from __future__ import absolute_import, division, print_function import time from iotbx.pdb.secondary_structure import annotation, pdb_helix, pdb_strand import iotbx import iotbx.cif from libtbx.test_utils import show_diff from six.moves import cStringIO as StringIO import libtbx.load_env import os from six.moves import range def test_helix_interface(): # helix_class_to_int. h_class_array = ['unknown','alpha', 'unknown', 'pi', 'unknown', '3_10', 'unknown', 'unknown', 'unknown', 'unknown', 'unknown'] for n, hc in enumerate(h_class_array): # print pdb_helix.helix_class_to_int(hc), n if hc == 'unknown': assert pdb_helix.helix_class_to_int(hc) == 0 else: assert pdb_helix.helix_class_to_int(hc) == n assert pdb_helix.helix_class_to_str(n) == hc h_string = \ "HELIX 1 1 ALA A 16 THR A 18 1 3" h_string_trunc = "HELIX 1 1 ALA A 16 THR A 18 1" got_exception = False try: h = pdb_helix.from_pdb_record(h_string_trunc) except ValueError: got_exception = True assert got_exception h = pdb_helix.from_pdb_record(h_string) assert h.serial == ' 1' assert h.helix_id == '1' assert h.start_resname == 'ALA' assert h.start_chain_id == 'A' assert h.start_resseq == ' 16' assert h.start_icode == ' ' assert h.end_resname == 'THR' assert h.end_chain_id == 'A' assert h.end_resseq == ' 18' assert h.end_icode == ' ' assert h.helix_class == 'alpha' assert h.comment == ' ' assert h.length == 3 assert h.hbond_list == [] assert h.helix_selection == None assert h.enabled == True assert h.sigma ==0.05 assert h.slack ==0 assert h.top_out == False assert h.get_start_resseq_as_int() == 16 assert h.get_end_resseq_as_int() == 18 for resseq in ['15', ' 15', ' 15', 15]: h.set_start_resseq(resseq) assert h.start_resseq == ' 15' assert h.get_start_resseq_as_int() == 15 for resseq in ['15', ' 15', ' 15', 15]: h.set_end_resseq(resseq) assert h.end_resseq == ' 15' assert h.get_end_resseq_as_int() == 15 for resseq in ['AA15', 23001]: h.set_start_resseq(resseq) assert h.start_resseq == 'AA15' assert h.get_start_resseq_as_int() == 23001 for resseq in ['AA19', 23005]: h.set_end_resseq(resseq) assert h.end_resseq == 'AA19' assert h.get_end_resseq_as_int() == 23005 def test_sheet_interface(): sheet_str = """\ SHEET 1 A 2 ARG A 13 ASP A 14 0 SHEET 2 A 2 LEU A 27 SER A 30 -1 O ARG A 29 N ARG A 13 """ ann = annotation.from_records(sheet_str.split("\n")) sh = ann.sheets[0] st = sh.strands[1] reg = sh.registrations[1] assert reg.cur_atom == ' O ' assert reg.cur_resname == 'ARG' assert reg.cur_chain_id == 'A' assert reg.cur_resseq == ' 29' assert reg.cur_icode == ' ' assert reg.prev_atom == ' N ' assert reg.prev_resname == 'ARG' assert reg.prev_chain_id == 'A' assert reg.prev_resseq == ' 13' assert reg.prev_icode == ' ' assert st.sheet_id == ' A', st.sheet_id assert st.strand_id == ' 2', st.strand_id assert st.start_resname == 'LEU' assert st.start_chain_id == 'A' assert st.start_resseq == ' 27', st.start_resseq assert st.start_icode == ' ' assert st.end_resname == 'SER' assert st.end_chain_id == 'A' assert st.end_resseq == ' 30' assert st.end_icode == ' ' assert st.sense == -1 for resseq in ['15', ' 15', ' 15', 15]: reg.set_cur_resseq(resseq) assert reg.cur_resseq == ' 15' assert reg.get_cur_resseq_as_int() == 15 for resseq in ['AA15', 23001]: reg.set_cur_resseq(resseq) assert reg.cur_resseq == 'AA15' assert reg.get_cur_resseq_as_int() == 23001 for resseq in ['15', ' 15', ' 15', 15]: reg.set_prev_resseq(resseq) assert reg.prev_resseq == ' 15' assert reg.get_prev_resseq_as_int() == 15 for resseq in ['AA15', 23001]: reg.set_prev_resseq(resseq) assert reg.prev_resseq == 'AA15' assert reg.get_prev_resseq_as_int() == 23001 for resseq in ['15', ' 15', ' 15', 15]: st.set_start_resseq(resseq) assert st.start_resseq == ' 15' assert st.get_start_resseq_as_int() == 15 for resseq in ['AA15', 23001]: st.set_start_resseq(resseq) assert st.start_resseq == 'AA15' assert st.get_start_resseq_as_int() == 23001 for resseq in ['15', ' 15', ' 15', 15]: st.set_end_resseq(resseq) assert st.end_resseq == ' 15' assert st.get_end_resseq_as_int() == 15 for resseq in ['AA15', 23001]: st.set_end_resseq(resseq) assert st.end_resseq == 'AA15' assert st.get_end_resseq_as_int() == 23001 cif_one_helix = """\ # _struct_conf.conf_type_id HELX_P _struct_conf.id HELX_P1 _struct_conf.pdbx_PDB_helix_id AA1 _struct_conf.beg_label_comp_id GLN _struct_conf.beg_label_asym_id A _struct_conf.beg_label_seq_id 149 _struct_conf.pdbx_beg_PDB_ins_code ? _struct_conf.end_label_comp_id GLY _struct_conf.end_label_asym_id A _struct_conf.end_label_seq_id 160 _struct_conf.pdbx_end_PDB_ins_code ? _struct_conf.beg_auth_comp_id GLN _struct_conf.beg_auth_asym_id A _struct_conf.beg_auth_seq_id 212 _struct_conf.end_auth_comp_id GLY _struct_conf.end_auth_asym_id A _struct_conf.end_auth_seq_id 223 _struct_conf.pdbx_PDB_helix_class 1 _struct_conf.details ? _struct_conf.pdbx_PDB_helix_length 12 # _struct_conf_type.id HELX_P _struct_conf_type.criteria ? _struct_conf_type.reference ? """ cif_4_helices = """\ loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.beg_auth_comp_id _struct_conf.beg_auth_asym_id _struct_conf.beg_auth_seq_id _struct_conf.end_auth_comp_id _struct_conf.end_auth_asym_id _struct_conf.end_auth_seq_id _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P HELX_P1 AA1 SER A 24 ? LYS A 28 ? SER A 26 LYS A 30 5 ? 5 HELX_P HELX_P2 AA2 LEU A 194 ? GLU A 197 ? LEU A 196 GLU A 199 5 ? 4 HELX_P HELX_P3 AA3 SER B 24 ? LYS B 28 ? SER B 26 LYS B 30 5 ? 5 HELX_P HELX_P4 AA4 LEU B 194 ? GLU B 197 ? LEU B 196 GLU B 199 5 ? 4 # """ cif_many_sheets = """\ # loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details AA1 ? 4 ? AA2 ? 3 ? AA3 ? 2 ? AA4 ? 4 ? AA5 ? 3 ? AA6 ? 4 ? AA7 ? 3 ? AA8 ? 2 ? AA9 ? 4 ? AB1 ? 3 ? # loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense AA1 1 2 ? parallel AA1 2 3 ? anti-parallel AA1 3 4 ? anti-parallel AA2 1 2 ? anti-parallel AA2 2 3 ? anti-parallel AA3 1 2 ? anti-parallel AA4 1 2 ? parallel AA4 2 3 ? anti-parallel AA4 3 4 ? anti-parallel AA5 1 2 ? anti-parallel AA5 2 3 ? anti-parallel AA6 1 2 ? parallel AA6 2 3 ? anti-parallel AA6 3 4 ? anti-parallel AA7 1 2 ? anti-parallel AA7 2 3 ? anti-parallel AA8 1 2 ? anti-parallel AA9 1 2 ? parallel AA9 2 3 ? anti-parallel AA9 3 4 ? anti-parallel AB1 1 2 ? anti-parallel AB1 2 3 ? anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id AA1 1 ILE A 5 ? PRO A 8 ? ILE A 7 PRO A 10 AA1 2 MET A 90 ? THR A 97 ? MET A 92 THR A 99 AA1 3 THR A 71 ? SER A 80 ? THR A 73 SER A 82 AA1 4 VAL A 32 ? THR A 37 ? VAL A 34 THR A 39 AA2 1 LYS A 17 ? GLN A 21 ? LYS A 19 GLN A 23 AA2 2 TRP A 57 ? VAL A 60 ? TRP A 59 VAL A 62 AA2 3 PHE A 49 ? ILE A 51 ? PHE A 51 ILE A 53 AA3 1 GLU A 105 ? PHE A 106 ? GLU A 107 PHE A 108 AA3 2 ALA A 130 ? THR A 131 ? ALA A 132 THR A 133 AA4 1 VAL A 110 ? MET A 116 ? VAL A 112 MET A 118 AA4 2 SER A 200 ? THR A 210 ? SER A 202 THR A 212 AA4 3 THR A 184 ? ALA A 192 ? THR A 186 ALA A 194 AA4 4 ALA A 145 ? ASP A 152 ? ALA A 147 ASP A 154 AA5 1 THR A 123 ? GLU A 127 ? THR A 125 GLU A 129 AA5 2 VAL A 169 ? VAL A 172 ? VAL A 171 VAL A 174 AA5 3 PHE A 161 ? ILE A 163 ? PHE A 163 ILE A 165 AA6 1 ILE B 5 ? PRO B 8 ? ILE B 7 PRO B 10 AA6 2 MET B 90 ? THR B 97 ? MET B 92 THR B 99 AA6 3 THR B 71 ? SER B 80 ? THR B 73 SER B 82 AA6 4 VAL B 32 ? GLY B 38 ? VAL B 34 GLY B 40 AA7 1 LYS B 17 ? GLN B 21 ? LYS B 19 GLN B 23 AA7 2 TRP B 57 ? VAL B 60 ? TRP B 59 VAL B 62 AA7 3 PHE B 49 ? ILE B 51 ? PHE B 51 ILE B 53 AA8 1 GLU B 105 ? PHE B 106 ? GLU B 107 PHE B 108 AA8 2 ALA B 130 ? THR B 131 ? ALA B 132 THR B 133 AA9 1 VAL B 110 ? MET B 116 ? VAL B 112 MET B 118 AA9 2 SER B 200 ? THR B 210 ? SER B 202 THR B 212 AA9 3 THR B 184 ? ALA B 192 ? THR B 186 ALA B 194 AA9 4 ALA B 145 ? ASP B 152 ? ALA B 147 ASP B 154 AB1 1 SER B 124 ? GLU B 127 ? SER B 126 GLU B 129 AB1 2 VAL B 169 ? VAL B 172 ? VAL B 171 VAL B 174 AB1 3 PHE B 161 ? ILE B 163 ? PHE B 163 ILE B 165 # loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_1_auth_atom_id _pdbx_struct_sheet_hbond.range_1_auth_comp_id _pdbx_struct_sheet_hbond.range_1_auth_asym_id _pdbx_struct_sheet_hbond.range_1_auth_seq_id _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_auth_atom_id _pdbx_struct_sheet_hbond.range_2_auth_comp_id _pdbx_struct_sheet_hbond.range_2_auth_asym_id _pdbx_struct_sheet_hbond.range_2_auth_seq_id AA1 1 2 N ILE A 5 ? N ILE A 7 O LEU A 93 ? O LEU A 95 AA1 2 3 O ILE A 92 ? O ILE A 94 N LEU A 74 ? N LEU A 76 AA1 3 4 O VAL A 79 ? O VAL A 81 N PHE A 33 ? N PHE A 35 AA2 1 2 N VAL A 20 ? N VAL A 22 O LEU A 58 ? O LEU A 60 AA2 2 3 O LYS A 59 ? O LYS A 61 N ILE A 50 ? N ILE A 52 AA3 1 2 N GLU A 105 ? N GLU A 107 O THR A 131 ? O THR A 133 AA4 1 2 N VAL A 115 ? N VAL A 117 O THR A 210 ? O THR A 212 AA4 2 3 O ALA A 205 ? O ALA A 207 N LEU A 187 ? N LEU A 189 AA4 3 4 O GLN A 190 ? O GLN A 192 N THR A 147 ? N THR A 149 AA5 1 2 N MET A 126 ? N MET A 128 O ILE A 170 ? O ILE A 172 AA5 2 3 O SER A 171 ? O SER A 173 N THR A 162 ? N THR A 164 AA6 1 2 N ILE B 5 ? N ILE B 7 O THR B 95 ? O THR B 97 AA6 2 3 O ILE B 92 ? O ILE B 94 N LEU B 74 ? N LEU B 76 AA6 3 4 O HIS B 77 ? O HIS B 79 N SER B 35 ? N SER B 37 AA7 1 2 N VAL B 20 ? N VAL B 22 O LEU B 58 ? O LEU B 60 AA7 2 3 O LYS B 59 ? O LYS B 61 N ILE B 50 ? N ILE B 52 AA8 1 2 N GLU B 105 ? N GLU B 107 O THR B 131 ? O THR B 133 AA9 1 2 N PHE B 111 ? N PHE B 113 O THR B 204 ? O THR B 206 