from __future__ import absolute_import, division, print_function from iotbx import pdb from cctbx.array_family import flex from libtbx.test_utils import Exception_expected, show_diff from six.moves import range from six.moves import zip def exercise_selection(): pdb_inp = pdb.input(source_info=None, lines=flex.split_lines("""\ CRYST1 50.800 50.800 155.300 90.00 90.00 90.00 P 43 21 2 8 MODEL 1 ATOM 4 N SER 1 8.753 29.755 61.685 1.00 49.13 ATOM 5 CA SER 1 9.242 30.200 62.974 1.00 46.62 ANISOU 5 CA SER 1 343 490 2719 -45 -169 617 ATOM 6 C SER 1 10.453 29.500 63.579 1.00 41.99 ATOM 7 O SER 1 10.593 29.607 64.814 1.00 43.24 ANISOU 7 O SER 1 343 490 2719 -45 -169 617 ATOM 8 CB SER 1 8.052 30.189 63.974 1.00 53.00 ATOM 9 OG SER 1 7.294 31.409 63.930 1.00 57.79 ATOM 10 N ARG 2 11.360 28.819 62.827 1.00 36.48 ATOM 11 CA ARG 2 12.548 28.316 63.532 1.00 30.20 ATOM 12 C ARG 2 13.502 29.501 63.500 1.00 25.54 ATOM 13 O ARG 2 13.730 30.037 62.407 1.00 23.86 ATOM 14 CB ARG 2 13.241 27.119 62.861 1.00 27.44 ATOM 15 CG ARG 2 12.412 25.849 62.964 1.00 23.66 ATOM 16 CD ARG 2 13.267 24.651 63.266 1.00 23.98 ATOM 17 NE ARG 2 13.948 24.115 62.135 1.00 22.71 ATOM 18 CZ ARG 2 15.114 23.487 62.201 1.00 21.38 ATOM 19 NH1 ARG 2 15.845 23.331 63.301 1.00 19.34 ATOM 20 NH2 ARG 2 15.575 23.030 61.051 1.00 26.66 ATOM 21 N PRO 3J 13.947 29.997 64.680 1.00 22.94 ATOM 22 CA PRO 3J 14.902 31.100 64.827 1.00 20.19 ATOM 23 C PRO 3J 16.195 30.718 64.086 1.00 18.44 ATOM 24 O PRO 3J 16.545 29.521 64.086 1.00 19.76 ATOM 25 CB PRO 3J 15.133 31.218 66.313 1.00 19.17 ATOM 26 CG PRO 3J 14.065 30.364 66.951 1.00 15.12 ATOM 27 CD PRO 3J 13.816 29.289 65.966 1.00 19.56 ATOM 28 N AILE 4 16.953 31.648 63.512 1.00 15.29 ATOM 29 CA AILE 4 18.243 31.372 62.859 1.00 14.32 ATOM 30 C AILE 4 19.233 32.112 63.743 1.00 13.54 ATOM 31 O AILE 4 19.105 33.315 64.009 1.00 11.84 ATOM 32 CB AILE 4 18.298 31.951 61.406 1.00 13.62 ATOM 33 CG1AILE 4 17.157 31.300 60.620 1.00 18.39 ATOM 34 CG2AILE 4 19.661 31.747 60.743 1.00 13.64 ATOM 35 CD1AILE 4 16.879 32.102 59.355 1.00 16.69 ATOM 28 N BILE 4 16.953 31.648 63.512 1.00 15.29 ATOM 29 CA BILE 4 18.243 31.372 62.859 1.00 14.32 ATOM 30 C BILE 4 19.233 32.112 63.743 1.00 13.54 ATOM 31 O BILE 4 19.105 33.315 64.009 1.00 11.84 ATOM 32 CB BILE 4 18.298 31.951 61.406 1.00 13.62 ATOM 33 CG1BILE 4 17.157 31.300 60.620 1.00 18.39 ATOM 34 CG2BILE 4 19.661 31.747 60.743 1.00 13.64 ATOM1200035 CD1BILE 4 16.879 32.102 59.355 1.00 16.69 TER 36 ILE 4 ENDMDL MODEL 2 HETATM 1451 PA 5GP H 187 29.875 44.488 69.823 1.00 19.62 HETATM 1452 O1A 5GP H 187 28.526 44.888 69.143 1.00 19.86 HETATM 1453 O2A 5GP H 187 30.764 44.617 68.702 1.00 23.42 HETATM 1454 O3A 5GP H 187 30.319 45.004 71.073 1.00 20.20 HETATM 1455 O5* 5GP H 187 29.683 43.016 70.027 1.00 20.32 HETATM 1456 C5* 5GP H 187 30.740 42.297 70.837 1.00 21.47 HETATM 1457 C4* 5GP H 187 30.677 40.747 70.770 1.00 21.56 HETATM 1458 O4* 5GP H 187 29.608 40.160 71.599 1.00 20.50 HETATM 1459 C3* 5GP H 187 30.547 40.121 69.352 1.00 20.18 HETATM 1460 O3* 5GP