diff --git a/package/AUTHORS b/package/AUTHORS index e412dac67fe..79e2ddc5643 100644 --- a/package/AUTHORS +++ b/package/AUTHORS @@ -121,6 +121,7 @@ Chronological list of authors - Yibo Zhang - Luís Pedro Borges Araújo - Abhishek A. Kognole + - Rocco Meli External code ------------- diff --git a/package/CHANGELOG b/package/CHANGELOG index d7d28302ab0..704597c61b1 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -16,7 +16,7 @@ The rules for this file: mm/dd/yy micaela-matta, xiki-tempula, zemanj, mattwthompson, orbeckst, aliehlen, dpadula85, jbarnoud, manuel.nuno.melo, richardjgowers, mattwthompson, ayushsuhane, picocentauri, NinadBhat, bieniekmateusz, p-j-smith, Lp0lp, - IAlibay, tyler.je.reddy, aakognole + IAlibay, tyler.je.reddy, aakognole, RMeli * 0.20.0 @@ -76,6 +76,7 @@ Changes Fixes * fixes ProgressMeter issues with older Jupyter Lab versions (Issue #2078) * fixes ProgressMeter behaviour for non-AnalysisBase methods (Issue #2084) + * fixed mol2 parser for status bit strings (Issue #2318) * fixed reading AMBER topologies with negative ATOMIC_NUMBERS (Issue #2306) * fixed reading bz2 compressed psf files (Issue #2232) * fixed mol2 comment header handling (Issue #2261) diff --git a/package/MDAnalysis/coordinates/MOL2.py b/package/MDAnalysis/coordinates/MOL2.py index 262903771fa..948ef58b7e2 100644 --- a/package/MDAnalysis/coordinates/MOL2.py +++ b/package/MDAnalysis/coordinates/MOL2.py @@ -129,6 +129,7 @@ class MOL2Reader(base.ReaderBase): previously created a new instance of Timestep each frame. .. versionchanged:: 0.20.0 Allows for comments at top of file. + Ignores status bit strings """ format = 'MOL2' units = {'time': None, 'length': 'Angstrom'} @@ -197,7 +198,8 @@ def parse_block(self, block): coords = np.zeros((self.n_atoms, 3), dtype=np.float32) for i, a in enumerate(atom_lines): - aid, name, x, y, z, atom_type, resid, resname, charge = a.split() + aid, name, x, y, z, atom_type, resid, resname, charge = a.split()[:9] + #x, y, z = float(x), float(y), float(z) coords[i, :] = x, y, z diff --git a/package/MDAnalysis/topology/MOL2Parser.py b/package/MDAnalysis/topology/MOL2Parser.py index 6a12fcb14f5..5a5bb733a9a 100644 --- a/package/MDAnalysis/topology/MOL2Parser.py +++ b/package/MDAnalysis/topology/MOL2Parser.py @@ -83,6 +83,7 @@ class MOL2Parser(TopologyReaderBase): Now subclasses TopologyReaderBase .. versionchanged:: 0.20.0 Allows for comments at the top of the file + Ignores status bit strings """ format = 'MOL2' @@ -139,7 +140,8 @@ def parse(self, **kwargs): charges = [] for a in atom_lines: - aid, name, x, y, z, atom_type, resid, resname, charge = a.split() + aid, name, x, y, z, atom_type, resid, resname, charge = a.split()[:9] + ids.append(aid) names.append(name) types.append(atom_type) @@ -174,7 +176,8 @@ def parse(self, **kwargs): bondorder = [] for b in bond_lines: # bond_type can be: 1, 2, am, ar - bid, a0, a1, bond_type = b.split() + bid, a0, a1, bond_type = b.split()[:4] + a0, a1 = int(a0) - 1, int(a1) - 1 bond = tuple(sorted([a0, a1])) bondorder.append(bond_type) diff --git a/testsuite/MDAnalysisTests/coordinates/test_mol2.py b/testsuite/MDAnalysisTests/coordinates/test_mol2.py index 76a7f2314ee..adc47447b2d 100644 --- a/testsuite/MDAnalysisTests/coordinates/test_mol2.py +++ b/testsuite/MDAnalysisTests/coordinates/test_mol2.py @@ -33,7 +33,7 @@ from MDAnalysisTests.datafiles import ( mol2_molecules, mol2_molecule, mol2_broken_molecule, - mol2_zinc, mol2_comments_header + mol2_zinc, mol2_comments_header, mol2_ligand ) from MDAnalysis import Universe import MDAnalysis as mda @@ -56,6 +56,11 @@ def test_read(self): u.trajectory[199] assert_array_almost_equal(u.atoms.positions[0], [1.7240, 11.2730, 14.1200]) + def test_read_statusbit(self): + u = Universe(mol2_ligand) + assert_equal(len(u.atoms), 297) + assert_equal(u.trajectory.n_frames, 1) + def test_write(self): ref = Universe(mol2_molecules) ref.atoms.write(self.outfile) diff --git a/testsuite/MDAnalysisTests/data/mol2/Ligand.mol2 b/testsuite/MDAnalysisTests/data/mol2/Ligand.mol2 new file mode 100644 index 00000000000..57fcbe5adf1 --- /dev/null +++ b/testsuite/MDAnalysisTests/data/mol2/Ligand.mol2 @@ -0,0 +1,630 @@ +# Ligand PDB 2w73 + +@MOLECULE +2w73_ligand + 297 297 17 0 2 +SMALL +GAST_HUCK + + +@DICT +BIOPOLYMER macromol +@ATOM + 1 H1 -4.3113 -22.6846 25.7277 H 1 VAL395 0.2015 + 2 H2 -4.8435 -22.5042 27.2748 H 1 VAL395 0.2015 + 3 H3 -3.3012 -22.0851 26.8808 H 1 VAL395 0.2015 + 4 H4 -4.0407 -20.3421 25.4793 H 1 VAL395 0.1101 + 5 H5 -6.3067 -19.7271 25.2880 H 1 VAL395 0.0376 + 6 H6 -7.4270 -21.7212 24.3277 H 1 VAL395 0.0236 + 7 H7 -6.1915 -22.7731 25.0984 H 1 VAL395 0.0236 + 8 H8 -5.7056 -21.5983 23.8293 H 1 VAL395 0.0236 + 9 H9 -6.9441 -20.0645 27.6590 H 1 VAL395 0.0236 + 10 H10 -7.0388 -21.8358 27.3764 H 1 VAL395 0.0236 + 11 H11 -8.1720 -20.7292 26.5291 H 1 VAL395 0.0236 + 12 H12 -3.9835 -21.7225 28.3784 H 2 ILE396 0.1885 + 13 H13 -4.9144 -19.7823 30.2232 H 2 ILE396 0.0803 + 14 H14 -4.1481 -22.0401 30.9262 H 2 ILE396 0.0345 + 15 H15 -2.9167 -19.6261 32.3177 H 2 ILE396 0.0267 + 16 H16 -3.1622 -21.2414 33.0640 H 2 ILE396 0.0267 + 17 H17 -2.0776 -22.1714 29.6048 H 2 ILE396 0.0235 + 18 H18 -1.7860 -22.4771 31.3507 H 2 ILE396 0.0235 + 19 H19 -1.3438 -20.8922 30.6303 H 2 ILE396 0.0235 + 20 H20 -4.9799 -19.6789 33.6862 H 2 ILE396 0.0230 + 21 H21 -5.6085 -21.0395 32.6962 H 2 ILE396 0.0230 + 22 H22 -5.3629 -19.4242 31.9498 H 2 ILE396 0.0230 + 23 H23 -1.8404 -20.0577 28.4801 H 3 ARG397 0.1883 + 24 H24 -0.6243 -17.9356 29.9536 H 3 ARG397 0.0800 + 25 H25 1.0426 -17.8156 28.1350 H 3 ARG397 0.0313 + 26 H26 0.1571 -19.1647 27.3461 H 3 ARG397 0.0313 + 27 H27 0.5136 -20.6364 29.2030 H 3 ARG397 0.0301 + 28 H28 0.9508 -19.2831 30.3004 H 3 ARG397 0.0301 + 29 H29 2.9417 -20.3978 29.7122 H 3 ARG397 0.0689 + 30 H30 2.9000 -18.8443 28.8113 H 3 ARG397 0.0689 + 31 H31 1.6682 -20.9054 27.2407 H 3 ARG397 0.2642 + 32 H32 4.5362 -21.6650 25.3981 H 3 ARG397 0.2615 + 33 H33 2.7611 -21.8039 25.5098 H 3 ARG397 0.2615 + 34 H34 4.8371 -19.8386 28.4325 H 3 ARG397 0.2615 + 35 H35 5.7110 -20.5531 27.0510 H 3 ARG397 0.2615 + 36 H36 -2.6236 -18.0169 27.0706 H 4 ASN398 0.1885 + 37 H37 -2.1286 -15.2940 26.2225 H 4 ASN398 0.0826 + 38 H38 -4.5198 -15.5571 25.2147 H 4 ASN398 0.0551 + 39 H39 -4.4377 -17.2391 25.8398 H 4 ASN398 0.0551 + 40 H40 -3.2447 -17.8339 22.5254 H 4 ASN398 0.1814 + 41 H41 -4.6687 -17.7780 23.5098 H 4 ASN398 0.1814 + 42 H42 -4.4228 -16.7536 28.3903 H 5 LYS399 0.1883 + 43 H43 -5.8526 -14.3952 29.0959 H 5 LYS399 0.0800 + 44 H44 -5.4384 -16.8297 30.8194 H 5 LYS399 0.0312 + 45 H45 -6.6656 -16.6732 29.5171 H 5 LYS399 0.0312 + 46 H46 -7.1981 -14.4645 30.9298 H 5 LYS399 0.0269 + 47 H47 -6.5698 -15.5308 32.2317 H 5 LYS399 0.0269 + 48 H48 -8.1447 -17.3311 31.3238 H 5 LYS399 0.0317 + 49 H49 -8.8948 -16.0350 30.3319 H 5 LYS399 0.0317 + 50 H50 -9.1890 -14.7285 32.5131 H 5 LYS399 0.0813 + 51 H51 -8.7403 -16.2432 33.3680 H 5 LYS399 0.0813 + 52 H52 -11.1001 -15.9652 33.2121 H 5 LYS399 0.1994 + 53 H53 -10.6341 -17.2888 32.3516 H 5 LYS399 0.1994 + 54 H54 -11.0453 -15.9008 31.5682 H 5 LYS399 0.1994 + 55 H55 -3.0113 -15.9378 30.5765 H 6 ILE400 0.1883 + 56 H56 -2.7947 -14.1531 32.7510 H 6 ILE400 0.0803 + 57 H57 -0.6708 -15.8276 31.3502 H 6 ILE400 0.0345 + 58 H58 -2.5731 -16.9420 32.5389 H 6 ILE400 0.0267 + 59 H59 -2.1683 -16.0088 34.0194 H 6 ILE400 0.0267 + 60 H60 0.4300 -13.9209 32.4605 H 6 ILE400 0.0235 + 61 H61 0.7163 -15.4530 33.3533 H 6 ILE400 0.0235 + 62 H62 -0.4857 -14.2674 33.9665 H 6 