AA9 2 3 O ALA B 205 ? O ALA B 207 N LEU B 187 ? N LEU B 189 AA9 3 4 O THR B 186 ? O THR B 188 N ASP B 152 ? N ASP B 154 AB1 1 2 N MET B 126 ? N MET B 128 O ILE B 170 ? O ILE B 172 AB1 2 3 O SER B 171 ? O SER B 173 N THR B 162 ? N THR B 164 # """ cif_one_sheet = """\ # _struct_sheet.id A _struct_sheet.type ? _struct_sheet.number_strands 2 _struct_sheet.details ? # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 _struct_sheet_order.offset ? _struct_sheet_order.sense anti-parallel # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code _struct_sheet_range.symmetry _struct_sheet_range.beg_auth_comp_id _struct_sheet_range.beg_auth_asym_id _struct_sheet_range.beg_auth_seq_id _struct_sheet_range.end_auth_comp_id _struct_sheet_range.end_auth_asym_id _struct_sheet_range.end_auth_seq_id A 1 SER A 4 ? ALA A 7 ? ? SER A 4 ALA A 7 A 2 MET A 22 ? GLU A 25 ? ? MET A 22 GLU A 25 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_comp_id SER _pdbx_struct_sheet_hbond.range_1_label_asym_id A _pdbx_struct_sheet_hbond.range_1_label_seq_id 4 _pdbx_struct_sheet_hbond.range_1_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_1_auth_atom_id N _pdbx_struct_sheet_hbond.range_1_auth_comp_id SER _pdbx_struct_sheet_hbond.range_1_auth_asym_id A _pdbx_struct_sheet_hbond.range_1_auth_seq_id 4 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_comp_id GLU _pdbx_struct_sheet_hbond.range_2_label_asym_id A _pdbx_struct_sheet_hbond.range_2_label_seq_id 25 _pdbx_struct_sheet_hbond.range_2_PDB_ins_code ? _pdbx_struct_sheet_hbond.range_2_auth_atom_id O _pdbx_struct_sheet_hbond.range_2_auth_comp_id GLU _pdbx_struct_sheet_hbond.range_2_auth_asym_id A _pdbx_struct_sheet_hbond.range_2_auth_seq_id 25 # """ def tst_from_cif_block(): test_str_1 = "data_4ZTE\n" + cif_4_helices + cif_many_sheets pdb_str = """\ HELIX 1 AA1 SER A 26 LYS A 30 5 5 HELIX 2 AA2 LEU A 196 GLU A 199 5 4 HELIX 3 AA3 SER B 26 LYS B 30 5 5 HELIX 4 AA4 LEU B 196 GLU B 199 5 4 SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7 SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94 SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81 SHEET 1 AA2 3 LYS A 19 GLN A 23 0 SHEET 2 AA2 3 TRP A 59 VAL A 62 -1 O LEU A 60 N VAL A 22 SHEET 3 AA2 3 PHE A 51 ILE A 53 -1 N ILE A 52 O LYS A 61 SHEET 1 AA3 2 GLU A 107 PHE A 108 0 SHEET 2 AA3 2 ALA A 132 THR A 133 -1 O THR A 133 N GLU A 107 SHEET 1 AA4 4 VAL A 112 MET A 118 0 SHEET 2 AA4 4 SER A 202 THR A 212 1 O THR A 212 N VAL A 117 SHEET 3 AA4 4 THR A 186 ALA A 194 -1 N LEU A 189 O ALA A 207 SHEET 4 AA4 4 ALA A 147 ASP A 154 -1 N THR A 149 O GLN A 192 SHEET 1 AA5 3 THR A 125 GLU A 129 0 SHEET 2 AA5 3 VAL A 171 VAL A 174 -1 O ILE A 172 N MET A 128 SHEET 3 AA5 3 PHE A 163 ILE A 165 -1 N THR A 164 O SER A 173 SHEET 1 AA6 4 ILE B 7 PRO B 10 0 SHEET 2 AA6 4 MET B 92 THR B 99 1 O THR B 97 N ILE B 7 SHEET 3 AA6 4 THR B 73 SER B 82 -1 N LEU B 76 O ILE B 94 SHEET 4 AA6 4 VAL B 34 GLY B 40 -1 N SER B 37 O HIS B 79 SHEET 1 AA7 3 LYS B 19 GLN B 23 0 SHEET 2 AA7 3 TRP B 59 VAL B 62 -1 O LEU B 60 N VAL B 22 SHEET 3 AA7 3 PHE B 51 ILE B 53 -1 N ILE B 52 O LYS B 61 SHEET 1 AA8 2 GLU B 107 PHE B 108 0 SHEET 2 AA8 2 ALA B 132 THR B 133 -1 O THR B 133 N GLU B 107 SHEET 1 AA9 4 VAL B 112 MET B 118 0 SHEET 2 AA9 4 SER B 202 THR B 212 1 O THR B 206 N PHE B 113 SHEET 3 AA9 4 THR B 186 ALA B 194 -1 N LEU B 189 O ALA B 207 SHEET 4 AA9 4 ALA B 147 ASP B 154 -1 N ASP B 154 O THR B 188 SHEET 1 AB1 3 SER B 126 GLU B 129 0 SHEET 2 AB1 3 VAL B 171 VAL B 174 -1 O ILE B 172 N MET B 128 SHEET 3 AB1 3 PHE B 163 ILE B 165 -1 N THR B 164 O SER B 173""" cif_model = iotbx.cif.reader(input_string=test_str_1).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) assert ann.get_n_helices() == 4 resnames = [x.start_resname for x in ann.helices] assert resnames == ["SER","LEU","SER","LEU"] resnames = [x.end_resname for x in ann.helices] assert resnames == ["LYS","GLU","LYS","GLU"] assert ann.get_n_sheets() == 10, ann.get_n_sheets() assert [len(x.strands) for x in ann.sheets] == [4, 3, 2, 4, 3, 4, 3, 2, 4, 3] # print ann.as_pdb_str() assert not show_diff(pdb_str, ann.as_pdb_str()) def tst_from_cif_block_2(): cif_str = "data_1UCS\n" + cif_4_helices + cif_one_sheet cif_model = iotbx.cif.reader(input_string=cif_str).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) assert ann.get_n_helices() == 4 resnames = [x.start_resname for x in ann.helices] assert resnames == ["SER","LEU","SER","LEU"] resnames = [x.end_resname for x in ann.helices] assert resnames == ["LYS","GLU","LYS","GLU"] assert ann.get_n_sheets() == 1 assert [len(x.strands) for x in ann.sheets] == [2] # print ann.as_pdb_str() def tst_from_cif_block_3(): "Only one helix" cif_str = "data_1UCS" + cif_one_helix cif_model = iotbx.cif.reader(input_string=cif_str).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) assert ann.get_n_helices() == 1 resnames = [x.start_resname for x in ann.helices] assert resnames == ["GLN"], resnames resnames = [x.end_resname for x in ann.helices] assert resnames == ["GLY"] assert ann.get_n_sheets() == 0 # print ann.as_pdb_str() def tst_from_cif_block_4(): "Only one sheet" cif_str = "data_1UCS" + cif_one_sheet cif_model = iotbx.cif.reader(input_string=cif_str).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) assert ann.get_n_helices() == 0, ann.get_n_helices() assert ann.get_n_sheets() == 1 assert [len(x.strands) for x in ann.sheets] == [2] # print ann.as_pdb_str() def tst_from_minimal_cif_helix(): """reading annotation that contains only required mmCIF records - http://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Categories/struct_conf.html """ cif_answer_minimal_helix = """\ loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P 1 1 ARG A 87 ? GLN A 92 ? 0 ? 5 HELX_P 2 2 ARG B 287 ? GLN B 292 ? 0 ? 5 HELX_P 3 3 PRO A 1 ? LEU A 5 ? 0 ? 4 """ cif_answer_conf_type_loop = """\ loop_ _struct_conf_type.id _struct_conf_type.criteria _struct_conf_type.reference HELX_P ? ? """ pdb_answer_minimal_helix = """\ HELIX 1 1 ARG A 87 GLN A 92 1 5 HELIX 2 2 ARG B 287 GLN B 292 1 5 HELIX 3 3 PRO A 1 LEU A 5 1 4""" minimal_helix = """\ data_4ZTE loop_ _struct_conf.id _struct_conf.conf_type_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id HELX1 HELX_RH_AL_P ARG A 87 GLN A 92 HELX2 HELX_RH_AL_P ARG B 287 GLN B 292 STRN1 STRN_P PRO A 1 LEU A 5 """ cif_model = iotbx.cif.reader(input_string=minimal_helix).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) assert not show_diff(ann.as_pdb_str(), pdb_answer_minimal_helix) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 2 for i, answer in enumerate([cif_answer_minimal_helix, cif_answer_conf_type_loop]): out = StringIO() cif_loops[i].show(out) v = out.getvalue() # print "\"%s\"" % v assert not show_diff(out.getvalue(), answer) def tst_from_minimal_cif_sheet(): cif_minimal_sheet = """\ data_4ZTE # _struct_sheet.id A # _struct_sheet_order.sheet_id A _struct_sheet_order.range_id_1 1 _struct_sheet_order.range_id_2 2 # loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id A 1 SER A 4 ALA A 7 A 2 MET A 22 GLU A 25 # _pdbx_struct_sheet_hbond.sheet_id A _pdbx_struct_sheet_hbond.range_id_1 1 _pdbx_struct_sheet_hbond.range_id_2 2 _pdbx_struct_sheet_hbond.range_1_label_atom_id N _pdbx_struct_sheet_hbond.range_1_label_seq_id 4 _pdbx_struct_sheet_hbond.range_2_label_atom_id O _pdbx_struct_sheet_hbond.range_2_label_seq_id 25 # """ pdb_answer_minimal_sheet = """\ SHEET 1 A 2 SER A 4 ALA A 7 0 SHEET 2 A 2 MET A 22 GLU A 25 0 O . . 25 N . . 4""" answer_struct_sheet_loops = ["""\ loop_ _struct_sheet.id _struct_sheet.type _struct_sheet.number_strands _struct_sheet.details A ? 2 ? ""","""\ loop_ _struct_sheet_order.sheet_id _struct_sheet_order.range_id_1 _struct_sheet_order.range_id_2 _struct_sheet_order.offset _struct_sheet_order.sense A 1 2 ? ? ""","""\ loop_ _struct_sheet_range.sheet_id _struct_sheet_range.id _struct_sheet_range.beg_label_comp_id _struct_sheet_range.beg_label_asym_id _struct_sheet_range.beg_label_seq_id _struct_sheet_range.pdbx_beg_PDB_ins_code _struct_sheet_range.end_label_comp_id _struct_sheet_range.end_label_asym_id _struct_sheet_range.end_label_seq_id _struct_sheet_range.pdbx_end_PDB_ins_code A 1 SER A 4 ? ALA A 7 ? A 2 MET A 22 ? GLU A 25 ? ""","""\ loop_ _pdbx_struct_sheet_hbond.sheet_id _pdbx_struct_sheet_hbond.range_id_1 _pdbx_struct_sheet_hbond.range_id_2 _pdbx_struct_sheet_hbond.range_1_label_atom_id _pdbx_struct_sheet_hbond.range_1_label_comp_id _pdbx_struct_sheet_hbond.range_1_label_asym_id _pdbx_struct_sheet_hbond.range_1_label_seq_id _pdbx_struct_sheet_hbond.range_1_PDB_ins_code _pdbx_struct_sheet_hbond.range_2_label_atom_id _pdbx_struct_sheet_hbond.range_2_label_comp_id _pdbx_struct_sheet_hbond.range_2_label_asym_id _pdbx_struct_sheet_hbond.range_2_label_seq_id _pdbx_struct_sheet_hbond.range_2_PDB_ins_code A 1 2 N . . 4 ? O . . 25 ? """] cif_model = iotbx.cif.reader(input_string=cif_minimal_sheet).model() cif_block = list(cif_model.values())[0] ann = annotation.from_cif_block(cif_block) # print ann.as_pdb_str() assert not show_diff(ann.as_pdb_str(), pdb_answer_minimal_sheet) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 4, len(cif_loops) for i, sheet_loop in enumerate(cif_loops): out = StringIO() sheet_loop.show(out) v = out.getvalue() # print "\"%s\"" % v assert not show_diff(out.getvalue(), answer_struct_sheet_loops[i]) def tst_to_cif_helix(): pdb_str = """\ HELIX 1 AA1 SER A 26 LYS A 30 5 5 HELIX 2 AA2 LEU A 196 GLU A 199 5 4 HELIX 3 AA3 SER B 26 LYS B 30 5 5 HELIX 4 AA4 LEU B 196 GLU B 199 5 4 """ answer = """\ loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P 1 AA1 SER A 26 ? LYS A 30 ? 