H 187 31.228 38.864 69.416 1.00 23.65 HETATM 1461 C2* 5GP H 187 29.031 39.871 69.248 1.00 18.78 HETATM 1462 O2* 5GP H 187 28.685 38.690 68.496 1.00 20.45 HETATM 1463 C1* 5GP H 187 28.634 39.641 70.688 1.00 17.09 HETATM 1464 N9 5GP H 187 27.238 39.525 71.076 1.00 15.35 HETATM 1465 C8 5GP H 187 26.330 40.535 70.852 1.00 12.57 HETATM 1466 N7' 5GP H 187 25.175 40.314 71.417 1.00 12.88 HETATM 1467 C5 5GP H 187 25.278 39.082 72.070 1.00 10.75 HETATM 1468 C6 5GP H 187 24.326 38.354 72.827 1.00 9.77 HETATM 1469 O6 5GP H 187 23.169 38.678 73.029 1.00 8.66 HETATM 1470 N1' 5GP H 187 24.836 37.190 73.270 1.00 9.67 HETATM 1471 C2 5GP H 187 26.075 36.701 73.001 1.00 9.84 HETATM 1472 N2 5GP H 187 26.361 35.490 73.520 1.00 9.77 HETATM 1473 N3 5GP H 187 27.005 37.353 72.310 1.00 10.31 HETATM 1474 C4 5GP H 187 26.583 38.559 71.844 1.00 12.50 ENDMDL MODEL 3 HETATM 1475 S SO4 S 188 31.424 42.923 60.396 1.00 55.69 S4+ HETATM 1476 O1 SO4 S 188 31.631 41.513 60.336 1.00 59.84 o1- HETATM 1477 O2 SO4 S 188 32.533 43.699 59.932 1.00 49.98 O1- HETATM 1478 O3 SO4 S 188 31.128 43.217 61.738 1.00 59.44 O1- HETATM 1479 O4 SO4 S 188 30.353 43.201 59.539 1.00 60.54 O1- HETATM 1480 O HOH W 200 29.478 23.354 61.364 1.00 8.67 WATE ATOM 2000 A1 AAA X 1 8.753 29.755 61.685 1.00 49.13 ATOM 2001 A2 AAA X 1 9.242 30.200 62.974 1.00 46.62 ATOM 2002 A1 BBB X 2 11.360 28.819 62.827 1.00 36.48 ATOM 2003 A2 BBB X 2 12.548 28.316 63.532 1.00 30.20 ATOM 2004 A1 AAA Y 1 8.753 29.755 61.685 1.00 49.13 ATOM 2005 A2 AAA Y 1 9.242 30.200 62.974 1.00 46.62 ATOM 2006 A1 CCC Y 5 9.242 30.200 62.974 1.00 46.62 ATOM 2007 A2 BBB Y 2 12.548 28.316 63.532 1.00 30.20 ATOM 2008 A1 AAA Z 1K 8.753 29.755 61.685 1.00 49.13 ATOM 2009 A1 BBB Z 2 11.360 28.819 62.827 1.00 36.48 ATOM 2010 A2 BBB Z 2 12.548 28.316 63.532 1.00 30.20 ATOM 2011 A1 AAAZZ 1K 8.753 29.755 61.685 1.00 49.13 ATOM 2012 A1 BBBZZ 2 11.360 28.819 62.827 1.00 36.48 ATOM 2013 A1 CCCZZ 5 9.242 30.200 62.974 1.00 46.62 ATOM 2014 A1 CCCZZA001 9.242 30.200 62.974 1.00 46.62 ATOM 2015 A1 CCCZZA002 9.242 30.200 62.974 1.00 46.62 ATOM 2016 A1 CCCZZA003 9.242 30.200 62.974 1.00 46.62 ATOM 2017 A1 AAAUU 1K 8.753 29.755 61.685 1.00 49.13 ENDMDL END """)) hierarchy = pdb_inp.construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache( special_position_settings=pdb_inp.special_position_settings()) assert sel_cache.n_seq == hierarchy.atoms_size() isel = sel_cache.iselection assert isel("").size() == 0 assert isel("all").size() == sel_cache.n_seq assert isel("none").size() == 0 assert isel("optional none", optional=True).size() == 0 assert isel("optional none", optional=False) is None assert isel("not all").size() == 0 assert isel("not none").size() == sel_cache.n_seq assert list(isel(r"name c?\*")) == [45,46,48,50,52] assert list(isel(r"name 'C?\*'")) == [] assert list(isel(r"name ' C?\*'")) == [45,46,48,50,52] assert list(isel(r"name ' c?