ILE400 0.0235 + 63 H63 -1.2937 -18.3199 34.1474 H 6 ILE400 0.0230 + 64 H64 0.0467 -17.1245 34.1171 H 6 ILE400 0.0230 + 65 H65 -0.3582 -18.0577 32.6366 H 6 ILE400 0.0230 + 66 H66 -1.4469 -14.0345 29.4861 H 7 ARG401 0.1883 + 67 H67 0.0353 -11.6241 29.7894 H 7 ARG401 0.0800 + 68 H68 -0.3142 -11.3722 27.2764 H 7 ARG401 0.0313 + 69 H69 -1.2088 -12.9276 27.3610 H 7 ARG401 0.0313 + 70 H70 0.6897 -14.1464 27.9503 H 7 ARG401 0.0301 + 71 H71 1.5569 -12.6976 28.5631 H 7 ARG401 0.0301 + 72 H72 1.8834 -11.9179 26.2366 H 7 ARG401 0.0689 + 73 H73 1.0342 -13.3812 25.6329 H 7 ARG401 0.0689 + 74 H74 2.8801 -14.7306 26.2658 H 7 ARG401 0.2642 + 75 H75 6.0605 -13.6158 27.1799 H 7 ARG401 0.2615 + 76 H76 5.0606 -14.9967 26.6547 H 7 ARG401 0.2615 + 77 H77 3.3801 -11.3171 27.1690 H 7 ARG401 0.2615 + 78 H78 5.1230 -11.5518 27.4689 H 7 ARG401 0.2615 + 79 H79 -3.3416 -12.2253 28.8698 H 8 ALA402 0.1883 + 80 H80 -4.0255 -9.4716 28.3980 H 8 ALA402 0.0797 + 81 H81 -6.3981 -10.1303 28.6760 H 8 ALA402 0.0277 + 82 H82 -5.8729 -11.7402 29.2753 H 8 ALA402 0.0277 + 83 H83 -5.5017 -11.2446 27.5891 H 8 ALA402 0.0277 + 84 H84 -3.9895 -11.3783 31.3213 H 9 ILE403 0.1883 + 85 H85 -5.2984 -9.5255 32.9994 H 9 ILE403 0.0803 + 86 H86 -3.3181 -11.8487 33.4975 H 9 ILE403 0.0345 + 87 H87 -5.7030 -12.1795 32.7774 H 9 ILE403 0.0267 + 88 H88 -6.1997 -11.4601 34.3466 H 9 ILE403 0.0267 + 89 H89 -2.8241 -10.1297 35.1655 H 9 ILE403 0.0235 + 90 H90 -3.6034 -11.5704 35.9029 H 9 ILE403 0.0235 + 91 H91 -4.5588 -10.0743 35.6284 H 9 ILE403 0.0235 + 92 H92 -6.2641 -13.9387 34.4343 H 9 ILE403 0.0230 + 93 H93 -5.0221 -13.2900 35.5582 H 9 ILE403 0.0230 + 94 H94 -4.5254 -14.0094 33.9890 H 9 ILE403 0.0230 + 95 H95 -1.9100 -10.1017 32.1624 H 10 GLY404 0.1881 + 96 H96 -0.0095 -8.8214 32.3559 H 10 GLY404 0.0763 + 97 H97 -0.7494 -8.1114 33.8308 H 10 GLY404 0.0763 + 98 H98 -1.9083 -8.0515 30.5085 H 11 LYS405 0.1883 + 99 H99 -1.0774 -5.3520 29.8236 H 11 LYS405 0.0800 + 100 H100 -2.9516 -5.4828 28.1567 H 11 LYS405 0.0312 + 101 H101 -3.3630 -7.0833 28.8609 H 11 LYS405 0.0312 + 102 H102 -1.1425 -7.8789 28.3151 H 11 LYS405 0.0269 + 103 H103 -0.7636 -6.2848 27.5789 H 11 LYS405 0.0269 + 104 H104 -2.3851 -6.5624 25.8671 H 11 LYS405 0.0317 + 105 H105 -3.2045 -7.9001 26.7423 H 11 LYS405 0.0317 + 106 H106 -2.0310 -9.1421 25.2645 H 11 LYS405 0.0813 + 107 H107 -0.7621 -8.9666 26.5238 H 11 LYS405 0.0813 + 108 H108 0.0573 -8.4146 24.3400 H 11 LYS405 0.1994 + 109 H109 0.0805 -7.0811 25.3047 H 11 LYS405 0.1994 + 110 H110 -1.0823 -7.2420 24.1508 H 11 LYS405 0.1994 + 111 H111 -4.0842 -6.6583 31.1724 H 12 MET406 0.1883 + 112 H112 -5.4147 -4.1110 31.2558 H 12 MET406 0.0800 + 113 H113 -7.0244 -5.1719 32.8314 H 12 MET406 0.0320 + 114 H114 -6.0089 -6.6535 32.8094 H 12 MET406 0.0320 + 115 H115 -7.9453 -6.8230 31.3447 H 12 MET406 0.0378 + 116 H116 -6.3905 -6.9256 30.4508 H 12 MET406 0.0378 + 117 H117 -6.6625 -4.0501 27.9289 H 12 MET406 0.0340 + 118 H118 -6.3139 -5.8019 28.1199 H 12 MET406 0.0340 + 119 H119 -5.4147 -4.5950 29.1005 H 12 MET406 0.0340 + 120 H120 -3.4027 -5.9084 33.5622 H 13 ALA407 0.1883 + 121 H121 -3.9668 -4.2689 35.7890 H 13 ALA407 0.0797 + 122 H122 -1.8113 -5.0366 36.7677 H 13 ALA407 0.0277 + 123 H123 -1.3589 -5.7701 35.1917 H 13 ALA407 0.0277 + 124 H124 -2.7702 -6.4032 36.1049 H 13 ALA407 0.0277 + 125 H125 -1.7819 -3.9532 33.0882 H 14 ARG408 0.1883 + 126 H126 -0.2179 -1.7811 34.1211 H 14 ARG408 0.0800 + 127 N -4.2550 -22.1130 26.5560 N.4 1 VAL395 0.2381 BACKBONE|DICT|DIRECT + 128 CA -4.6970 -20.7760 26.2480 C.3 1 VAL395 0.0673 BACKBONE|DICT|DIRECT + 129 C -4.5810 -20.0070 27.5200 C.2 1 VAL395 0.2270 BACKBONE|DICT|DIRECT + 130 O -4.8570 -18.8150 27.5880 O.2 1 VAL395 -0.3907 BACKBONE|DICT|DIRECT + 131 CB -6.1500 -20.7130 25.7500 C.3 1 VAL395 0.0139 