5 ? 5 HELX_P 2 AA2 LEU A 196 ? GLU A 199 ? 5 ? 4 HELX_P 3 AA3 SER B 26 ? LYS B 30 ? 5 ? 5 HELX_P 4 AA4 LEU B 196 ? GLU B 199 ? 5 ? 4 """ pdb_str2 = """\ HELIX 1 AA1 SER A 26 LYS A 30 5 5 """ answer2 = """\ loop_ _struct_conf.conf_type_id _struct_conf.id _struct_conf.pdbx_PDB_helix_id _struct_conf.beg_label_comp_id _struct_conf.beg_label_asym_id _struct_conf.beg_label_seq_id _struct_conf.pdbx_beg_PDB_ins_code _struct_conf.end_label_comp_id _struct_conf.end_label_asym_id _struct_conf.end_label_seq_id _struct_conf.pdbx_end_PDB_ins_code _struct_conf.pdbx_PDB_helix_class _struct_conf.details _struct_conf.pdbx_PDB_helix_length HELX_P 1 AA1 SER A 26 ? LYS A 30 ? 5 ? 5\n""" ann = annotation.from_records(pdb_str.split("\n")) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 2 helix_loop = cif_loops[0] out = StringIO() helix_loop.show(out) v = out.getvalue() print("\"%s\"" % v) assert not show_diff(out.getvalue(), answer) # hmmm... when there's only one chain, there is one less 'space' # between resname and resnum. Guess: in previous case extra space is # needed to make nice columns. ann = annotation.from_records(pdb_str2.split("\n")) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 2 helix_loop = cif_loops[0] out = StringIO() helix_loop.show(out) v = out.getvalue() # print "\"%s\"" % v assert not show_diff(out.getvalue(), answer2) def tst_to_cif_sheet(): pdb_str1 = """\ SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7 SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94 SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81 SHEET 1 AA2 3 LYS A 19 GLN A 23 0 SHEET 2 AA2 3 TRP A 59 VAL A 62 -1 O LEU A 60 N VAL A 22 SHEET 3 AA2 3 PHE A 51 ILE A 53 -1 N ILE A 52 O LYS A 61""" ann = annotation.from_records(pdb_str1.split("\n")) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 4, len(cif_loops) out = StringIO() cif_block = iotbx.cif.model.block() for loop in cif_loops: loop.show(out) cif_block.add_loop(loop) v = out.getvalue() # print "\"%s\"" % v ann_back = annotation.from_cif_block(cif_block) assert ann_back.get_n_helices() == 0 assert ann_back.get_n_sheets() == 2 assert [len(x.strands) for x in ann_back.sheets] == [4, 3] # print ann_back.as_pdb_str() assert not show_diff(ann_back.as_pdb_str(), pdb_str1) pdb_str2 = """\ SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7 SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94 SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81""" ann = annotation.from_records(pdb_str2.split("\n")) cif_loops = ann.as_cif_loops() assert len(cif_loops) == 4, len(cif_loops) out = StringIO() cif_block = iotbx.cif.model.block() for loop in cif_loops: loop.show(out) cif_block.add_loop(loop) v = out.getvalue() # print "\"%s\"" % v ann_back = annotation.from_cif_block(cif_block) assert ann_back.get_n_helices() == 0 assert ann_back.get_n_sheets() == 1 assert [len(x.strands) for x in ann_back.sheets] == [4] # print ann_back.as_pdb_str() assert not show_diff(ann_back.as_pdb_str(), pdb_str2) pdb_records_2 = """\ HELIX 10 10 MET B 3 TYR B 15 1 13 HELIX 11 11 TYR B 220 LEU B 241 1 22 HELIX 12 12 GLU B 247 LEU B 275 1 29 HELIX 13 13 ILE B 281 ARG B 307 1 27 HELIX 14 14 GLU B 403 TYR B 430 1 28 HELIX 15 15 ALA B 432 VAL B 462 1 31 HELIX 16 16 PRO B 463 ASN B 466 5 4 SHEET 1 BA 6 ASP B 77 PRO B 81 0 SHEET 2 BA 6 ASN B 107 GLN B 111 -1 O VAL B 108 N ILE B 80 SHEET 3 BA 6 ALA B 115 TRP B 118 -1 O ALA B 115 N GLN B 111 SHEET 4 BA 6 ASN B 57 THR B 61 -1 O LEU B 58 N TRP B 118 SHEET 5 BA 6 THR B 30 GLY B 34 -1 O ARG B 32 N ALA B 59 SHEET 6 BA 6 ILE B 157 GLN B 159 1 O ILE B 157 N VAL B 31 SHEET 1 BB 4 LEU B 37 ASN B 44 0 SHEET 2 BB 4 GLU B 49 PHE B 55 -1 O GLU B 49 N ASN B 44 SHEET 3 BB 4 SER B 121 SER B 126 -1 O ALA B 122 N VAL B 54 SHEET 4 BB 4 PHE B 100 GLU B 101 -1 O GLU B 101 N ILE B 123 SHEET 1 BC 4 ILE B 90 LEU B 92 0 SHEET 2 BC 4 THR B 143 SER B 148 -1 O LYS B 147 N VAL B 91 SHEET 3 BC 4 VAL B 207 TYR B 210 -1 O VAL B 207 N PHE B 146 SHEET 4 BC 4 SER B 193 LYS B 195 -1 O ARG B 194 N THR B 208 SHEET 1 BD 2 SER B 187 ILE B 188 0 SHEET 2 BD 2 ILE B 213 GLN B 214 -1 O GLN B 214 N SER B 187 """ pdb_string_2 = """\ ATOM 4705 N TYR B 220 236.756 243.825 262.336 1.00 10.00 N ATOM 4706 CA TYR B 220 236.027 243.470 261.100 1.00 10.00 C ATOM 4707 C TYR B 220 235.677 244.591 260.121 1.00 10.00 C ATOM 4708 O TYR B 220 235.299 244.306 258.994 1.00 10.00 O ATOM 4709 CB TYR B 220 234.714 242.742 261.381 1.00 10.00 C ATOM 4710 CG TYR B 220 234.735 241.529 262.275 1.00 10.00 C ATOM 4711 CD1 TYR B 220 235.783 241.294 263.193 1.00 10.00 C ATOM 4712 CD2 TYR B 220 233.619 240.688 262.302 1.00 10.00 C ATOM 4713 CE1 TYR B 220 235.700 240.257 264.107 1.00 10.00 C ATOM 4714 CE2 TYR B 220 233.517 239.671 263.204 1.00 10.00 C ATOM 4715 CZ TYR B 220 234.545 239.451 264.103 1.00 10.00 C ATOM 4716 OH TYR B 220 234.389 238.416 264.996 1.00 10.00 O ATOM 4717 N ILE B 221 235.740 245.846 260.556 1.00 10.00 N ATOM 4718 CA ILE B 221 235.458 246.970 259.704 1.00 10.00 C ATOM 4719 C ILE B 221 236.494 246.879 258.537 1.00 10.00 C ATOM 4720 O ILE B 221 236.314 247.422 257.427 1.00 10.00 O ATOM 4721 CB ILE B 221 235.531 248.227 260.635 1.00 10.00 C ATOM 4722 CG1 ILE B 221 236.909 248.327 261.313 1.00 10.00 C ATOM 4723 CG2 ILE B 221 234.481 248.053 261.770 1.00 10.00 C ATOM 4724 CD1 ILE B 221 236.886 248.507 262.830 1.00 10.00 C ATOM 4725 N VAL B 222 237.527 246.072 258.779 1.00 10.00 N ATOM 4726 CA VAL B 222 238.611 245.866 257.840 1.00 10.00 C ATOM 4727 C VAL B 222 238.076 245.079 256.678 1.00 10.00 C ATOM 4728 O VAL B 222 238.190 245.501 255.525 1.00 10.00 O ATOM 4729 CB VAL B 222 239.767 245.051 258.480 1.00 10.00 C ATOM 4730 CG1 VAL B 222 241.030 245.163 257.617 1.00 10.00 C ATOM 4731 CG2 VAL B 222 239.993 245.505 259.937 1.00 10.00 C ATOM 4732 N TYR B 223 237.498 243.916 256.959 1.00 10.00 N ATOM 4733 CA TYR B 223 236.998 243.193 255.797 1.00 10.00 C ATOM 4734 C TYR B 223 235.642 243.731 255.357 1.00 10.00 C ATOM 4735 O TYR B 223 235.112 243.268 254.374 1.00 10.00 O ATOM 4736 CB TYR B 223 236.908 241.695 256.094 1.00 10.00 C ATOM 4737 CG TYR B 223 235.804 241.324 257.057 1.00 10.00 C ATOM 4738 CD1 TYR B 223 234.480 241.272 256.641 1.00 10.00 C ATOM 4739 CD2 TYR B 223 236.085 241.027 258.384 1.00 10.00 C ATOM 4740 CE1 TYR B 223 233.468 240.932 257.518 1.00 10.00 C ATOM 4741 CE2 TYR B 223 235.080 240.686 259.269 1.00 10.00 C ATOM 4742 CZ TYR B 223 233.774 240.641 258.831 1.00 10.00 C ATOM 4743 OH TYR B 223 232.772 240.302 259.711 1.00 10.00 O ATOM 4744 N THR B 224 235.127 244.742 256.068 1.00 10.00 N ATOM 4745 CA THR B 224 233.888 245.465 255.737 1.00 10.00 C ATOM 4746 C THR B 224 234.274 246.452 254.592 1.00 10.00 C ATOM 4747 O THR B 224 233.527 246.682 253.621 1.00 10.00 O ATOM 4748 CB THR B 224 233.390 246.267 256.985 1.00 10.00 C ATOM 4749 OG1 THR B 224 232.815 245.365 257.938 1.00 10.00 O ATOM 4750 CG2 THR B 224 232.338 247.298 256.604 1.00 10.00 C ATOM 4751 N ILE B 225 235.481 246.993 254.709 1.00 10.00 N ATOM 4752 CA ILE B 225 236.079 247.939 253.743 1.00 10.00 C ATOM 4753 C ILE B 225 236.203 247.150 252.435 1.00 10.00 C ATOM 4754 O ILE B 225 235.800 247.601 251.358 1.00 10.00 O ATOM 4755 CB ILE B 225 237.546 248.405 254.230 1.00 10.00 C ATOM 4756 CG1 ILE B 225 237.487 249.823 254.873 1.00 10.00 C ATOM 4757 CG2 ILE B 225 238.554 248.277 253.078 1.00 10.00 C ATOM 4758 CD1 ILE B 225 238.802 250.372 255.483 1.00 10.00 C ATOM 4759 N VAL B 226 236.723 245.926 252.549 1.00 10.00 N ATOM 4760 CA VAL B 226 236.904 245.129 251.334 1.00 10.00 C ATOM 4761 C VAL B 226 235.606 245.025 250.571 1.00 10.00 C ATOM 4762 O VAL B 226 235.621 245.119 249.364 1.00 10.00 O ATOM 4763 CB VAL B 226 237.478 243.708 251.567 1.00 10.00 C ATOM 4764 CG1 VAL B 226 238.787 243.804 252.297 1.00 10.00 C ATOM 4765 CG2 VAL B 226 236.480 242.836 252.257 1.00 10.00 C ATOM 4766 N PRO B 227 234.471 244.784 251.253 1.00 10.00 N ATOM 4767 CA PRO B 227 233.225 244.717 250.484 1.00 10.00 C ATOM 4768 C PRO B 227 233.110 246.013 249.736 1.00 10.00 C ATOM 4769 O PRO B 227 233.251 246.069 248.522 1.00 10.00 O ATOM 4770 CB PRO B 227 232.142 244.666 251.550 1.00 10.00 C ATOM 4771 CG PRO B 227 232.785 243.987 252.657 1.00 10.00 C ATOM 4772 CD PRO B 227 234.206 244.487 252.661 1.00 10.00 C ATOM 4773 N CYS B 228 232.868 247.074 250.497 1.00 10.00 N ATOM 4774 CA CYS B 228 232.716 248.396 249.898 1.00 10.00 C ATOM 4775 C CYS B 228 233.629 248.546 248.681 1.00 10.00 C ATOM 4776 O CYS B 228 233.127 248.848 247.618 1.00 10.00 O ATOM 4777 CB CYS B 228 232.947 249.541 250.931 1.00 10.00 C ATOM 4778 SG CYS B 228 231.542 249.841 252.106 1.00 10.00 S ATOM 4779 N ILE B 229 234.929 248.269 248.819 1.00 10.00 N ATOM 4780 CA ILE B 229 235.889 248.399 247.719 1.00 10.00 C ATOM 4781 C ILE B 229 235.932 247.224 246.730 1.00 10.00 C ATOM 4782 O ILE B 229 236.051 247.422 245.518 1.00 10.00 O ATOM 4783 CB ILE B 229 237.313 248.607 248.276 1.00 10.00 C ATOM 4784 CG1 ILE B 229 237.316 249.781 249.260 1.00 10.00 C ATOM 4785 CG2 ILE B 229 238.288 248.863 247.136 1.00 10.00 C ATOM 4786 CD1 ILE B 229 238.648 250.007 