\*'")) == [45,46,48,50,52] assert list(isel(r"name n?'")) == [55, 59] for conj in ["and ", ""]: assert list(isel(r"altloc a %sname n" % conj)) == [24] assert list(isel(r"altloc b %sname n" % conj)) == [32] assert list(isel(r"altloc ' ' %sname n" % conj)) == [0,6,17] assert list(isel(r"altid ' ' %sname n" % conj)) == [0,6,17] assert list(isel(r"resname hoh")) == [69] assert list(isel(r"resname SO4")) == [64,65,66,67,68] assert list(isel(r"resname so4")) == [64,65,66,67,68] assert list(isel(r"resname So4")) == [64,65,66,67,68] assert list(isel(r"resname S?4")) == [64,65,66,67,68] assert list(isel(r"resname pro and name cg")) == [22] assert list(isel(r"resname pro and (name cg or name ca)")) == [18,22] assert list(isel(r"resname pro AND (name cg or name ca)")) == [18,22] assert list(isel(r"resname pro and (name cg OR name ca)")) == [18,22] assert list(isel(r"resname pro AND (name cg OR name ca)")) == [18,22] assert list(isel(r"not resname pro and (name cg or name ca)") ) == [1,7,11,25,33] assert list(isel(r"chain h and name o*")) == [41,42,43,44,47,49,51,58] assert list(isel(r"(chain h or chain s) and name o[2-46]")) == [58,66,67,68] assert list(isel(r"resseq 188")) == [64,65,66,67,68] assert list(isel(r"resseq 188")) == [64,65,66,67,68] assert list(isel(r"resseq 1:1")) == [0,1,2,3,4,5,70,71,74,75,78,81] assert list(isel(r"resseq 2:2")) == list(range(6,17)) + [72,73,77,79,80,82] assert list(isel(r"resseq 5:5")) == [76,83] assert list(isel(r"resseq 1:5")) == list(range(40))+list(range(70,84)) assert list(isel(r"resseq 2:3")) == list(range(6,24))+[72,73,77,79,80,82] assert list(isel(r"resseq 188:188")) == [64,65,66,67,68] assert list(isel(r"resseq 200:200")) == [69] assert list(isel(r"resseq 188:200")) == [64,65,66,67,68,69] assert list(isel(r"resseq 9999:A002")) == [84,85] assert list(isel(r"resseq A002:A003")) == [85,86] assert list(isel(r"resseq :")) == list(range(88)) assert list(isel(r"resseq :2 and name n*")) == [0,6,13,15,16] assert list(isel(r"resseq 2: and name cb")) == [10,21,28,36] assert list(isel(r"resseq 1:2 and name n*")) == [0,6,13,15,16] assert list(isel(r"resseq 2:4 and name cb")) == [10,21,28,36] assert list(isel(r"model 1 and name cb")) == [4,10,21,28,36] assert list(isel(r"model 2:3 and name o1*")) == [41,65] assert list(isel(r"icode j and name c?")) == [18,21,22,23] assert list(isel(r"resid 188")) == [64,65,66,67,68] assert list(isel(r"resid 3J")) == [17,18,19,20,21,22,23] assert list(isel(r"resid 1K")) == [78,81,87] assert list(isel(r"resid ' 1K'")) == [78,81] assert list(isel(r"resid ' 1K '")) == [87] assert list(isel(r"resi ' 1K'")) == [] assert list(isel(r"resid 1:2")) \ == list(range(17)) + [70,71,72,73,74,75,77,78,79,80,81,82] expected = list(range(6,17)) + [72,73,77,78,79,80,81,82] assert list(isel(r"resid 1K:2")) == expected assert list(isel(r"resid ' 1K:2'")) == expected assert list(isel(r"resid ' 1K:2'")) == expected expected = list(range(6,40)) + [72,73,76,77,78,79,80,81,82,83,87] assert list(isel(r"resi ' 1K: 1K '")) == expected # expected = [7,18,25,33] assert list(isel(r"resseq 2:4 and name ca")) == expected assert list(isel(r"resseq 2 : 4 and name ca")) == expected