DICT + 132 CG1 -6.3850 -21.7760 24.6760 C.3 1 VAL395 -0.0553 DICT + 133 CG2 -7.1470 -20.8450 26.9110 C.3 1 VAL395 -0.0553 DICT + 134 N -4.1610 -20.7500 28.5290 N.am 2 ILE396 -0.2607 BACKBONE|DICT|DIRECT + 135 CA -3.9470 -20.1760 29.8780 C.3 2 ILE396 0.1336 BACKBONE|DICT|DIRECT + 136 C -2.9720 -19.0280 29.7890 C.2 2 ILE396 0.2042 BACKBONE|DICT|DIRECT + 137 O -3.1790 -17.9780 30.4160 O.2 2 ILE396 -0.3944 BACKBONE|DICT|DIRECT + 138 CB -3.4600 -21.1820 30.9330 C.3 2 ILE396 -0.0037 DICT + 139 CG1 -3.5420 -20.5310 32.3150 C.3 2 ILE396 -0.0491 DICT + 140 CG2 -2.0700 -21.7180 30.6070 C.3 2 ILE396 -0.0582 DICT + 141 CD1 -4.9740 -20.1410 32.6880 C.3 2 ILE396 -0.0648 DICT + 142 N -1.9200 -19.2140 29.0110 N.am 3 ARG397 -0.2637 BACKBONE|DICT|DIRECT + 143 CA -0.8800 -18.2080 28.9190 C.3 3 ARG397 0.1311 BACKBONE|DICT|DIRECT + 144 C -1.4170 -16.9450 28.2530 C.2 3 ARG397 0.2040 BACKBONE|DICT|DIRECT + 145 O -1.0050 -15.8510 28.5760 O.2 3 ARG397 -0.3944 BACKBONE|DICT|DIRECT + 146 CB 0.3710 -18.6700 28.3050 C.3 3 ARG397 -0.0092 DICT + 147 CG 1.0270 -19.6660 29.2720 C.3 3 ARG397 -0.0156 DICT + 148 CD 2.4300 -19.8330 28.9190 C.3 3 ARG397 0.0627 DICT + 149 NE 2.5370 -20.5550 27.6690 N.pl3 3 ARG397 -0.2723 DICT + 150 CZ 3.6750 -20.7950 27.0400 C.cat 3 ARG397 0.2882 DICT + 151 NH1 3.6560 -21.4720 25.8970 N.pl3 3 ARG397 -0.2849 DICT + 152 NH2 4.8280 -20.3630 27.5460 N.pl3 3 ARG397 -0.2849 DICT + 153 N -2.3290 -17.0960 27.3260 N.am 4 ASN398 -0.2616 BACKBONE|DICT|DIRECT + 154 CA -2.9390 -15.9090 26.6410 C.3 4 ASN398 0.1476 BACKBONE|DICT|DIRECT + 155 C -3.7270 -15.0630 27.6070 C.2 4 ASN398 0.2063 BACKBONE|DICT|DIRECT + 156 O -3.7400 -13.8130 27.5660 O.2 4 ASN398 -0.3942 BACKBONE|DICT|DIRECT + 157 CB -3.8450 -16.3810 25.4900 C.3 4 ASN398 0.0773 DICT + 158 CG -3.0640 -16.8030 24.2520 C.2 4 ASN398 0.1780 DICT + 159 OD1 -1.8930 -16.4750 24.1080 O.2 4 ASN398 -0.3970 DICT + 160 ND2 -3.7120 -17.5310 23.3560 N.am 4 ASN398 -0.3007 DICT + 161 N -4.4220 -15.7570 28.4730 N.am 5 LYS399 -0.2636 BACKBONE|DICT|DIRECT + 162 CA -5.1980 -15.1500 29.5560 C.3 5 LYS399 0.1310 BACKBONE|DICT|DIRECT + 163 C -4.3070 -14.4360 30.5510 C.2 5 LYS399 0.2039 BACKBONE|DICT|DIRECT + 164 O -4.5990 -13.3100 30.9790 O.2 5 LYS399 -0.3944 BACKBONE|DICT|DIRECT + 165 CB -6.0790 -16.1250 30.2690 C.3 5 LYS399 -0.0122 DICT + 166 CG -7.0170 -15.5080 31.2270 C.3 5 LYS399 -0.0440 DICT + 167 CD -8.3420 -16.2510 31.2580 C.3 5 LYS399 -0.0124 DICT + 168 CE -9.1950 -15.8270 32.4570 C.3 5 LYS399 -0.0354 DICT + 169 NZ -10.6070 -16.2820 32.3920 N.4 5 LYS399 0.2185 DICT + 170 N -3.2050 -15.0230 30.9310 N.am 6 ILE400 -0.2635 BACKBONE|DICT|DIRECT + 171 CA -2.2480 -14.4250 31.8360 C.3 6 ILE400 0.1335 BACKBONE|DICT|DIRECT + 172 C -1.6720 -13.1420 31.2450 C.2 6 ILE400 0.2042 BACKBONE|DICT|DIRECT + 173 O -1.5270 -12.0970 31.9480 O.2 6 ILE400 -0.3944 BACKBONE|DICT|DIRECT + 174 CB -1.1220 -15.3860 32.2510 C.3 6 ILE400 -0.0037 DICT + 175 CG1 -1.7580 -16.4760 33.1120 C.3 6 ILE400 -0.0491 DICT + 176 CG2 -0.0420 -14.7110 33.0630 C.3 6 ILE400 -0.0582 DICT + 177 CD1 -0.7710 -17.5720 33.5330 C.3 6 ILE400 -0.0648 DICT + 178 N -1.3510 -13.1720 29.9830 N.am 7 ARG401 -0.2637 BACKBONE|DICT|DIRECT + 179 CA -0.8530 -11.9920 29.2550 C.3 7 ARG401 0.1311 BACKBONE|DICT|DIRECT + 180 C -1.8970 -10.8870 29.2680 C.2 7 ARG401 0.2039 BACKBONE|DICT|DIRECT + 181 O -1.5600 -9.6950 29.4580 O.2 7 ARG401 -0.3944 BACKBONE|DICT|DIRECT + 182 CB -0.4260 -12.3150 27.8320 C.3 7 ARG401 -0.0092 DICT + 183 CG 0.9030 -13.0830 27.7670 C.3 7 ARG401 -0.0156 DICT + 184 CD 1.6590 -12.9750 26.4420 C.3 7 ARG401 0.0627 DICT + 185 NE 2.9120 -13.7310 26.5120 N.pl3 7 ARG401 -0.2723 DICT + 186 CZ 4.0880 -13.2220 26.8700 C.cat 7 ARG401 0.2882 DICT + 187 NH1 5.1460 -14.0010 26.9040 N.pl3 7 ARG401 -0.2849 DICT + 