249.947 1.00 10.00 C ATOM 4787 N LEU B 230 235.860 246.004 247.250 1.00 10.00 N ATOM 4788 CA LEU B 230 235.889 244.785 246.426 1.00 10.00 C ATOM 4789 C LEU B 230 234.553 244.686 245.700 1.00 10.00 C ATOM 4790 O LEU B 230 234.483 244.299 244.538 1.00 10.00 O ATOM 4791 CB LEU B 230 236.102 243.542 247.297 1.00 10.00 C ATOM 4792 CG LEU B 230 237.259 243.504 248.306 1.00 10.00 C ATOM 4793 CD1 LEU B 230 237.222 242.152 248.975 1.00 10.00 C ATOM 4794 CD2 LEU B 230 238.606 243.767 247.657 1.00 10.00 C ATOM 4795 N ILE B 231 233.483 245.047 246.402 1.00 10.00 N ATOM 4796 CA ILE B 231 232.175 245.042 245.773 1.00 10.00 C ATOM 4797 C ILE B 231 232.270 246.087 244.707 1.00 10.00 C ATOM 4798 O ILE B 231 231.634 245.986 243.664 1.00 10.00 O ATOM 4799 CB ILE B 231 231.097 245.478 246.713 1.00 10.00 C ATOM 4800 CG1 ILE B 231 231.185 244.615 247.972 1.00 10.00 C ATOM 4801 CG2 ILE B 231 229.721 245.466 245.969 1.00 10.00 C ATOM 4802 CD1 ILE B 231 230.710 243.195 247.766 1.00 10.00 C ATOM 4803 N SER B 232 233.034 247.118 245.052 1.00 10.00 N ATOM 4804 CA SER B 232 233.308 248.151 244.061 1.00 10.00 C ATOM 4805 C SER B 232 234.054 247.577 242.862 1.00 10.00 C ATOM 4806 O SER B 232 233.835 247.929 241.753 1.00 10.00 O ATOM 4807 CB SER B 232 234.101 249.298 244.687 1.00 10.00 C ATOM 4808 OG SER B 232 233.261 250.136 245.462 1.00 10.00 O ATOM 4809 N ILE B 233 234.905 246.580 243.194 1.00 10.00 N ATOM 4810 CA ILE B 233 235.644 245.926 242.139 1.00 10.00 C ATOM 4811 C ILE B 233 234.665 245.443 241.097 1.00 10.00 C ATOM 4812 O ILE B 233 234.778 245.798 239.927 1.00 10.00 O ATOM 4813 CB ILE B 233 236.469 244.734 242.640 1.00 10.00 C ATOM 4814 CG1 ILE B 233 237.195 245.075 243.948 1.00 10.00 C ATOM 4815 CG2 ILE B 233 237.521 244.395 241.583 1.00 10.00 C ATOM 4816 CD1 ILE B 233 238.246 244.065 244.374 1.00 10.00 C ATOM 4817 N LEU B 234 233.675 244.677 241.533 1.00 10.00 N ATOM 4818 CA LEU B 234 232.673 244.134 240.627 1.00 10.00 C ATOM 4819 C LEU B 234 231.791 245.340 240.186 1.00 10.00 C ATOM 4820 O LEU B 234 231.322 245.402 239.046 1.00 10.00 O ATOM 4821 CB LEU B 234 231.877 242.962 241.316 1.00 10.00 C ATOM 4822 CG LEU B 234 232.447 241.937 242.366 1.00 10.00 C ATOM 4823 CD1 LEU B 234 231.422 240.857 242.578 1.00 10.00 C ATOM 4824 CD2 LEU B 234 233.763 241.285 241.947 1.00 10.00 C ATOM 4825 N ALA B 235 231.631 246.334 241.067 1.00 10.00 N ATOM 4826 CA ALA B 235 230.861 247.525 240.769 1.00 10.00 C ATOM 4827 C ALA B 235 231.553 248.274 239.623 1.00 10.00 C ATOM 4828 O ALA B 235 231.035 248.323 238.503 1.00 10.00 O ATOM 4829 CB ALA B 235 230.785 248.393 242.002 1.00 10.00 C ATOM 4830 N ILE B 236 232.691 248.903 239.910 1.00 10.00 N ATOM 4831 CA ILE B 236 233.475 249.607 238.866 1.00 10.00 C ATOM 4832 C ILE B 236 233.551 248.710 237.664 1.00 10.00 C ATOM 4833 O ILE B 236 233.594 249.167 236.534 1.00 10.00 O ATOM 4834 CB ILE B 236 234.979 249.942 239.255 1.00 10.00 C ATOM 4835 CG1 ILE B 236 235.762 250.300 237.985 1.00 10.00 C ATOM 4836 CG2 ILE B 236 235.693 248.763 239.889 1.00 10.00 C ATOM 4837 CD1 ILE B 236 236.838 251.361 238.197 1.00 10.00 C ATOM 4838 N LEU B 237 233.558 247.415 237.957 1.00 10.00 N ATOM 4839 CA LEU B 237 233.632 246.343 236.959 1.00 10.00 C ATOM 4840 C LEU B 237 232.360 246.328 236.119 1.00 10.00 C ATOM 4841 O LEU B 237 232.416 246.266 234.898 1.00 10.00 O ATOM 4842 CB LEU B 237 233.818 244.973 237.656 1.00 10.00 C ATOM 4843 CG LEU B 237 235.119 244.111 237.601 1.00 10.00 C ATOM 4844 CD1 LEU B 237 236.403 244.933 237.384 1.00 10.00 C ATOM 4845 CD2 LEU B 237 235.234 243.311 238.886 1.00 10.00 C ATOM 4846 N VAL B 238 231.212 246.422 236.778 1.00 10.00 N ATOM 4847 CA VAL B 238 229.915 246.397 236.074 1.00 10.00 C ATOM 4848 C VAL B 238 229.713 247.710 235.345 1.00 10.00 C ATOM 4849 O VAL B 238 228.903 247.810 234.436 1.00 10.00 O ATOM 4850 CB VAL B 238 228.702 246.194 237.050 1.00 10.00 C ATOM 4851 CG1 VAL B 238 227.400 246.551 236.389 1.00 10.00 C ATOM 4852 CG2 VAL B 238 228.631 244.739 237.510 1.00 10.00 C ATOM 4853 N PHE B 239 230.476 248.722 235.747 1.00 10.00 N ATOM 4854 CA PHE B 239 230.405 250.061 235.171 1.00 10.00 C ATOM 4855 C PHE B 239 231.509 250.132 234.127 1.00 10.00 C ATOM 4856 O PHE B 239 231.467 250.917 233.179 1.00 10.00 O ATOM 4857 CB PHE B 239 230.634 251.028 236.310 1.00 10.00 C ATOM 4858 CG PHE B 239 229.961 250.592 237.595 1.00 10.00 C ATOM 4859 CD1 PHE B 239 228.755 249.886 237.561 1.00 10.00 C ATOM 4860 CD2 PHE B 239 230.531 250.863 238.836 1.00 10.00 C ATOM 4861 CE1 PHE B 239 228.132 249.453 238.735 1.00 10.00 C ATOM 4862 CE2 PHE B 239 229.914 250.434 240.016 1.00 10.00 C ATOM 4863 CZ PHE B 239 228.711 249.724 239.965 1.00 10.00 C ATOM 4864 N TYR B 240 232.465 249.220 234.293 1.00 10.00 N ATOM 4865 CA TYR B 240 233.634 249.123 233.423 1.00 10.00 C ATOM 4866 C TYR B 240 233.399 248.048 232.375 1.00 10.00 C ATOM 4867 O TYR B 240 233.905 248.138 231.261 1.00 10.00 O ATOM 4868 CB TYR B 240 234.847 248.758 234.275 1.00 10.00 C ATOM 4869 CG TYR B 240 236.188 249.041 233.699 1.00 10.00 C ATOM 4870 CD1 TYR B 240 236.368 249.237 232.358 1.00 10.00 C ATOM 4871 CD2 TYR B 240 237.291 249.069 234.516 1.00 10.00 C ATOM 4872 CE1 TYR B 240 237.606 249.449 231.854 1.00 10.00 C ATOM 4873 CE2 TYR B 240 238.527 249.277 234.016 1.00 10.00 C ATOM 4874 CZ TYR B 240 238.675 249.463 232.688 1.00 10.00 C ATOM 4875 OH TYR B 240 239.923 249.641 232.191 1.00 10.00 O ATOM 4876 N LEU B 241 232.624 247.038 232.756 1.00 10.00 N ATOM 4877 CA LEU B 241 232.280 245.893 231.900 1.00 10.00 C ATOM 4878 C LEU B 241 231.473 246.333 230.662 1.00 10.00 C ATOM 4879 O LEU B 241 231.580 245.705 229.611 1.00 10.00 O ATOM 4880 CB LEU B 241 231.532 244.785 232.730 1.00 10.00 C ATOM 4881 CG LEU B 241 230.971 243.450 232.158 1.00 10.00 C ATOM 4882 CD1 LEU B 241 232.007 242.657 231.452 1.00 10.00 C ATOM 4883 CD2 LEU B 241 230.426 242.604 233.258 1.00 10.00 C ATOM 4884 N PRO B 242 230.679 247.430 230.757 1.00 10.00 N ATOM 4885 CA PRO B 242 229.911 247.858 229.579 1.00 10.00 C ATOM 4886 C PRO B 242 230.801 248.243 228.376 1.00 10.00 C ATOM 4887 O PRO B 242 230.582 247.785 227.252 1.00 10.00 O ATOM 4888 CB PRO B 242 229.064 249.002 230.127 1.00 10.00 C ATOM 4889 CG PRO B 242 229.728 249.370 231.472 1.00 10.00 C ATOM 4890 CD PRO B 242 230.222 248.099 231.985 1.00 10.00 C ATOM 4891 N PRO B 243 231.814 249.099 228.594 1.00 10.00 N ATOM 4892 CA PRO B 243 232.577 249.351 227.367 1.00 10.00 C ATOM 4893 C PRO B 243 233.753 248.371 227.292 1.00 10.00 C ATOM 4894 O PRO B 243 234.662 248.514 226.477 1.00 10.00 O ATOM 4895 CB PRO B 243 233.035 250.797 227.536 1.00 10.00 C ATOM 4896 CG PRO B 243 233.181 250.938 228.993 1.00 10.00 C ATOM 4897 CD PRO B 243 231.933 250.254 229.505 1.00 10.00 C ATOM 4898 N ASP B 244 233.711 247.382 228.180 1.00 10.00 N ATOM 4899 CA ASP B 244 234.715 246.317 228.295 1.00 10.00 C ATOM 4900 C ASP B 244 234.177 245.111 227.532 1.00 10.00 C ATOM 4901 O ASP B 244 234.866 244.491 226.708 1.00 10.00 O ATOM 4902 CB ASP B 244 234.922 245.955 229.765 1.00 10.00 C ATOM 4903 CG ASP B 244 236.381 245.800 230.130 1.00 10.00 C ATOM 4904 OD1 ASP B 244 237.220 245.632 229.218 1.00 10.00 O ATOM 4905 OD2 ASP B 244 236.685 245.845 231.339 1.00 10.00 O ATOM 4906 N ALA B 245 232.915 244.822 227.773 1.00 10.00 N ATOM 4907 CA ALA B 245 232.240 243.722 227.116 1.00 10.00 C ATOM 4908 C ALA B 245 230.748 244.083 227.062 1.00 10.00 C ATOM 4909 O ALA B 245 229.918 243.550 227.807 1.00 10.00 O ATOM 4910 CB ALA B 245 232.453 242.495 227.884 1.00 10.00 C ATOM 4911 N GLY B 246 230.420 245.050 226.199 1.00 10.00 N ATOM 4912 CA GLY B 246 229.039 245.509 226.032 1.00 10.00 C ATOM 4913 C GLY B 246 228.022 244.400 226.236 1.00 10.00 C ATOM 4914 O GLY B 246 226.971 244.623 226.816 1.00 10.00 O ATOM 4915 N GLU B 247 228.338 243.213 225.704 1.00 10.00 N ATOM 4916 CA GLU B 247 227.477 242.051 225.888 1.00 10.00 C ATOM 4917 C GLU B 247 227.187 241.806 227.364 1.00 10.00 C ATOM 4918 O GLU B 247 226.485 240.913 227.745 1.00 10.00 O ATOM 4919 CB GLU B 247 228.111 240.810 225.256 1.00 10.00 C ATOM 4920 CG GLU B 247 228.267 240.893 223.745 1.00 10.00 C ATOM 4921 CD GLU B 247 229.511 241.652 223.330 1.00 10.00 C ATOM 4922 OE1 GLU B 247 230.289 242.054 224.223 1.00 10.00 O ATOM 4923 OE2 GLU B 247 229.711 241.846 222.113 1.00 10.00 O ATOM 4924 N LYS B 248 227.836 242.656 228.158 1.00 10.00 N ATOM 4925 CA LYS B 248 227.703 242.635 229.601 1.00 10.00 C ATOM 4926 C LYS B 248 226.199 242.758 229.827 1.00 10.00 C ATOM 4927 O LYS B 248 225.647 242.319 230.840 1.00 10.00 O ATOM 4928 CB LYS B 248 228.497 243.831 230.186 1.00 10.00 C ATOM 4929 CG LYS B 248 227.758 245.140 230.358 1.00 10.00 C ATOM 4930 CD LYS B 248 227.205 245.217 231.753 1.00 10.00 C ATOM 4931 CE LYS B 248 228.297 245.156 232.785 1.00 10.00 C ATOM 4932 NZ LYS B 248 227.742 245.174 234.142 1.00 10.00 N ATOM 4933 N MET B 249 225.551 243.310 228.807 1.00 10.00 N ATOM 4934 CA MET B 249 224.123 243.560 228.763 1.00 10.00 C ATOM 4935 C MET B 249 223.315 242.787 229.811 1.00 10.00 C ATOM 4936 O MET B 249 222.738 243.375 230.729 1.00 10.00 O ATOM 4937 CB MET B 249 223.631 243.270 227.335 1.00 10.00 C ATOM 4938 CG MET B 249 224.404 242.140 226.624 1.00 10.00 C ATOM 4939 SD MET B 249 224.187 240.510 227.326 1.00 10.00 S ATOM 4940 CE MET B 249 222.349 240.281 227.080 1.00 10.00 C ATOM 4941 N SER B 250 223.305 241.467 229.682 1.00 10.00 N ATOM 4942 CA SER B 