assert list(isel(r"resseq 2: 4 and name ca")) == expected assert list(isel(r"resseq 2 :4 and name ca")) == expected expected = [1,7,18] assert list(isel(r"resseq :3 and name ca")) == expected assert list(isel(r"resseq : 3 and name ca")) == expected assert list(isel(r"name ca and resseq :3")) == expected assert list(isel(r"name ca and resseq : 3")) == expected expected = [18,25,33] assert list(isel(r"resseq 3: and name ca")) == expected assert list(isel(r"resseq 3 : and name ca")) == expected assert list(isel(r"name ca and resseq 3:")) == expected assert list(isel(r"name ca and resseq 3 :")) == expected assert list(isel(r"name ca and resseq 3")) == [18] expected = [1,7,18,25,33] assert list(isel(r"resseq : and name ca")) == expected assert list(isel(r"name ca and resseq :")) == expected # assert list(isel(r"segid wate")) == [69] assert list(isel(r"element o")) == [65,66,67,68] assert list(isel(r"charge 4+")) == [64] assert list(isel(r"anisou")) == [1, 3] assert list(isel(r"pepnames")) == list(range(40)) assert list(isel(r"single_atom_residue")) == [ 69, 76, 77, 78, 81, 82, 83, 84, 85, 86, 87] assert list(isel(r"hetero")) == list(isel(r"hetatm")) == [ 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69] assert list(isel("within(3, resname PRO)")) == [7, 8, 9, 17, 18, 19, 20, 21, 22, 23, 24, 25, 32, 33, 73, 77, 80] assert list(isel("residues_within(3, resname PRO)")) == \ list(range(6, 40)) + [72, 73, 77, 79, 80] # try: isel(r"resseq") except pdb.atom_selection.AtomSelectionError as e: assert str(e).find( "Missing argument for resseq.") >= 0 else: raise Exception_expected try: isel(r"resseq 3:2") except pdb.atom_selection.AtomSelectionError as e: assert str(e).find( "range with first index > last index: resseq 3:2") >= 0 else: raise Exception_expected try: isel(r"resid ' 1K :2'") except pdb.atom_selection.AtomSelectionError as e: assert str(e).find( "range with first index > last index: resid 1K :2") >= 0 else: raise Exception_expected for s in ["altloc a and and name n", "altloc a and or name n", "altloc a or and name n", "altloc a or or name n", "and name n", "or name n", "not", "not not", "altloc a optional", "optional optional altloc a"]: try: isel(string=s) except pdb.atom_selection.AtomSelectionError as e: assert str(e).endswith("""\ Atom selection string leading to error: %s""" % s), str(e) else: raise Exception_expected # sel = sel_cache.get_labels(name=" CA ") assert len(sel) == 1 assert list(sel[0]) == [1,7,18,25,33] atoms = hierarchy.atoms() for i_seq in sel[0]: assert atoms[i_seq].name == " CA " sel = sel_cache.get_labels(resseq=" 5") assert len(sel) == 1 assert list(sel[0]) == [76, 83] # atoms.reset_i_seq() sel = sel_cache.selection("resname 5GP and name C6") assert sel.count(True) == 1 sel_complete = pdb.atom_selection.expand_selection_to_entire_atom_groups( selection=sel, pdb_atoms=atoms) assert sel_complete.count(True) == 24 # link_records = [ pdb.records.link(pdb_str=pdb_str) for pdb_str in """\ LINK S SO4 S 188 O1 SO4 S 188 LINK S SO4 S 188 