188 NH2 4.2060 -11.9320 27.1940 N.pl3 7 ARG401 -0.2849 DICT + 189 N -3.1460 -11.2630 29.0590 N.am 8 ALA402 -0.2640 BACKBONE|DICT|DIRECT + 190 CA -4.2740 -10.2820 29.0990 C.3 8 ALA402 0.1282 BACKBONE|DICT|DIRECT + 191 C -4.3940 -9.6750 30.4570 C.2 8 ALA402 0.2036 BACKBONE|DICT|DIRECT + 192 O -4.6440 -8.4140 30.6380 O.2 8 ALA402 -0.3944 BACKBONE|DICT|DIRECT + 193 CB -5.6070 -10.8930 28.6260 C.3 8 ALA402 -0.0244 DICT + 194 N -4.2140 -10.4170 31.4810 N.am 9 ILE403 -0.2635 BACKBONE|DICT|DIRECT + 195 CA -4.3090 -9.9780 32.8370 C.3 9 ILE403 0.1335 BACKBONE|DICT|DIRECT + 196 C -3.2430 -8.9310 33.0690 C.2 9 ILE403 0.2040 BACKBONE|DICT|DIRECT + 197 O -3.4870 -7.8540 33.6730 O.2 9 ILE403 -0.3944 BACKBONE|DICT|DIRECT + 198 CB -4.1380 -11.2090 33.8560 C.3 9 ILE403 -0.0037 DICT + 199 CG1 -5.4140 -12.0290 33.8280 C.3 9 ILE403 -0.0491 DICT + 200 CG2 -3.7550 -10.7120 35.2320 C.3 9 ILE403 -0.0582 DICT + 201 CD1 -5.2980 -13.4170 34.5010 C.3 9 ILE403 -0.0648 DICT + 202 N -2.0460 -9.2240 32.6220 N.am 10 GLY404 -0.2664 BACKBONE|DICT|DIRECT + 203 CA -0.9050 -8.3300 32.7640 C.3 10 GLY404 0.1201 BACKBONE|DICT|DIRECT + 204 C -1.1430 -7.0140 32.0110 C.2 10 GLY404 0.2007 BACKBONE|DICT|DIRECT + 205 O -0.7900 -5.9570 32.5320 O.2 10 GLY404 -0.3947 BACKBONE|DICT|DIRECT + 206 N -1.6870 -7.1380 30.8500 N.am 11 LYS405 -0.2640 BACKBONE|DICT|DIRECT + 207 CA -1.9990 -5.9290 29.9900 C.3 11 LYS405 0.1310 BACKBONE|DICT|DIRECT + 208 C -3.0040 -5.0710 30.6970 C.2 11 LYS405 0.2039 BACKBONE|DICT|DIRECT + 209 O -2.8500 -3.8130 30.7650 O.2 11 LYS405 -0.3944 BACKBONE|DICT|DIRECT + 210 CB -2.5500 -6.3660 28.6750 C.3 11 LYS405 -0.0122 DICT + 211 CG -1.5670 -7.0010 27.8060 C.3 11 LYS405 -0.0440 DICT + 212 CD -2.2320 -7.4410 26.5110 C.3 11 LYS405 -0.0124 DICT + 213 CE -1.3860 -8.4270 25.7960 C.3 11 LYS405 -0.0354 DICT + 214 NZ -0.5130 -7.7360 24.8200 N.4 11 LYS405 0.2185 DICT + 215 N -4.0220 -5.6620 31.2310 N.am 12 MET406 -0.2637 BACKBONE|DICT|DIRECT + 216 CA -5.0950 -4.9250 31.9230 C.3 12 MET406 0.1317 BACKBONE|DICT|DIRECT + 217 C -4.5740 -4.3120 33.1850 C.2 12 MET406 0.2039 BACKBONE|DICT|DIRECT + 218 O -4.9610 -3.1770 33.5900 O.2 12 MET406 -0.3944 BACKBONE|DICT|DIRECT + 219 CB -6.3300 -5.7760 32.2290 C.3 12 MET406 -0.0034 DICT + 220 CG -7.0610 -6.2590 31.0130 C.3 12 MET406 -0.0024 DICT + 221 SD -7.6130 -4.9450 29.9020 S.3 12 MET406 -0.1639 DICT + 222 CE -6.3860 -4.8380 28.6450 C.3 12 MET406 -0.0181 DICT + 223 N -3.6880 -5.0070 33.8880 N.am 13 ALA407 -0.2640 BACKBONE|DICT|DIRECT + 224 CA -3.1290 -4.4890 35.1110 C.3 13 ALA407 0.1282 BACKBONE|DICT|DIRECT + 225 C -2.3960 -3.1590 34.8150 C.2 13 ALA407 0.2036 BACKBONE|DICT|DIRECT + 226 O -2.4440 -2.2060 35.5670 O.2 13 ALA407 -0.3944 BACKBONE|DICT|DIRECT + 227 CB -2.1990 -5.4990 35.8480 C.3 13 ALA407 -0.0244 DICT + 228 N -1.7230 -3.1560 33.6890 N.am 14 ARG408 -0.2637 BACKBONE|DICT|DIRECT + 229 CA -0.8880 -2.0230 33.2830 C.3 14 ARG408 0.1311 BACKBONE|DICT|DIRECT + 230 C -1.7880 -0.8100 33.0260 C.2 14 ARG408 0.2039 BACKBONE|DICT|DIRECT + 231 O -1.5070 0.2850 33.4770 O.2 14 ARG408 -0.3944 BACKBONE|DICT|DIRECT + 232 CB -0.0030 -2.3340 32.0630 C.3 14 ARG408 -0.0092 DICT + 233 CG 0.8420 -1.1440 31.6250 C.3 14 ARG408 -0.0156 DICT + 234 CD 1.6930 -1.4790 30.4210 C.3 14 ARG408 0.0627 DICT + 235 NE 1.8090 -0.2950 29.5830 N.pl3 14 ARG408 -0.2723 DICT + 236 CZ 2.5550 0.7620 29.8870 C.cat 14 ARG408 0.2882 DICT + 237 NH1 2.5890 1.7890 29.0600 N.pl3 14 ARG408 -0.2849 DICT + 238 NH2 3.2670 0.7930 31.0090 N.pl3 14 ARG408 -0.2849 DICT + 239 N -2.8790 -1.0290 32.3180 N.am 15 VAL409 -0.2635 BACKBONE|DICT|DIRECT + 240 CA -3.7200 0.0870 31.8530 C.3 15 VAL409 0.1333 BACKBONE|DICT|DIRECT + 241 C -4.7440 0.5430 32.8440 C.2 15 VAL409 0.2043 BACKBONE|DICT|DIRECT + 242 O -5.1800 1.7320 32.8080 O.2 