250 222.578 240.589 230.594 1.00 10.00 C ATOM 4943 C SER B 250 223.411 240.238 231.807 1.00 10.00 C ATOM 4944 O SER B 250 222.980 240.431 232.947 1.00 10.00 O ATOM 4945 CB SER B 250 222.169 239.291 229.891 1.00 10.00 C ATOM 4946 OG SER B 250 223.305 238.557 229.461 1.00 10.00 O ATOM 4947 N LEU B 251 224.606 239.715 231.551 1.00 10.00 N ATOM 4948 CA LEU B 251 225.518 239.325 232.623 1.00 10.00 C ATOM 4949 C LEU B 251 225.545 240.419 233.656 1.00 10.00 C ATOM 4950 O LEU B 251 225.767 240.166 234.844 1.00 10.00 O ATOM 4951 CB LEU B 251 226.933 239.153 232.107 1.00 10.00 C ATOM 4952 CG LEU B 251 227.965 240.219 232.443 1.00 10.00 C ATOM 4953 CD1 LEU B 251 228.397 240.185 233.875 1.00 10.00 C ATOM 4954 CD2 LEU B 251 229.133 239.974 231.566 1.00 10.00 C ATOM 4955 N SER B 252 225.330 241.645 233.189 1.00 10.00 N ATOM 4956 CA SER B 252 225.347 242.803 234.075 1.00 10.00 C ATOM 4957 C SER B 252 224.316 242.658 235.188 1.00 10.00 C ATOM 4958 O SER B 252 224.646 242.763 236.359 1.00 10.00 O ATOM 4959 CB SER B 252 225.100 244.087 233.281 1.00 10.00 C ATOM 4960 OG SER B 252 223.934 243.978 232.483 1.00 10.00 O ATOM 4961 N ILE B 253 223.079 242.406 234.777 1.00 10.00 N ATOM 4962 CA ILE B 253 221.984 242.215 235.701 1.00 10.00 C ATOM 4963 C ILE B 253 222.318 241.079 236.674 1.00 10.00 C ATOM 4964 O ILE B 253 221.966 241.155 237.861 1.00 10.00 O ATOM 4965 CB ILE B 253 220.637 241.967 234.909 1.00 10.00 C ATOM 4966 CG1 ILE B 253 219.873 243.313 234.717 1.00 10.00 C ATOM 4967 CG2 ILE B 253 219.812 240.846 235.566 1.00 10.00 C ATOM 4968 CD1 ILE B 253 218.952 243.807 235.863 1.00 10.00 C ATOM 4969 N SER B 254 223.006 240.035 236.210 1.00 10.00 N ATOM 4970 CA SER B 254 223.376 238.942 237.101 1.00 10.00 C ATOM 4971 C SER B 254 224.230 239.445 238.260 1.00 10.00 C ATOM 4972 O SER B 254 224.153 238.954 239.385 1.00 10.00 O ATOM 4973 CB SER B 254 224.117 237.850 236.327 1.00 10.00 C ATOM 4974 OG SER B 254 225.519 237.973 236.484 1.00 10.00 O ATOM 4975 N ALA B 255 225.086 240.395 237.894 1.00 10.00 N ATOM 4976 CA ALA B 255 226.037 241.048 238.788 1.00 10.00 C ATOM 4977 C ALA B 255 225.307 241.739 239.912 1.00 10.00 C ATOM 4978 O ALA B 255 225.642 241.558 241.078 1.00 10.00 O ATOM 4979 CB ALA B 255 226.895 242.082 238.010 1.00 10.00 C ATOM 4980 N LEU B 256 224.309 242.534 239.561 1.00 10.00 N ATOM 4981 CA LEU B 256 223.576 243.237 240.619 1.00 10.00 C ATOM 4982 C LEU B 256 222.698 242.283 241.429 1.00 10.00 C ATOM 4983 O LEU B 256 222.629 242.451 242.637 1.00 10.00 O ATOM 4984 CB LEU B 256 222.714 244.357 240.023 1.00 10.00 C ATOM 4985 CG LEU B 256 223.454 245.455 239.256 1.00 10.00 C ATOM 4986 CD1 LEU B 256 222.475 246.489 238.720 1.00 10.00 C ATOM 4987 CD2 LEU B 256 224.499 246.119 240.141 1.00 10.00 C ATOM 4988 N LEU B 257 222.022 241.325 240.800 1.00 10.00 N ATOM 4989 CA LEU B 257 221.351 240.362 241.696 1.00 10.00 C ATOM 4990 C LEU B 257 222.312 239.918 242.800 1.00 10.00 C ATOM 4991 O LEU B 257 222.010 239.941 243.992 1.00 10.00 O ATOM 4992 CB LEU B 257 220.902 239.113 240.928 1.00 10.00 C ATOM 4993 CG LEU B 257 219.677 239.334 240.039 1.00 10.00 C ATOM 4994 CD1 LEU B 257 218.840 238.062 239.860 1.00 10.00 C ATOM 4995 CD2 LEU B 257 218.716 240.394 240.581 1.00 10.00 C ATOM 4996 N ALA B 258 223.421 239.380 242.242 1.00 10.00 N ATOM 4997 CA ALA B 258 224.562 239.012 243.063 1.00 10.00 C ATOM 4998 C ALA B 258 225.004 240.169 243.948 1.00 10.00 C ATOM 4999 O ALA B 258 225.149 240.011 245.189 1.00 10.00 O ATOM 5000 CB ALA B 258 225.713 238.543 242.190 1.00 10.00 C ATOM 5001 N LEU B 259 225.248 241.342 243.377 1.00 10.00 N ATOM 5002 CA LEU B 259 225.691 242.450 244.206 1.00 10.00 C ATOM 5003 C LEU B 259 224.678 242.839 245.284 1.00 10.00 C ATOM 5004 O LEU B 259 225.062 243.145 246.415 1.00 10.00 O ATOM 5005 CB LEU B 259 226.049 243.676 243.341 1.00 10.00 C ATOM 5006 CG LEU B 259 227.151 244.631 243.850 1.00 10.00 C ATOM 5007 CD1 LEU B 259 227.592 245.577 242.736 1.00 10.00 C ATOM 5008 CD2 LEU B 259 226.652 245.413 245.048 1.00 10.00 C ATOM 5009 N THR B 260 223.399 242.829 244.948 1.00 10.00 N ATOM 5010 CA THR B 260 222.387 243.200 245.924 1.00 10.00 C ATOM 5011 C THR B 260 222.189 242.157 247.018 1.00 10.00 C ATOM 5012 O THR B 260 222.041 242.522 248.180 1.00 10.00 O ATOM 5013 CB THR B 260 221.034 243.494 245.252 1.00 10.00 C ATOM 5014 OG1 THR B 260 221.208 244.520 244.268 1.00 10.00 O ATOM 5015 CG2 THR B 260 220.017 243.972 246.288 1.00 10.00 C ATOM 5016 N VAL B 261 222.180 240.871 246.671 1.00 10.00 N ATOM 5017 CA VAL B 261 222.004 239.850 247.696 1.00 10.00 C ATOM 5018 C VAL B 261 223.159 239.978 248.701 1.00 10.00 C ATOM 5019 O VAL B 261 222.934 240.017 249.908 1.00 10.00 O ATOM 5020 CB VAL B 261 221.950 238.444 247.085 1.00 10.00 C ATOM 5021 CG1 VAL B 261 223.254 237.708 247.343 1.00 10.00 C ATOM 5022 CG2 VAL B 261 220.760 237.676 247.653 1.00 10.00 C ATOM 5023 N PHE B 262 224.382 240.077 248.191 1.00 10.00 N ATOM 5024 CA PHE B 262 225.569 240.246 249.018 1.00 10.00 C ATOM 5025 C PHE B 262 225.380 241.384 250.006 1.00 10.00 C ATOM 5026 O PHE B 262 225.689 241.251 251.207 1.00 10.00 O ATOM 5027 CB PHE B 262 226.797 240.499 248.145 1.00 10.00 C ATOM 5028 CG PHE B 262 227.078 239.399 247.169 1.00 10.00 C ATOM 5029 CD1 PHE B 262 226.127 238.427 246.917 1.00 10.00 C ATOM 5030 CD2 PHE B 262 228.290 239.340 246.505 1.00 10.00 C ATOM 5031 CE1 PHE B 262 226.382 237.410 246.017 1.00 10.00 C ATOM 5032 CE2 PHE B 262 228.554 238.326 245.601 1.00 10.00 C ATOM 5033 CZ PHE B 262 227.597 237.358 245.358 1.00 10.00 C ATOM 5034 N LEU B 263 225.005 242.562 249.524 1.00 10.00 N ATOM 5035 CA LEU B 263 224.853 243.689 250.414 1.00 10.00 C ATOM 5036 C LEU B 263 223.675 243.543 251.357 1.00 10.00 C ATOM 5037 O LEU B 263 223.652 244.130 252.450 1.00 10.00 O ATOM 5038 CB LEU B 263 224.762 244.980 249.601 1.00 10.00 C ATOM 5039 CG LEU B 263 226.093 245.735 249.527 1.00 10.00 C ATOM 5040 CD1 LEU B 263 226.330 246.117 248.086 1.00 10.00 C ATOM 5041 CD2 LEU B 263 226.123 246.953 250.472 1.00 10.00 C ATOM 5042 N LEU B 264 222.686 242.760 250.956 1.00 10.00 N ATOM 5043 CA LEU B 264 221.542 242.579 251.816 1.00 10.00 C ATOM 5044 C LEU B 264 221.924 241.605 252.925 1.00 10.00 C ATOM 5045 O LEU B 264 221.463 241.743 254.065 1.00 10.00 O ATOM 5046 CB LEU B 264 220.334 242.083 251.014 1.00 10.00 C ATOM 5047 CG LEU B 264 219.755 243.159 250.078 1.00 10.00 C ATOM 5048 CD1 LEU B 264 218.653 242.565 249.216 1.00 10.00 C ATOM 5049 CD2 LEU B 264 219.225 244.338 250.898 1.00 10.00 C ATOM 5050 N LEU B 265 222.774 240.622 252.620 1.00 10.00 N ATOM 5051 CA LEU B 265 223.222 239.669 253.669 1.00 10.00 C ATOM 5052 C LEU B 265 224.032 240.505 254.652 1.00 10.00 C ATOM 5053 O LEU B 265 223.988 240.274 255.858 1.00 10.00 O ATOM 5054 CB LEU B 265 224.166 238.569 253.144 1.00 10.00 C ATOM 5055 CG LEU B 265 224.020 237.888 251.787 1.00 10.00 C ATOM 5056 CD1 LEU B 265 225.443 237.601 251.239 1.00 10.00 C ATOM 5057 CD2 LEU B 265 223.153 236.632 251.913 1.00 10.00 C ATOM 5058 N LEU B 266 224.807 241.449 254.109 1.00 10.00 N ATOM 5059 CA LEU B 266 225.613 242.341 254.936 1.00 10.00 C ATOM 5060 C LEU B 266 224.650 243.101 255.827 1.00 10.00 C ATOM 5061 O LEU B 266 224.959 243.415 256.978 1.00 10.00 O ATOM 5062 CB LEU B 266 226.400 243.325 254.070 1.00 10.00 C ATOM 5063 CG LEU B 266 227.671 242.791 253.407 1.00 10.00 C ATOM 5064 CD1 LEU B 266 228.218 243.833 252.445 1.00 10.00 C ATOM 5065 CD2 LEU B 266 228.705 242.448 254.474 1.00 10.00 C ATOM 5066 N ALA B 267 223.483 243.402 255.267 1.00 10.00 N ATOM 5067 CA ALA B 267 222.436 244.089 255.989 1.00 10.00 C ATOM 5068 C ALA B 267 222.023 243.185 257.154 1.00 10.00 C ATOM 5069 O ALA B 267 221.667 243.655 258.244 1.00 10.00 O ATOM 5070 CB ALA B 267 221.285 244.310 255.082 1.00 10.00 C ATOM 5071 N ASP B 268 222.131 241.880 256.924 1.00 10.00 N ATOM 5072 CA ASP B 268 221.777 240.836 257.862 1.00 10.00 C ATOM 5073 C ASP B 268 222.713 240.754 259.077 1.00 10.00 C ATOM 5074 O ASP B 268 222.260 240.620 260.224 1.00 10.00 O ATOM 5075 CB ASP B 268 221.764 239.492 257.131 1.00 10.00 C ATOM 5076 CG ASP B 268 220.507 239.255 256.337 1.00 10.00 C ATOM 5077 OD1 ASP B 268 219.399 239.480 256.867 1.00 10.00 O ATOM 5078 OD2 ASP B 268 220.644 238.809 255.181 1.00 10.00 O ATOM 5079 N LYS B 269 224.017 240.864 258.839 1.00 10.00 N ATOM 5080 CA LYS B 269 224.982 240.732 259.921 1.00 10.00 C ATOM 5081 C LYS B 269 225.111 242.032 260.702 1.00 10.00 C ATOM 5082 O LYS B 269 225.405 241.979 261.910 1.00 10.00 O ATOM 5083 CB LYS B 269 226.344 240.301 259.377 1.00 10.00 C ATOM 5084 CG LYS B 269 226.919 241.244 258.332 1.00 10.00 C ATOM 5085 CD LYS B 269 227.543 242.471 258.979 1.00 10.00 C ATOM 5086 CE LYS B 269 227.861 243.539 257.944 1.00 10.00 C ATOM 5087 NZ LYS B 269 229.289 243.957 257.999 1.00 10.00 N ATOM 5088 N VAL B 270 224.951 243.183 260.068 1.00 10.00 N ATOM 5089 CA VAL B 270 225.061 244.484 260.753 1.00 10.00 C ATOM 5090 C VAL B 270 224.046 244.754 261.883 1.00 10.00 C ATOM 5091 O VAL B 270 224.421 245.251 262.949 1.00 10.00 O ATOM 5092 CB VAL B 270 224.953 245.662 259.753 1.00 10.00 C ATOM 5093 CG1 VAL B 270 225.245 246.971 260.475 1.00 10.00 C ATOM 5094 CG2 VAL B 270 225.921 245.468 258.594 1.00 10.00 C ATOM 5095 N PRO B 271 222.758 244.423 261.663 1.00 10.00 N ATOM 5096 CA PRO B 271 221.782 244.685 262.718 1.00 10.00 C ATOM 5097 C PRO B 271 221.942 243.734 263.890 1.00 10.00 