O2 SO4 S 188 LINK NZ LYS A 680 1.260 C4A PLP D 1 LYS-PLP """.splitlines()] expected_results = [ [[64], [65]], [[64], [66]], [[], []]] for link_record,expected in zip(link_records, expected_results): assert [list(sel) for sel in sel_cache.link_iselections(link_record)] \ == expected # hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA Asn A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN a 4 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN a 5 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN a 6 6.831 2.310 4.318 1.00 12.30 C END """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("chain A")) == [0,1,2] assert list(isel("chain a")) == [3,4,5] assert list(isel("name ca")) == list(range(6)) assert list(isel("resname asn")) == [1,2,5] assert list(isel("resname ASN")) == [1,2,5] assert list(isel("resname Asn")) == [1,2,5] hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 2 CA GLY A 1 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 2 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 3 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN b 4 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN b 5 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN b 6 6.831 2.310 4.318 1.00 12.30 C END """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("resname asn")) == [1,2,5] assert list(isel("resname ASN")) == [1,2,5] assert list(isel("resname Asn")) == [1,2,5] assert list(isel("chain A")) == [0,1,2] assert list(isel("chain a")) == [] assert list(isel("chain B")) == [] assert list(isel("chain b")) == [3,4,5] # hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 5 CA SER 1 9.242 30.200 62.974 1.00 46.62 ATOM 11 CA ARG 2 12.548 28.316 63.532 1.00 30.20 ATOM 21 N NON 3J 13.947 29.997 64.680 1.00 22.94 ATOM 22 CA NON 3J 14.902 31.100 64.827 1.00 20.19 ATOM 24 O NON 3J 16.545 29.521 64.086 1.00 19.76 ATOM 28 N AILE 4 16.953 31.648 63.512 1.00 15.29 ATOM 29 CA AILE 4 18.243 31.372 62.859 1.00 14.32 ATOM 30 C AILE 4 19.233 32.112 63.743 1.00 13.54 ATOM 31 O AILE 4 19.105 33.315 64.009 1.00 11.84 ATOM 41 N PRO 5 13.947 29.997 64.680 1.00 22.94 ATOM 42 CA PRO 5 14.902 31.100 64.827 1.00 20.19 ATOM 44 O PRO 5 16.545 29.521 64.086 1.00 19.76 ATOM 45 CA CA 6 16.545 29.521 64.086 1.00 19.76 """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("pepnames")) == [0,1,5,6,7,8,9,10,11] # for s in ["peptide", "protein"]: assert list(isel(s)) == [0, 1, 5, 6, 7, 8, 9, 10, 11] try: isel("chain A or (peptyde and name ca)") except pdb.atom_selection.AtomSelectionError as e: assert not show_diff(str(e), """\ RuntimeError: Atom selection syntax error at word "peptyde". Atom selection string leading to error: chain A or (peptyde and name ca)""") else: raise Exception_expected # hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 459 CA SER A 58 ATOM 463 OG ASER A 58 ATOM 464 OG BSER A 58 """)).construct_hierarchy() sel_cache = hierarchy.atom_selection_cache() assert sel_cache.iselection("single_atom_residue").size() == 0 hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 2 CA GLY A 666 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 777 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 1 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 2 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 3 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA ASN A 4 6.831 2.310 4.318 1.00 12.30 C TER ATOM 6 CA ASN B 777 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN B 1 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN B 2 0.384 1.888 3.199 1.00 10.53 C END """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() sele = sel_cache.iselection("resid 777 through 3 and chain A") assert (sele.size() == 4) sele = sel_cache.iselection("resid 777 through 3") assert (sele.size() == 7) try : sele = sel_cache.iselection("resid 777 through chain A") except pdb.atom_selection.AtomSelectionError as e : pass else : raise Exception_expected hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ CRYST1 21.937 4.866 23.477 90.00 107.08 90.00 P 1 21 1 2 ATOM 6 CA ASN B 777 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN B 1 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN B 2 0.384 1.888 3.199 1.00 10.53 C TER ATOM 2 CA GLY A 666 -9.052 4.207 4.651 1.00 16.57 C ATOM 6 CA ASN A 777 -6.522 2.038 2.831 1.00 14.10 C ATOM 14 CA ASN A 1 -3.193 1.904 4.589 1.00 11.74 C ATOM 22 CA GLN A 2 0.384 1.888 3.199 1.00 10.53 C ATOM 31 CA GLN A 3 3.270 2.361 5.640 1.00 11.39 C ATOM 40 CA AASN A 4 6.831 2.310 4.318 1.00 12.30 C ATOM 41 CA BASN A 4 6.831 2.310 4.318 1.00 12.30 C TER END """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() sele = sel_cache.iselection("resid 2 through 4") assert (list(sele) == [2,6,7,8,9]) sele = sel_cache.iselection("chain A and resid 2 through 4") assert (list(sele) == [6,7,8,9]) # hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 5 CA SER 1 9.242 30.200 62.974 1.00 46.62 ATOM 11 O HOH 2 12.548 28.316 63.532 1.00 30.20 ATOM 21 O WAT C 3J 13.947 29.997 64.680 1.00 22.94 O ATOM 22 CA NON 3J 14.902 31.100 64.827 0.50 20.19 ATOM 42 CA PRO 5 14.902 31.100 64.827 1.00 20.19 ATOM 44 O PRO 5 16.545 29.521 64.086 1.00 19.76 HETATM 45 O ZHOH 6 16.545 29.521 64.086 0.00 19.76 HETATM 4 O KHOH 6 16.545 29.521 64.086 0.00 19.76 """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("water")) == [1,2,6,7] # assert list(isel("bfactor < 20")) == [5,6,7] assert list(isel("name CA and bfactor = 20.19")) == [3,4] assert list(isel("occupancy > 0")) == [0,1,2,3,4,5] assert list(isel("occupancy < 1")) == [3,6,7] assert list(isel("occupancy = 0")) == [6,7] try : isel("within(5, resname PRO)") except pdb.atom_selection.AtomSelectionError : pass else : raise Exception_expected # make sure that hybrid-36 numbers work with and without insertion codes hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 2 CA SER A13L 33.163 16.115 17.936 1.00 26.68 C ATOM 8 CA ASP A13M 34.633 18.762 20.254 1.00 22.59 C ATOM 16 CA LYS A13N 36.047 17.704 23.610 1.00 19.79 C ATOM 25 CA ILE A002 35.551 