15 VAL409 -0.3944 BACKBONE|DICT|DIRECT + 243 CB -4.2890 -0.1670 30.5220 C.3 15 VAL409 -0.0063 DICT + 244 CG1 -3.2210 -0.4690 29.4970 C.3 15 VAL409 -0.0584 DICT + 245 CG2 -5.3100 -1.1160 30.5700 C.3 15 VAL409 -0.0584 DICT + 246 N -5.1430 -0.3270 33.7460 N.am 16 PHE410 -0.2619 BACKBONE|DICT|DIRECT + 247 CA -6.0180 0.0910 34.8900 C.3 16 PHE410 0.1404 BACKBONE|DICT|DIRECT + 248 C -5.3340 0.4860 36.1550 C.2 16 PHE410 0.2055 BACKBONE|DICT|DIRECT + 249 O -5.8280 1.3190 36.9120 O.2 16 PHE410 -0.3942 BACKBONE|DICT|DIRECT + 250 CB -7.0260 -0.9470 35.3070 C.3 16 PHE410 0.0214 DICT + 251 CG -8.1730 -1.0060 34.4300 C.ar 16 PHE410 -0.0386 DICT + 252 CD1 -9.2550 -0.1360 34.5780 C.ar 16 PHE410 -0.0601 DICT + 253 CD2 -8.1840 -1.8940 33.4210 C.ar 16 PHE410 -0.0601 DICT + 254 CE1 -10.3290 -0.2080 33.7290 C.ar 16 PHE410 -0.0686 DICT + 255 CE2 -9.2100 -1.9750 32.5900 C.ar 16 PHE410 -0.0686 DICT + 256 CZ -10.3190 -1.1310 32.7110 C.ar 16 PHE410 -0.0687 DICT + 257 N -4.2000 -0.0980 36.4000 N.am 17 SER411 -0.2671 BACKBONE|DICT|DIRECT + 258 CA -3.5370 0.1010 37.6940 C.3 17 SER411 0.1173 BACKBONE|DICT|DIRECT + 259 C -2.0510 0.4310 37.5630 C.2 17 SER411 0.0623 BACKBONE|DICT|DIRECT + 260 O -1.5560 0.6640 36.4610 O.co2 17 SER411 -0.5665 BACKBONE|DICT|DIRECT + 261 CB -3.7570 -1.1350 38.5750 C.3 17 SER411 0.0789 DICT + 262 OG -3.2060 -2.2870 37.9660 O.3 17 SER411 -0.3910 DICT + 263 OXT -1.2930 0.4850 38.5420 O.co2 17 SER411 -0.5665 CAP|DICT + 264 H127 -0.6514 -2.6313 31.2256 H 14 ARG408 0.0313 + 265 H128 0.6690 -3.1661 32.3198 H 14 ARG408 0.0313 + 266 H129 1.4995 -0.8480 32.4557 H 14 ARG408 0.0301 + 267 H130 0.1751 -0.3075 31.3692 H 14 ARG408 0.0301 + 268 H131 1.2207 -2.2914 29.8492 H 14 ARG408 0.0689 + 269 H132 2.6927 -1.7967 30.7520 H 14 ARG408 0.0689 + 270 H133 1.2801 -0.2749 28.6994 H 14 ARG408 0.2642 + 271 H134 3.1639 2.6133 29.2859 H 14 ARG408 0.2615 + 272 H135 2.0407 1.7667 28.1883 H 14 ARG408 0.2615 + 273 H136 3.2425 -0.0074 31.6568 H 14 ARG408 0.2615 + 274 H137 3.8432 1.6175 31.2307 H 14 ARG408 0.2615 + 275 H138 -3.1394 -1.9680 32.0933 H 15 VAL409 0.1883 + 276 H139 -3.0354 0.9390 31.7286 H 15 VAL409 0.0802 + 277 H140 -4.7613 0.7730 30.2005 H 15 VAL409 0.0343 + 278 H141 -3.6919 -0.6517 28.5198 H 15 VAL409 0.0234 + 279 H142 -2.6586 -1.3625 29.8058 H 15 VAL409 0.0234 + 280 H143 -2.5350 0.3873 29.4190 H 15 VAL409 0.0234 + 281 H144 -6.0441 -0.8263 31.3363 H 15 VAL409 0.0234 + 282 H145 -4.8854 -2.0990 30.8220 H 15 VAL409 0.0234 + 283 H146 -5.8058 -1.1711 29.5896 H 15 VAL409 0.0234 + 284 H147 -4.8584 -1.2825 33.6678 H 16 PHE410 0.1885 + 285 H148 -6.5708 0.9712 34.5298 H 16 PHE410 0.0823 + 286 H149 -7.3738 -0.7093 36.3231 H 16 PHE410 0.0474 + 287 H150 -6.5351 -1.9314 35.3084 H 16 PHE410 0.0474 + 288 H151 -9.2457 0.6028 35.3712 H 16 PHE410 0.0557 + 289 H152 -7.3364 -2.5560 33.2858 H 16 PHE410 0.0557 + 290 H153 -11.1763 0.4555 33.8592 H 16 PHE410 0.0599 + 291 H154 -9.1910 -2.7130 31.7963 H 16 PHE410 0.0599 + 292 H155 -11.1500 -1.2033 32.0188 H 16 PHE410 0.0559 + 293 H156 -3.7788 -0.6831 35.7070 H 17 SER411 0.1876 + 294 H157 -4.0190 0.9586 38.1861 H 17 SER411 0.0749 + 295 H158 -4.8366 -1.2859 38.7226 H 17 SER411 0.0599 + 296 H159 -3.2725 -0.9749 39.5495 H 17 SER411 0.0599 + 297 H160 -3.3516 -3.0411 38.5251 H 17 SER411 0.2096 +@BOND + 1 127 1 1 + 2 127 2 1 + 3 127 3 1 + 4 128 4 1 + 5 131 5 1 + 6 132 6 1 + 7 132 7 1 + 8 132 8 1 + 9 133 9 1 + 10 133 10 1 + 11 133 11 1 + 12 134 12 1 + 13 135 13 1 + 14 138 14 1 + 15 139 15 1 + 16 139 16 1 + 17 140 17 1 + 18 140 18 1 + 19 140 19 1 + 20 141 20 1 + 21 141 21 1 + 22 141 22 1 + 23 142 23 1 + 24 143 24 1 + 25 146 25 1 + 26 146 26 1 + 27 147 27 1 + 28 147 28 1 + 29 148 29 1 + 30 148 30 1 + 31 149 31 1 + 32 151 32 1 + 33 151 33 1 + 34 152 34 1 + 35 152 35 1 + 36 