C ATOM 5098 O PRO B 271 221.722 244.111 265.044 1.00 10.00 O ATOM 5099 CB PRO B 271 220.463 244.476 262.003 1.00 10.00 C ATOM 5100 CG PRO B 271 220.768 243.256 261.202 1.00 10.00 C ATOM 5101 CD PRO B 271 222.173 243.534 260.649 1.00 10.00 C ATOM 5102 N GLU B 272 222.323 242.506 263.582 1.00 10.00 N ATOM 5103 CA GLU B 272 222.482 241.519 264.642 1.00 10.00 C ATOM 5104 C GLU B 272 223.812 241.696 265.365 1.00 10.00 C ATOM 5105 O GLU B 272 224.014 241.153 266.456 1.00 10.00 O ATOM 5106 CB GLU B 272 222.365 240.101 264.078 1.00 10.00 C ATOM 5107 CG GLU B 272 222.283 239.016 265.139 1.00 10.00 C ATOM 5108 CD GLU B 272 222.192 237.626 264.543 1.00 10.00 C ATOM 5109 OE1 GLU B 272 223.250 237.045 264.224 1.00 10.00 O ATOM 5110 OE2 GLU B 272 221.061 237.115 264.397 1.00 10.00 O ATOM 5111 N THR B 273 224.746 242.448 264.783 1.00 10.00 N ATOM 5112 CA THR B 273 226.022 242.664 265.441 1.00 10.00 C ATOM 5113 C THR B 273 225.966 243.896 266.325 1.00 10.00 C ATOM 5114 O THR B 273 226.650 243.953 267.352 1.00 10.00 O ATOM 5115 CB THR B 273 227.158 242.804 264.429 1.00 10.00 C ATOM 5116 OG1 THR B 273 226.789 243.755 263.422 1.00 10.00 O ATOM 5117 CG2 THR B 273 227.462 241.462 263.782 1.00 10.00 C ATOM 5118 N SER B 274 225.184 244.913 265.951 1.00 10.00 N ATOM 5119 CA SER B 274 225.097 246.091 266.795 1.00 10.00 C ATOM 5120 C SER B 274 224.192 245.616 267.923 1.00 10.00 C ATOM 5121 O SER B 274 224.236 246.155 269.001 1.00 10.00 O ATOM 5122 CB SER B 274 224.482 247.284 266.043 1.00 10.00 C ATOM 5123 OG SER B 274 223.149 247.015 265.626 1.00 10.00 O ATOM 5124 N LEU B 275 223.413 244.582 267.657 1.00 10.00 N ATOM 5125 CA LEU B 275 222.480 243.986 268.618 1.00 10.00 C ATOM 5126 C LEU B 275 223.102 243.867 270.011 1.00 10.00 C ATOM 5127 O LEU B 275 222.364 243.617 270.970 1.00 10.00 O ATOM 5128 CB LEU B 275 222.019 242.605 268.137 1.00 10.00 C ATOM 5129 CG LEU B 275 221.032 242.583 266.968 1.00 10.00 C ATOM 5130 CD1 LEU B 275 220.269 241.268 266.933 1.00 10.00 C ATOM 5131 CD2 LEU B 275 220.068 243.757 267.056 1.00 10.00 C ATOM 5132 N SER B 276 224.404 243.994 270.159 1.00 10.00 N ATOM 5133 CA SER B 276 224.994 243.862 271.497 1.00 10.00 C ATOM 5134 C SER B 276 225.986 244.956 271.827 1.00 10.00 C ATOM 5135 O SER B 276 226.479 245.038 272.953 1.00 10.00 O ATOM 5136 CB SER B 276 225.691 242.501 271.672 1.00 10.00 C ATOM 5137 OG SER B 276 226.767 242.591 272.594 1.00 10.00 O ATOM 5138 N VAL B 277 226.289 245.806 270.856 1.00 10.00 N ATOM 5139 CA VAL B 277 227.258 246.856 271.114 1.00 10.00 C ATOM 5140 C VAL B 277 227.014 248.142 270.273 1.00 10.00 C ATOM 5141 O VAL B 277 227.956 248.785 269.847 1.00 10.00 O ATOM 5142 CB VAL B 277 228.758 246.256 270.941 1.00 10.00 C ATOM 5143 CG1 VAL B 277 228.913 244.967 271.745 1.00 10.00 C ATOM 5144 CG2 VAL B 277 229.100 245.960 269.475 1.00 10.00 C ATOM 5145 N PRO B 278 225.737 248.571 270.094 1.00 10.00 N ATOM 5146 CA PRO B 278 225.400 249.757 269.312 1.00 10.00 C ATOM 5147 C PRO B 278 225.702 251.104 269.972 1.00 10.00 C ATOM 5148 O PRO B 278 225.755 251.223 271.199 1.00 10.00 O ATOM 5149 CB PRO B 278 223.904 249.567 269.050 1.00 10.00 C ATOM 5150 CG PRO B 278 223.440 249.030 270.354 1.00 10.00 C ATOM 5151 CD PRO B 278 224.540 248.034 270.745 1.00 10.00 C ATOM 5152 N ILE B 279 225.950 252.080 269.159 1.00 10.00 N ATOM 5153 CA ILE B 279 226.182 253.473 269.507 1.00 10.00 C ATOM 5154 C ILE B 279 225.797 254.381 268.330 1.00 10.00 C ATOM 5155 O ILE B 279 225.022 253.864 267.510 1.00 10.00 O ATOM 5156 CB ILE B 279 227.633 253.732 269.931 1.00 10.00 C ATOM 5157 CG1 ILE B 279 227.947 252.979 271.225 1.00 10.00 C ATOM 5158 CG2 ILE B 279 227.875 255.224 270.100 1.00 10.00 C ATOM 5159 CD1 ILE B 279 229.127 252.039 271.115 1.00 10.00 C ATOM 5160 N ILE B 280 226.353 255.538 268.171 1.00 10.00 N ATOM 5161 CA ILE B 280 225.965 256.355 267.010 1.00 10.00 C ATOM 5162 C ILE B 280 226.157 255.647 265.686 1.00 10.00 C ATOM 5163 O ILE B 280 227.025 254.789 265.543 1.00 10.00 O ATOM 5164 CB ILE B 280 226.687 257.771 266.906 1.00 10.00 C ATOM 5165 CG1 ILE B 280 228.143 257.730 267.425 1.00 10.00 C ATOM 5166 CG2 ILE B 280 225.779 258.833 267.568 1.00 10.00 C ATOM 5167 CD1 ILE B 280 228.263 257.823 268.900 1.00 10.00 C """ def tst_to_cif_annotation(): pass def tst_remove_empty_annotations(): ann = annotation.from_records(pdb_records_2.split("\n")) pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_string_2.split('\n')).\ construct_hierarchy() ann.remove_empty_annotations(hierarchy=pdb_h) # print ann assert ann.get_n_helices() == 2 assert ann.get_n_sheets() == 0 def tst_split_helices_with_prolines(): ann = annotation.from_records(pdb_records_2.split("\n")) pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_string_2.split('\n')).\ construct_hierarchy() # pdb_h.write_pdb_file(file_name='1.pdb') ann.remove_empty_annotations(hierarchy=pdb_h) # print ann ann.split_helices_with_prolines(hierarchy=pdb_h) # print "="*50 # print ann assert ann.get_n_helices() == 4 h_sizes = [x.length for x in ann.helices] assert h_sizes == [7, 15, 24, 5], h_sizes def tst_split_helices_with_prolines_2(): """ Corner case when the helix begins with PRO, 2nd residue is also PRO""" pro_ann = "HELIX 16 16 PRO B 463 ALA B 467 5 5" pdb_str = """\ ATOM 5910 N PRO B 463 239.715 263.725 264.122 1.00 10.00 N ATOM 5911 CA PRO B 463 238.974 264.849 264.695 1.00 10.00 C ATOM 5912 C PRO B 463 238.267 264.611 266.069 1.00 10.00 C ATOM 5913 O PRO B 463 238.533 265.320 267.055 1.00 10.00 O ATOM 5914 CB PRO B 463 237.997 265.183 263.567 1.00 10.00 C ATOM 5915 CG PRO B 463 238.911 265.060 262.343 1.00 10.00 C ATOM 5916 CD PRO B 463 239.700 263.801 262.637 1.00 10.00 C ATOM 5917 N PRO B 464 237.359 263.619 266.160 1.00 10.00 N ATOM 5918 CA PRO B 464 236.693 263.407 267.459 1.00 10.00 C ATOM 5919 C PRO B 464 237.446 262.481 268.415 1.00 10.00 C ATOM 5920 O PRO B 464 236.830 261.688 269.109 1.00 10.00 O ATOM 5921 CB PRO B 464 235.345 262.820 267.063 1.00 10.00 C ATOM 5922 CG PRO B 464 235.738 261.949 265.934 1.00 10.00 C ATOM 5923 CD PRO B 464 236.751 262.765 265.124 1.00 10.00 C ATOM 5924 N ASP B 465 238.768 262.633 268.474 1.00 10.00 N ATOM 5925 CA ASP B 465 239.620 261.794 269.304 1.00 10.00 C ATOM 5926 C ASP B 465 240.116 262.429 270.606 1.00 10.00 C ATOM 5927 O ASP B 465 240.198 261.761 271.642 1.00 10.00 O ATOM 5928 CB ASP B 465 240.822 261.329 268.465 1.00 10.00 C ATOM 5929 CG ASP B 465 241.926 262.387 268.361 1.00 10.00 C ATOM 5930 OD1 ASP B 465 241.627 263.557 268.042 1.00 10.00 O ATOM 5931 OD2 ASP B 465 243.106 262.040 268.593 1.00 10.00 O ATOM 5932 N ASN B 466 240.420 263.721 270.572 1.00 10.00 N ATOM 5933 CA ASN B 466 240.960 264.382 271.760 1.00 10.00 C ATOM 5934 C ASN B 466 240.023 264.651 272.935 1.00 10.00 C ATOM 5935 O ASN B 466 240.482 265.044 273.998 1.00 10.00 O ATOM 5936 CB ASN B 466 241.654 265.686 271.349 1.00 10.00 C ATOM 5937 CG ASN B 466 240.831 266.505 270.376 1.00 10.00 C ATOM 5938 OD1 ASN B 466 239.714 266.921 270.685 1.00 10.00 O ATOM 5939 ND2 ASN B 466 241.380 266.739 269.189 1.00 10.00 N ATOM 5940 N ALA B 467 238.694 264.465 272.767 1.00 10.00 N ATOM 5941 CA ALA B 467 237.910 264.755 273.973 1.00 10.00 C ATOM 5942 C ALA B 467 238.085 263.704 275.100 1.00 10.00 C ATOM 5943 O ALA B 467 237.157 263.430 275.874 1.00 10.00 O ATOM 5944 CB ALA B 467 236.468 264.889 273.432 1.00 10.00 C """ ann = annotation.from_records(pro_ann.split("\n")) pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str.split('\n')).\ construct_hierarchy() assert ann.get_n_helices() == 1 ann.split_helices_with_prolines(hierarchy=pdb_h) # print ann assert ann.get_n_helices() == 1 assert ann.helices[0].length == 4 def tst_split_helices_with_prolines_3(): """ Corner case when the helix ends with PRO""" pro_ann = "HELIX 16 16 THR B 223 PRO B 227 5 5" pdb_str = """\ ATOM 4732 N TYR B 223 237.498 243.916 256.959 1.00 10.00 N ATOM 4733 CA TYR B 223 236.998 243.193 255.797 1.00 10.00 C ATOM 4734 C TYR B 223 235.642 243.731 255.357 1.00 10.00 C ATOM 4735 O TYR B 223 235.112 243.268 254.374 1.00 10.00 O ATOM 4736 CB TYR B 223 236.908 241.695 256.094 1.00 10.00 C ATOM 4737 CG TYR B 223 235.804 241.324 257.057 1.00 10.00 C ATOM 4738 CD1 TYR B 223 234.480 241.272 256.641 1.00 10.00 C ATOM 4739 CD2 TYR B 223 236.085 241.027 258.384 1.00 10.00 C ATOM 4740 CE1 TYR B 223 233.468 240.932 257.518 1.00 10.00 C ATOM 4741 CE2 TYR B 223 235.080 240.686 259.269 1.00 10.00 C ATOM 4742 CZ TYR B 223 233.774 240.641 258.831 1.00 10.00 C ATOM 4743 OH TYR B 223 232.772 240.302 259.711 1.00 10.00 O ATOM 4744 N THR B 224 235.127 244.742 256.068 1.00 10.00 N ATOM 4745 CA THR B 224 233.888 245.465 255.737 1.00 10.00 C ATOM 4746 C THR B 224 234.274 246.452 254.592 1.00 10.00 C ATOM 4747 O THR B 224 233.527 246.682 253.621 1.00 10.00 O ATOM 4748 CB THR B 224 233.390 246.267 256.985 1.00 10.00 C ATOM 4749 OG1 THR B 224 232.815 245.365 257.938 1.00 10.00 O ATOM 4750 CG2 THR B 224 232.338 247.298 256.604 1.00 10.00 C ATOM 4751 N ILE B 225 235.481 246.993 254.709 1.00 10.00 N ATOM 4752 CA ILE B 225 236.079 247.939 253.743 1.00 10.00 C ATOM 4753 C ILE B 225 236.203 247.150 252.435 1.00 10.00 C ATOM 4754 O ILE B 225 235.800 247.601 251.358 1.00 10.00 O ATOM 4755 CB ILE B 225 237.546 248.405 254.230 1.00 10.00 C ATOM 4756 CG1 ILE B 225 237.487 249.823 254.873 1.00 10.00 C ATOM 4757 CG2 ILE B 225 238.554 248.277 253.078 1.00 10.00 C ATOM 4758 CD1 ILE B 225 238.802 250.372 255.483 1.00 10.00 C ATOM 4759 N VAL B 226 236.723 245.926 252.549 1.00 10.00 N ATOM 4760 CA VAL B 226 236.904 245.129 251.334 1.00 10.00 C ATOM 4761 C VAL B 226 235.606 245.025 250.571 1.00 10.00 C ATOM 4762 O VAL B 226 235.621 245.119 249.364 1.00 10.00 O ATOM 4763 CB VAL B 226 237.478 243.708 251.567 1.00 10.00 C ATOM 4764 CG1 VAL B 226 238.787 243.804 252.297 1.00 10.00 C ATOM 4765 CG2 VAL B 226 236.480 242.836 252.257 1.00 10.00 C ATOM 4766 N PRO B 227 234.471 244.784 251.253 1.00 10.00 N ATOM 4767 CA PRO B 227 233.225 244.717 250.484 1.00 10.00 C ATOM 4768 C PRO B 227 233.110 246.013 249.736 1.00 10.00 C ATOM 4769 O PRO B 227 233.251 246.069 248.522 1.00 10.00 O ATOM 4770 CB PRO B 227 232.142 244.666 251.550 1.00 10.00 C ATOM 4771 CG PRO B 227 232.785 243.987 252.657 1.00 10.00 C ATOM 4772 CD PRO B 227 234.206 244.487 252.661 1.00 10.00 C """ ann = annotation.from_records(pro_ann.split("\n")) pdb_h = iotbx.pdb.input(source_info=None, lines=pdb_str.split('\n')).