19.482 26.886 1.00 19.33 C ATOM 34 CA AHIS A003X 38.649 21.223 28.218 0.50 19.79 C ATOM 5 N TYR A 2 27.208 -20.701 0.590 1.00 7.29 N ATOM 17 N SER A 2A 26.854 -17.177 0.412 1.00 6.66 N ATOM 26 N CYS A 2B 25.627 -14.135 -0.995 1.00 5.11 N ATOM 32 N ARG A 5 25.486 -10.691 -2.002 1.00 4.69 N ATOM 43 N ALA A 6 24.325 -7.563 -3.358 1.00 4.39 N ATOM 48 N VAL A 7 24.165 -4.139 -3.284 1.00 4.97 N ATOM 204 N MET A 31 18.177 -3.966 -4.656 1.00 4.72 N ATOM 212 N ALA A 32 19.899 -6.986 -4.412 1.00 3.90 N ATOM 217 N SER A 33 20.230 -10.407 -3.567 1.00 4.02 N ATOM 223 N GLY A 34 21.415 -13.600 -2.283 1.00 4.96 N ATOM 227 N THR A 35 21.521 -17.105 -1.329 1.00 4.35 N ATOM 234 N SER A 35A 23.294 -20.178 -1.426 1.00 4.63 N """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("resid A13L through A13N")) == [0, 1, 2] assert list(isel("resid A002 through A003X")) == [3, 4] assert list(isel("(resid A002 through A003X) and (altloc ' ' or altloc 'A') "))== [3, 4] assert list(isel("(chain 'A' and resid 2A through 7 ) and (name N) and (altloc 'A' or altloc ' ')"))==[6, 7, 8, 9, 10] # exercise peptide, protein hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 5 CA SER 1 9.242 30.200 62.974 1.00 46.62 ATOM 11 CA ARG 2 12.548 28.316 63.532 1.00 30.20 ATOM 21 N 2AG 3J 13.947 29.997 64.680 1.00 22.94 ATOM 22 CA 2AG 3J 14.902 31.100 64.827 1.00 20.19 ATOM 24 O 2AG 3J 16.545 29.521 64.086 1.00 19.76 ATOM 28 N AILE 4 16.953 31.648 63.512 1.00 15.29 ATOM 29 CA AILE 4 18.243 31.372 62.859 1.00 14.32 ATOM 30 C AILE 4 19.233 32.112 63.743 1.00 13.54 ATOM 31 O AILE 4 19.105 33.315 64.009 1.00 11.84 ATOM 41 N PRO 5 13.947 29.997 64.680 1.00 22.94 ATOM 42 CA HOH 6 14.902 31.100 64.827 1.00 20.19 ATOM 44 O HOH 7 16.545 29.521 64.086 1.00 19.76 ATOM 45 CA CA 8 16.545 29.521 64.086 1.00 19.76 """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection for s in ["peptide", "protein"]: assert list(isel(s)) == [0,1,2,3,4,5,6,7,8,9], list(isel(s)) # exercise nucleotide hierarchy = pdb.input(source_info=None, lines=flex.split_lines("""\ ATOM 5 CA A 1 9.242 30.200 62.974 1.00 46.62 ATOM 11 CA C 2 12.548 28.316 63.532 1.00 30.20 ATOM 21 N DA 3J 13.947 29.997 64.680 1.00 22.94 ATOM 22 CA DA 3J 14.902 31.100 64.827 1.00 20.19 ATOM 24 O DA 3J 16.545 29.521 64.086 1.00 19.76 ATOM 28 N A6MA 4 16.953 31.648 63.512 1.00 15.29 ATOM 29 CA A6MA 4 18.243 31.372 62.859 1.00 14.32 ATOM 30 C A6MA 4 19.233 32.112 63.743 1.00 13.54 ATOM 31 O A6MA 4 19.105 33.315 64.009 1.00 11.84 ATOM 41 N PRO 5 13.947 29.997 64.680 1.00 22.94 ATOM 42 CA HOH 6 14.902 31.100 64.827 1.00 20.19 ATOM 44 O HOH 7 16.545 29.521 64.086 1.00 19.76 ATOM 45 CA CA 8 16.545 29.521 64.086 1.00 19.76 """)).construct_hierarchy(sort_atoms=False) sel_cache = hierarchy.atom_selection_cache() isel = sel_cache.iselection assert list(isel("nucleotide")) == [0,1,2,3,4,5,6,7,8], 'found %s' % list(isel("nucleotide")) assert list(isel("nucleotide or protein")) == [0,1,2,3,4,5,6,7,8,9] def run(): exercise_selection() print("OK") if (__name__ == "__main__"): run()