153 36 1 + 37 154 37 1 + 38 157 38 1 + 39 157 39 1 + 40 160 40 1 + 41 160 41 1 + 42 161 42 1 + 43 162 43 1 + 44 165 44 1 + 45 165 45 1 + 46 166 46 1 + 47 166 47 1 + 48 167 48 1 + 49 167 49 1 + 50 168 50 1 + 51 168 51 1 + 52 169 52 1 + 53 169 53 1 + 54 169 54 1 + 55 170 55 1 + 56 171 56 1 + 57 174 57 1 + 58 175 58 1 + 59 175 59 1 + 60 176 60 1 + 61 176 61 1 + 62 176 62 1 + 63 177 63 1 + 64 177 64 1 + 65 177 65 1 + 66 178 66 1 + 67 179 67 1 + 68 182 68 1 + 69 182 69 1 + 70 183 70 1 + 71 183 71 1 + 72 184 72 1 + 73 184 73 1 + 74 185 74 1 + 75 187 75 1 + 76 187 76 1 + 77 188 77 1 + 78 188 78 1 + 79 189 79 1 + 80 190 80 1 + 81 193 81 1 + 82 193 82 1 + 83 193 83 1 + 84 194 84 1 + 85 195 85 1 + 86 198 86 1 + 87 199 87 1 + 88 199 88 1 + 89 200 89 1 + 90 200 90 1 + 91 200 91 1 + 92 201 92 1 + 93 201 93 1 + 94 201 94 1 + 95 202 95 1 + 96 203 96 1 + 97 203 97 1 + 98 206 98 1 + 99 207 99 1 + 100 210 100 1 + 101 210 101 1 + 102 211 102 1 + 103 211 103 1 + 104 212 104 1 + 105 212 105 1 + 106 213 106 1 + 107 213 107 1 + 108 214 108 1 + 109 214 109 1 + 110 214 110 1 + 111 215 111 1 + 112 216 112 1 + 113 219 113 1 + 114 219 114 1 + 115 220 115 1 + 116 220 116 1 + 117 222 117 1 + 118 222 118 1 + 119 222 119 1 + 120 223 120 1 + 121 224 121 1 + 122 227 122 1 + 123 227 123 1 + 124 227 124 1 + 125 128 127 1 BACKBONE|DICT + 126 128 131 1 DICT + 127 128 129 1 BACKBONE|DICT + 128 129 130 2 BACKBONE|DICT + 129 131 133 1 DICT + 130 131 132 1 DICT + 131 135 134 1 BACKBONE|DICT + 132 135 138 1 DICT + 133 135 136 1 BACKBONE|DICT + 134 136 137 2 BACKBONE|DICT + 135 138 140 1 DICT + 136 138 139 1 DICT + 137 139 141 1 DICT + 138 129 134 am BACKBONE|DICT|INTERRES + 139 143 142 1 BACKBONE|DICT + 140 143 146 1 DICT + 141 143 144 1 BACKBONE|DICT + 142 144 145 2 BACKBONE|DICT + 143 146 147 1 DICT + 144 147 148 1 DICT + 145 148 149 1 DICT + 146 149 150 ar DICT + 147 150 152 ar DICT + 148 150 151 ar DICT + 149 136 142 am BACKBONE|DICT|INTERRES + 150 154 153 1 BACKBONE|DICT + 151 154 157 1 DICT + 152 154 155 1 BACKBONE|DICT + 153 155 156 2 BACKBONE|DICT + 154 157 158 1 DICT + 155 158 160 am DICT + 156 158 159 2 DICT + 157 144 153 am BACKBONE|DICT|INTERRES + 158 162 161 1 BACKBONE|DICT + 159 162 165 1 DICT + 160 162 163 1 BACKBONE|DICT + 161 163 164 2 BACKBONE|DICT + 162 165 166 1 DICT + 163 166 167 1 DICT + 164 167 168 1 DICT + 165 168 169 1 DICT + 166 155 161 am BACKBONE|DICT|INTERRES + 167 171 170 1 BACKBONE|DICT + 168 171 174 1 DICT + 169 171 172 1 BACKBONE|DICT + 170 172 173 2 BACKBONE|DICT + 171 174 176 1 DICT + 172 174 175 1 DICT + 173 175 177 1 DICT + 174 163 170 am BACKBONE|DICT|INTERRES + 175 179 178 1 BACKBONE|DICT + 176 179 182 1 DICT + 177 179 180 1 BACKBONE|DICT + 178 180 181 2 BACKBONE|DICT + 179 182 183 1 DICT + 180 183 184 1 DICT + 181 184 185 1 DICT + 182 185 186 ar DICT + 183 186 188 ar DICT + 184 186 187 ar DICT + 185 172 178 am BACKBONE|DICT|INTERRES + 186 190 189 1 BACKBONE|DICT + 187 190 193 1 DICT + 188 190 191 1 BACKBONE|DICT + 189 191 192 2 BACKBONE|DICT + 190 180 189 am BACKBONE|DICT|INTERRES + 191 195 194 1 BACKBONE|DICT + 192 195 198 1 DICT + 193 195 196 1 BACKBONE|DICT + 194 196 197 2 BACKBONE|DICT + 195 198 200 1 DICT + 196 198 199 1 DICT + 197 199 201 1 DICT + 198 191 194 am BACKBONE|DICT|INTERRES + 199 203 202 1 BACKBONE|DICT + 200 203 204 1 BACKBONE|DICT + 201 204 205 2 BACKBONE|DICT + 202 196 202 am BACKBONE|DICT|INTERRES + 203 207 206 1 BACKBONE|DICT + 204 207 210 1 DICT + 205 207 208 1 BACKBONE|DICT + 206 208 209 2 BACKBONE|DICT + 207 210 211 1 DICT + 208 211 212 1 DICT + 209 212 213 1 DICT + 210 213 214 1 DICT + 211 204 206 am BACKBONE|DICT|INTERRES + 212 216 215 1 BACKBONE|DICT + 213 216 219 1 DICT + 214 216 217 1 BACKBONE|DICT + 215 217 218 2 BACKBONE|DICT + 216 219 220 