\ construct_hierarchy() assert ann.get_n_helices() == 1 ann.split_helices_with_prolines(hierarchy=pdb_h) # print ann assert ann.get_n_helices() == 1 assert ann.helices[0].length == 4 def tst_remove_short_annotations(): ann = annotation.from_records(pdb_records_2.split("\n")) assert ann.get_n_helices() == 7 assert ann.get_n_sheets() == 4 ann.remove_short_annotations() assert ann.get_n_helices() == 6, ann.get_n_helices() assert ann.get_n_sheets() == 3, ann.get_n_sheets() nstr = [x.n_strands for x in ann.sheets] # print ann assert nstr == [5,3,2], nstr def tst_remove_3_10_helices(): ann = annotation.from_records(pdb_records_2.split("\n")) assert ann.get_n_helices() == 7 assert ann.get_n_sheets() == 4 ann.remove_3_10_helices() assert ann.get_n_helices() == 6, ann.get_n_helices() assert ann.get_n_sheets() == 4, ann.get_n_sheets() # print ann def tst_concatenate_consecutive_helices(): ann_str = """\ HELIX 233 233 PHE Z 12 CYS Z 43 1 32 HELIX 234 234 LEU Z 49 ILE Z 54 1 6 HELIX 235 235 ILE Z 54 ILE Z 62 1 9 HELIX 236 236 ILE Z 62 SER Z 77 1 16 HELIX 237 237 ALA Z 83 GLN Z 122 1 40 HELIX 238 238 LEU Z 125 ALA Z 136 1 12 """ ann = annotation.from_records(ann_str.split("\n")) assert ann.get_n_helices() == 6 assert ann.get_n_sheets() == 0 ann.concatenate_consecutive_helices() assert ann.get_n_helices() == 4 # print ann h_sizes = [x.length for x in ann.helices] assert h_sizes == [32, 29, 40, 12], h_sizes def tst_concatenate_consecutive_helices2(): """ Very tight turn between two consecutive helices results in their concatenation. """ if (not libtbx.env.has_module(name="ksdssp")): print("Skipped: required module ksdssp not present") return file_path = libtbx.env.find_in_repositories( relative_path="cctbx_project/iotbx/regression/secondary_structure/5a63_chainCp.pdb", test=os.path.isfile) if (file_path is None): print('WARNING: Skipping tst_concatenate_consecutive_helices2("%s"): input file not available' % file_path) return inp = iotbx.pdb.input(file_name=file_path) original_ann = inp.extract_secondary_structure() assert original_ann.get_n_helices() == 2 assert original_ann.get_n_sheets() == 0 assert original_ann.helices[0].get_start_resseq_as_int() == 155 assert original_ann.helices[0].get_end_resseq_as_int() == 185 assert original_ann.helices[1].get_start_resseq_as_int() == 186 assert original_ann.helices[1].get_end_resseq_as_int() == 206 h = inp.construct_hierarchy() ann = original_ann.deep_copy() ann.concatenate_consecutive_helices(hierarchy=h) assert ann.get_n_helices() == 2 assert ann.get_n_sheets() == 0 # and make sure they got 'spreaded' assert ann.helices[0].get_start_resseq_as_int() == 155 assert ann.helices[0].get_end_resseq_as_int() == 184 assert ann.helices[1].get_start_resseq_as_int() == 187 assert ann.helices[1].get_end_resseq_as_int() == 206 # print ann def tst_concatenate_consecutive_helices3(): """ Very tight turn between two consecutive helices. They are separated by PRO residue, but this is not enough, they should be spreaded like in previous test. """ if (not libtbx.env.has_module(name="ksdssp")): print("Skipped: required module ksdssp not present") return file_path = libtbx.env.find_in_repositories( relative_path="cctbx_project/iotbx/regression/secondary_structure/5a63_chainBp.pdb", test=os.path.isfile) if (file_path is None): print('WARNING: Skipping tst_concatenate_consecutive_helices2("%s"): input file not available' % file_path) return inp = iotbx.pdb.input(file_name=file_path) original_ann = inp.extract_secondary_structure() assert original_ann.get_n_helices() == 2 assert original_ann.get_n_sheets() == 0 assert original_ann.helices[0].get_start_resseq_as_int() == 218 assert original_ann.helices[0].get_end_resseq_as_int() == 241 assert original_ann.helices[1].get_start_resseq_as_int() == 242 assert original_ann.helices[1].get_end_resseq_as_int() == 260 h = inp.construct_hierarchy() ann = original_ann.deep_copy() ann.concatenate_consecutive_helices(hierarchy=h) assert ann.get_n_helices() == 2 assert ann.get_n_sheets() == 0 # and make sure they got 'spreaded' assert ann.helices[0].get_start_resseq_as_int() == 218 assert ann.helices[0].get_end_resseq_as_int() == 240 assert ann.helices[1].get_start_resseq_as_int() == 243 assert ann.helices[1].get_end_resseq_as_int() == 260 def tst_concatenate_consecutive_helices4(): pdb_str = """\ HELIX 130 AO4 ASP i 421 GLY i 433 1 25 HELIX 131 AO5 GLY i 434 UNK i 441 1 8 ATOM 29887 N ASP i 421 299.903 227.017 234.954 1.00 60.00 N ATOM 29888 CA ASP i 421 298.473 226.790 234.820 1.00 60.00 C ATOM 29889 C ASP i 421 298.155 226.535 233.351 1.00 60.00 C ATOM 29890 O ASP i 421 297.473 225.562 233.002 1.00 60.00 O ATOM 29891 CB ASP i 421 297.680 227.986 235.352 1.00 60.00 C ATOM 29892 CG ASP i 421 296.231 227.646 235.639 1.00 60.00 C ATOM 29893 OD1 ASP i 421 295.733 226.637 235.095 1.00 60.00 O ATOM 29894 OD2 ASP i 421 295.586 228.390 236.409 1.00 60.00 O1- ATOM 29895 N ASP i 422 298.673 227.411 232.492 1.00 60.00 N ATOM 29896 CA ASP i 422 298.476 227.272 231.053 1.00 60.00 C ATOM 29897 C ASP i 422 299.031 225.943 230.539 1.00 60.00 C ATOM 29898 O ASP i 422 298.395 225.273 229.722 1.00 60.00 O ATOM 29899 CB ASP i 422 299.132 228.437 230.309 1.00 60.00 C ATOM 29900 CG ASP i 422 298.563 229.783 230.718 1.00 60.00 C ATOM 29901 OD1 ASP i 422 297.410 229.825 231.194 1.00 60.00 O ATOM 29902 OD2 ASP i 422 299.274 230.798 230.560 1.00 60.00 O1- ATOM 29903 N MET i 423 300.208 225.559 231.027 1.00 60.00 N ATOM 29904 CA MET i 423 300.834 224.314 230.589 1.00 60.00 C ATOM 29905 C MET i 423 300.122 223.092 231.164 1.00 60.00 C ATOM 29906 O MET i 423 300.167 222.012 230.579 1.00 60.00 O ATOM 29907 CB MET i 423 302.314 224.291 230.974 1.00 60.00 C ATOM 29908 CG MET i 423 303.096 225.488 230.468 1.00 60.00 C ATOM 29909 SD MET i 423 302.799 225.820 228.722 1.00 60.00 S ATOM 29910 CE MET i 423 302.434 227.573 228.771 1.00 60.00 C ATOM 29911 N GLN i 424 299.477 223.265 232.315 1.00 60.00 N ATOM 29912 CA GLN i 424 298.638 222.217 232.893 1.00 60.00 C ATOM 29913 C GLN i 424 297.452 221.966 231.973 1.00 60.00 C ATOM 29914 O GLN i 424 297.170 220.820 231.589 1.00 60.00 O ATOM 29915 CB GLN i 424 298.157 222.611 234.295 1.00 60.00 C ATOM 29916 CG GLN i 424 297.207 221.609 234.945 1.00 60.00 C ATOM 29917 CD GLN i 424 296.714 222.061 236.312 1.00 60.00 C ATOM 29918 OE1 GLN i 424 297.059 221.470 237.336 1.00 60.00 O ATOM 29919 NE2 GLN i 424 295.895 223.107 236.333 1.00 60.00 N ATOM 29920 N ARG i 425 296.767 223.051 231.620 1.00 60.00 N ATOM 29921 CA ARG i 425 295.650 222.977 230.687 1.00 60.00 C ATOM 29922 C ARG i 425 296.091 222.293 229.399 1.00 60.00 C ATOM 29923 O ARG i 425 295.457 221.346 228.945 1.00 60.00 O ATOM 29924 CB ARG i 425 295.092 224.370 230.377 1.00 60.00 C ATOM 29925 CG ARG i 425 293.590 224.512 230.605 1.00 60.00 C ATOM 29926 CD ARG i 425 292.980 225.574 229.700 1.00 60.00 C ATOM 29927 NE ARG i 425 291.868 226.275 230.339 1.00 60.00 N ATOM 29928 CZ ARG i 425 291.310 227.385 229.870 1.00 60.00 C ATOM 29929 NH1 ARG i 425 291.756 227.932 228.749 1.00 60.00 N1+ ATOM 29930 NH2 ARG i 425 290.306 227.953 230.524 1.00 60.00 N ATOM 29931 N MET i 426 297.200 222.769 228.837 1.00 60.00 N ATOM 29932 CA MET i 426 297.726 222.249 227.576 1.00 60.00 C ATOM 29933 C MET i 426 298.063 220.762 227.672 1.00 60.00 C ATOM 29934 O MET i 426 297.832 220.003 226.728 1.00 60.00 O ATOM 29935 CB MET i 426 298.965 223.045 227.158 1.00 60.00 C ATOM 29936 CG MET i 426 299.272 222.986 225.672 1.00 60.00 C ATOM 29937 SD MET i 426 297.903 223.582 224.659 1.00 60.00 S ATOM 29938 CE MET i 426 297.647 225.215 225.350 1.00 60.00 C ATOM 29939 N MET i 427 298.608 220.357 228.815 1.00 60.00 N ATOM 29940 CA MET i 427 298.910 218.957 229.074 1.00 60.00 C ATOM 29941 C MET i 427 297.629 218.130 229.045 1.00 60.00 C ATOM 29942 O MET i 427 297.599 217.034 228.481 1.00 60.00 O ATOM 29943 CB MET i 427 299.623 218.797 230.420 1.00 60.00 C ATOM 29944 CG MET i 427 299.974 217.361 230.776 1.00 60.00 C ATOM 29945 SD MET i 427 301.027 216.576 229.543 1.00 60.00 S ATOM 29946 CE MET i 427 302.516 217.559 229.687 1.00 60.00 C ATOM 29947 N LYS i 428 296.566 218.668 229.639 1.00 60.00 N ATOM 29948 CA LYS i 428 295.287 217.960 229.648 1.00 60.00 C ATOM 29949 C LYS i 428 294.684 217.856 228.244 1.00 60.00 C ATOM 29950 O LYS i 428 294.204 216.790 227.846 