTYR A 7 10.746 2.569 11.248 0.41 13.46 C ATOM 79 CE2BTYR A 7 11.968 0.749 10.405 0.41 14.33 C ATOM 80 CZ BTYR A 7 11.858 1.724 11.252 0.41 15.09 C ATOM 81 OH BTYR A 7 12.921 1.747 12.113 0.41 14.39 O ATOM 82 OXTBTYR A 7 11.408 3.001 7.529 0.41 17.49 O TER HETATM 83 O HOH A 8 -6.471 5.227 7.124 1.00 22.62 O HETATM 84 O HOH A 9 10.431 1.858 3.216 1.00 19.71 O HETATM 85 O HOH A 10 -11.286 1.756 -1.468 1.00 17.08 O HETATM 86 O AHOH A 11 11.808 4.179 9.970 0.60 23.99 O HETATM 87 O HOH A 12 13.605 1.327 9.198 1.00 26.17 O HETATM 88 O HOH A 13 -2.749 3.429 10.024 1.00 39.15 O HETATM 89 O HOH A 14 -1.500 0.682 10.967 1.00 43.49 O TER """ pdb_in = "%s_in.pdb" % prefix with open(pdb_in, "w") as f: f.write(pdb_raw) if (create_mtz): args = [ pdb_in, "high_resolution=%g" % d_min, "type=real", "label=F", "add_sigmas=True", "r_free_flags_fraction=0.1", "random_seed=12345", "output.file_name=%s.mtz" % prefix, ] fmodel.run(args=args, log=null_out()) pdb_file = file_reader.any_file(pdb_in) hierarchy = pdb_file.file_object.hierarchy xrs = pdb_file.file_object.xray_structure_simple() for atom in hierarchy.atoms(): atom.b = 5 if (atom.occ < 1.0): atom.occ = 0.5 with open("%s_start.pdb" % prefix, "w") as f: f.write(hierarchy.as_pdb_string(crystal_symmetry=xrs)) def exercise_regroup_3d(verbose): if (verbose): log = sys.stdout else: log = StringIO() prepare_correlated_occupancy_inputs() # File #1 (with homogenized occupancies) should work # File #2 should fail due to inconsistent occupancies pdb_files = [ "tst_group_correlated_occupancy_start.pdb", "tst_group_correlated_occupancy_in.pdb", ] for i_file, pdb_file in enumerate(pdb_files): model = get_model(pdb_file, log) try : constraint_groups = occupancy_selections( model = model, constrain_correlated_3d_groups=True, log=null_out()) except Sorry as s : if (i_file == 0): raise else : assert ("Inconsistent occupancies" in str(s)), str(s) else : if (i_file == 1): raise Exception_expected else : assert (len(constraint_groups) == 1) def run(): verbose = "--verbose" in sys.argv[1:] exercise_00(verbose=verbose) exercise_01(verbose=verbose) exercise_02(verbose=verbose) exercise_03(verbose=verbose) exercise_05(verbose=verbose) exercise_06(verbose=verbose) exercise_07(verbose=verbose) exercise_08(verbose=verbose) exercise_09(verbose=verbose) exercise_10(verbose=verbose) exercise_11(verbose=verbose) exercise_12(verbose=verbose) exercise_13(verbose=verbose) exercise_14(verbose=verbose) exercise_15(verbose=verbose) exercise_16(verbose=verbose) exercise_17(verbose=verbose) exercise_18(verbose=verbose) exercise_19(verbose=verbose) exercise_20(verbose=verbose) exercise_21(verbose=verbose) exercise_22(verbose=verbose) exercise_23(verbose=verbose) exercise_24(verbose=verbose) exercise_25(verbose=verbose) exercise_26(verbose=verbose) exercise_27(verbose=verbose) exercise_28(verbose=verbose) exercise_29(verbose=verbose) exercise_30(verbose=verbose) exercise_regroup_3d(verbose=verbose) print(format_cpu_times()) if (__name__ == "__main__"): run()