1 DICT + 217 220 221 1 DICT + 218 221 222 1 DICT + 219 208 215 am BACKBONE|DICT|INTERRES + 220 224 223 1 BACKBONE|DICT + 221 224 227 1 DICT + 222 224 225 1 BACKBONE|DICT + 223 225 226 2 BACKBONE|DICT + 224 217 223 am BACKBONE|DICT|INTERRES + 225 229 228 1 BACKBONE|DICT + 226 229 232 1 DICT + 227 229 230 1 BACKBONE|DICT + 228 230 231 2 BACKBONE|DICT + 229 232 233 1 DICT + 230 233 234 1 DICT + 231 234 235 1 DICT + 232 235 236 ar DICT + 233 236 238 ar DICT + 234 236 237 ar DICT + 235 225 228 am BACKBONE|DICT|INTERRES + 236 240 239 1 BACKBONE|DICT + 237 240 243 1 DICT + 238 240 241 1 BACKBONE|DICT + 239 241 242 2 BACKBONE|DICT + 240 243 245 1 DICT + 241 243 244 1 DICT + 242 230 239 am BACKBONE|DICT|INTERRES + 243 247 246 1 BACKBONE|DICT + 244 247 250 1 DICT + 245 247 248 1 BACKBONE|DICT + 246 248 249 2 BACKBONE|DICT + 247 250 251 1 DICT + 248 251 252 ar DICT + 249 251 253 ar DICT + 250 253 255 ar DICT + 251 255 256 ar DICT + 252 256 254 ar DICT + 253 254 252 ar DICT + 254 241 246 am BACKBONE|DICT|INTERRES + 255 258 257 1 BACKBONE|DICT + 256 258 261 1 DICT + 257 258 259 1 BACKBONE|DICT + 258 259 260 ar BACKBONE|DICT + 259 259 263 ar CAP|DICT + 260 261 262 1 DICT + 261 248 257 am BACKBONE|DICT|INTERRES + 262 228 125 1 + 263 229 126 1 + 264 232 264 1 + 265 232 265 1 + 266 233 266 1 + 267 233 267 1 + 268 234 268 1 + 269 234 269 1 + 270 235 270 1 + 271 237 271 1 + 272 237 272 1 + 273 238 273 1 + 274 238 274 1 + 275 239 275 1 + 276 240 276 1 + 277 243 277 1 + 278 244 278 1 + 279 244 279 1 + 280 244 280 1 + 281 245 281 1 + 282 245 282 1 + 283 245 283 1 + 284 246 284 1 + 285 247 285 1 + 286 250 286 1 + 287 250 287 1 + 288 252 288 1 + 289 253 289 1 + 290 254 290 1 + 291 255 291 1 + 292 256 292 1 + 293 257 293 1 + 294 258 294 1 + 295 261 295 1 + 296 261 296 1 + 297 262 297 1 +@SUBSTRUCTURE + 1 VAL395 128 RESIDUE 4 L VAL 1 ROOT VAL L 395 + 2 ILE396 135 RESIDUE 4 L ILE 2 **** ILE L 396 + 3 ARG397 143 RESIDUE 4 L ARG 2 **** ARG L 397 + 4 ASN398 154 RESIDUE 4 L ASN 2 **** ASN L 398 + 5 LYS399 162 RESIDUE 4 L LYS 2 **** LYS L 399 + 6 ILE400 171 RESIDUE 4 L ILE 2 **** ILE L 400 + 7 ARG401 179 RESIDUE 4 L ARG 2 **** ARG L 401 + 8 ALA402 190 RESIDUE 4 L ALA 2 **** ALA L 402 + 9 ILE403 195 RESIDUE 4 L ILE 2 **** ILE L 403 + 10 GLY404 203 RESIDUE 4 L GLY 2 **** GLY L 404 + 11 LYS405 207 RESIDUE 4 L LYS 2 **** LYS L 405 + 12 MET406 216 RESIDUE 4 L MET 2 **** MET L 406 + 13 ALA407 224 RESIDUE 4 L ALA 2 **** ALA L 407 + 14 ARG408 229 RESIDUE 4 L ARG 2 **** ARG L 408 + 15 VAL409 240 RESIDUE 4 L VAL 2 **** VAL L 409 + 16 PHE410 247 RESIDUE 4 L PHE 2 **** PHE L 410 + 17 SER411 258 RESIDUE 4 L SER 1 **** SER L 411 +@SET +CHAIN_HEAD STATIC SUBSTS AMSOM **** +2 0 128 +CHAIN_TAIL STATIC SUBSTS AMSOM **** +2 0 258 diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index 21d7df7d42d..61e34009e10 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -115,7 +115,7 @@ "TRR_multi_frame", "merge_protein", "merge_ligand", "merge_water", "mol2_molecules", "mol2_molecule", "mol2_broken_molecule", - "mol2_zinc", "mol2_comments_header", + "mol2_zinc", "mol2_comments_header", "mol2_ligand", "capping_input", "capping_output", "capping_ace", "capping_nma", "contacts_villin_folded", "contacts_villin_unfolded", "contacts_file", "LAMMPSdata", "trz4data", "LAMMPSdata_mini", @@ -383,6 +383,7 @@ mol2_molecules = resource_filename(__name__, "data/mol2/Molecules.mol2") mol2_molecule = resource_filename(__name__, "data/mol2/Molecule.mol2") +mol2_ligand = resource_filename(__name__, "data/mol2/Ligand.mol2") mol2_broken_molecule = resource_filename(__name__, "data/mol2/BrokenMolecule.mol2") mol2_comments_header = resource_filename(__name__, "data/mol2/Molecule_comments_header.mol2") # MOL2 file without substructure field