1.00 60.00 O ATOM 29951 CB LYS i 428 294.293 218.638 230.591 1.00 60.00 C ATOM 29952 CG LYS i 428 292.995 217.862 230.757 1.00 60.00 C ATOM 29953 CD LYS i 428 293.268 216.449 231.255 1.00 60.00 C ATOM 29954 CE LYS i 428 292.556 215.408 230.404 1.00 60.00 C ATOM 29955 NZ LYS i 428 292.980 214.020 230.745 1.00 60.00 N1+ ATOM 29956 N LYS i 429 294.712 218.960 227.504 1.00 60.00 N ATOM 29957 CA LYS i 429 294.172 218.989 226.148 1.00 60.00 C ATOM 29958 C LYS i 429 294.929 218.009 225.261 1.00 60.00 C ATOM 29959 O LYS i 429 294.346 217.366 224.388 1.00 60.00 O ATOM 29960 CB LYS i 429 294.242 220.400 225.555 1.00 60.00 C ATOM 29961 CG LYS i 429 293.617 221.490 226.417 1.00 60.00 C ATOM 29962 CD LYS i 429 292.188 221.161 226.813 1.00 60.00 C ATOM 29963 CE LYS i 429 291.587 222.262 227.676 1.00 60.00 C ATOM 29964 NZ LYS i 429 290.229 221.908 228.178 1.00 60.00 N1+ ATOM 29965 N MET i 430 296.234 217.901 225.494 1.00 60.00 N ATOM 29966 CA MET i 430 297.067 216.954 224.765 1.00 60.00 C ATOM 29967 C MET i 430 296.716 215.527 225.165 1.00 60.00 C ATOM 29968 O MET i 430 296.753 214.611 224.342 1.00 60.00 O ATOM 29969 CB MET i 430 298.549 217.227 225.033 1.00 60.00 C ATOM 29970 CG MET i 430 299.494 216.622 224.008 1.00 60.00 C ATOM 29971 SD MET i 430 299.571 217.597 222.493 1.00 60.00 S ATOM 29972 CE MET i 430 300.171 219.160 223.133 1.00 60.00 C ATOM 29973 N LYS i 431 296.369 215.348 226.436 1.00 60.00 N ATOM 29974 CA LYS i 431 296.049 214.027 226.968 1.00 60.00 C ATOM 29975 C LYS i 431 294.744 213.476 226.401 1.00 60.00 C ATOM 29976 O LYS i 431 294.664 212.306 226.030 1.00 60.00 O ATOM 29977 CB LYS i 431 295.967 214.077 228.496 1.00 60.00 C ATOM 29978 N LYS i 432 293.725 214.326 226.335 1.00 60.00 N ATOM 29979 CA LYS i 432 292.386 213.879 225.955 1.00 60.00 C ATOM 29980 C LYS i 432 292.198 213.671 224.449 1.00 60.00 C ATOM 29981 O LYS i 432 291.551 212.713 224.030 1.00 60.00 O ATOM 29982 CB LYS i 432 291.343 214.877 226.461 1.00 60.00 C ATOM 29983 CG LYS i 432 291.590 216.291 225.986 1.00 60.00 C ATOM 29984 CD LYS i 432 290.369 217.161 226.134 1.00 60.00 C ATOM 29985 CE LYS i 432 290.549 218.436 225.337 1.00 60.00 C ATOM 29986 NZ LYS i 432 289.514 219.436 225.680 1.00 60.00 N1+ ATOM 29987 N GLY i 433 292.750 214.573 223.643 1.00 60.00 N ATOM 29988 CA GLY i 433 292.514 214.550 222.211 1.00 60.00 C ATOM 29989 C GLY i 433 293.553 213.806 221.400 1.00 60.00 C ATOM 29990 O GLY i 433 294.685 213.618 221.845 1.00 60.00 O ATOM 29991 N GLY i 434 293.168 213.376 220.205 1.00 60.00 N ATOM 29992 CA GLY i 434 294.107 212.724 219.309 1.00 60.00 C ATOM 29993 C GLY i 434 295.180 213.712 218.931 1.00 60.00 C ATOM 29994 O GLY i 434 294.922 214.909 218.843 1.00 60.00 O TER END """ pdb_inp = iotbx.pdb.input(lines=pdb_str, source_info=None) h = pdb_inp.construct_hierarchy() ss_ann = pdb_inp.extract_secondary_structure() assert ss_ann.get_n_helices() == 2 ss_ann.concatenate_consecutive_helices(hierarchy=h) assert ss_ann.get_n_helices() == 1 # print ss_ann assert ss_ann.helices[0].get_start_resseq_as_int() == 421 assert ss_ann.helices[0].get_end_resseq_as_int() == 433 def tst_simple_elements(): ann_str = """\ HELIX 3 AA3 SER B 26 LYS B 30 5 5 HELIX 4 AA4 LEU B 196 GLU B 199 5 4 SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7 SHEET 3 AA1 4 THR A 73 SER A 82 -1 N LEU A 76 O ILE A 94 SHEET 4 AA1 4 VAL A 34 THR A 39 -1 N PHE A 35 O VAL A 81 """ ann = annotation.from_records(ann_str.split("\n")) assert ann.get_n_helices() == 2 assert ann.get_n_sheets() == 1 n_h = 0 n_st = 0 se = ann.simple_elements() assert len(se) == 6 for e in se: if isinstance(e, pdb_helix): n_h += 1 if isinstance(e, pdb_strand): n_st += 1 assert n_h == 2 assert n_st == 4 s = ann.as_pdb_str() def tst_filter_sheets_with_long_hbonds(): """ Attention. In this case there are 2 almost identical SHEET annotations.""" if (not libtbx.env.has_module(name="ksdssp")): print("Skipped: required module ksdssp not present") return file_path = libtbx.env.find_in_repositories( relative_path="cctbx_project/iotbx/regression/secondary_structure/3jd6_noh.pdb", test=os.path.isfile) if (file_path is None): print('WARNING: Skipping tst_filter_sheets_with_long_hbonds("%s"): input file not available' % file_path) return inp = iotbx.pdb.input(file_name=file_path) original_ann = inp.extract_secondary_structure() assert original_ann.get_n_helices() == 1 assert original_ann.get_n_sheets() == 2 h = inp.construct_hierarchy() ann = original_ann.deep_copy() ann.filter_sheets_with_long_hbonds(hierarchy=h) assert ann.get_n_helices() == 1, ann.get_n_helices() assert ann.get_n_sheets() == 3, ann.get_n_sheets() # with filtering out short ones def tst_filter_sheets_with_long_hbonds2(): """ bug found in 4a7h where ksdssp defines sheet 200 residues long sheet for rather small selection. A 2 ILE C 384 ARG C 586 1 N LEU C 385 O VAL C 97 correct definition can be provided by any other method in ss_manager. """ if (not libtbx.env.has_module(name="ksdssp")): print("Skipped: required module ksdssp not present") return file_path = libtbx.env.find_in_repositories( relative_path="cctbx_project/iotbx/regression/secondary_structure/4a7h_chainC.pdb", test=os.path.isfile) if (file_path is None): print('WARNING: Skipping tst_filter_sheets_with_long_hbonds2("%s"): input file not available' % file_path) return inp = iotbx.pdb.input(file_name=file_path) original_ann = inp.extract_secondary_structure() assert original_ann.get_n_helices() == 0 assert original_ann.get_n_sheets() == 3 h = inp.construct_hierarchy() ann = original_ann.deep_copy() try: ann.filter_sheets_with_long_hbonds(hierarchy=h) except Exception as e: if e.args[0].startswith("It is 4a7h"): pass else: raise e else: # disable for now pass # assert 0 def tst_filter_sheets_with_long_hbonds3(): """ bug found in 1qmo: want to remove all sheets, but they appear not sorted.""" if (not libtbx.env.has_module(name="ksdssp")): print("Skipped: required module ksdssp not present") return file_path = libtbx.env.find_in_repositories( relative_path="cctbx_project/iotbx/regression/secondary_structure/1ubf_cutted.pdb", test=os.path.isfile) if (file_path is None): print('WARNING: Skipping tst_filter_sheets_with_long_hbonds3("%s"): input file not available' % file_path) return inp = iotbx.pdb.input(file_name=file_path) original_ann = inp.extract_secondary_structure() assert original_ann.get_n_helices() == 11 assert original_ann.get_n_sheets() == 2 h = inp.construct_hierarchy() ann = original_ann.deep_copy() ann.filter_sheets_with_long_hbonds(hierarchy=h) print(ann) assert ann.get_n_helices() == 11, ann.get_n_helices() assert ann.get_n_sheets() == 2, ann.get_n_sheets() def tst_reset_sheet_ids(): ann_str = """\ SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA1 4 MET A 92 THR A 99 1 O LEU A 95 N ILE A 7 """ ann_str2 = """\ SHEET 1 AA1 4 ILE A 7 PRO A 10 0 SHEET 2 AA2 4 MET A 92 THR A 99 0 """ # One sheet ann = annotation.from_records(ann_str.split("\n")) assert ann.get_n_helices() == 0 assert ann.get_n_sheets() == 1 assert ann.sheets[0].sheet_id == 'AA1' ann.reset_sheet_ids() assert ann.get_n_helices() == 0 assert ann.get_n_sheets() == 1 assert ann.sheets[0].sheet_id == '0', ann.sheets[0].sheet_id # Two sheets ann = annotation.from_records(ann_str2.split("\n")) assert ann.get_n_helices() == 0 assert ann.get_n_sheets() == 2 assert ann.sheets[0].sheet_id == 'AA1' assert ann.sheets[1].sheet_id == 'AA2' ann.reset_sheet_ids() assert ann.get_n_helices() == 0 assert ann.get_n_sheets() == 2 assert ann.sheets[0].sheet_id == '0', ann.sheets[0].sheet_id assert ann.sheets[1].sheet_id == '1', ann.sheets[0].sheet_id # 11 sheets ann = annotation.from_records(ann_str.split("\n")) for x in range(10): ann.sheets.append(ann.sheets[0].deep_copy()) assert ann.get_n_sheets() == 11 ann.reset_sheet_ids() sheet_ids = [x.sheet_id for x in ann.sheets] assert sheet_ids ==['0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A'], sheet_ids # 51 sheets ann = annotation.from_records(ann_str.split("\n")) for x in range(50): ann.sheets.append(ann.sheets[0].deep_copy()) assert ann.get_n_sheets() == 51 ann.reset_sheet_ids() sheet_ids = [x.sheet_id for x in ann.sheets] assert sheet_ids ==['00', '01', '02', '03', '04', '05', '06', '07', '08', '09', '0A', '0B', '0C', '0D', '0E', '0F', '0G', '0H', '0I', '0J', '0K', '0L', '0M', '0N', '0O', '0P', '0Q', '0R', '0S', '0T', '0U', '0V', '0W', '0X', '0Y', '0Z', '10', '11', '12', '13', '14', '15', '16', '17', '18', '19', '1A', '1B', '1C', '1D', '1E'], sheet_ids if (__name__ == "__main__"): t0 = time.time() test_helix_interface() test_sheet_interface() tst_from_cif_block() tst_from_cif_block_2() tst_from_cif_block_3() tst_from_cif_block_4() tst_from_minimal_cif_helix() tst_from_minimal_cif_sheet() tst_to_cif_helix() tst_to_cif_sheet() tst_to_cif_annotation() tst_remove_empty_annotations() tst_split_helices_with_prolines() tst_split_helices_with_prolines_2() tst_split_helices_with_prolines_3() tst_remove_short_annotations() tst_remove_3_10_helices() tst_concatenate_consecutive_helices() tst_concatenate_consecutive_helices2() tst_concatenate_consecutive_helices3() tst_concatenate_consecutive_helices4() tst_filter_sheets_with_long_hbonds() tst_filter_sheets_with_long_hbonds2() tst_filter_sheets_with_long_hbonds3() tst_reset_sheet_ids() tst_simple_elements() print("OK time =%8.3f"%(time.time() - t0))