From 773e9a2a56dfc305b75af8d73068f2d8fa59816a Mon Sep 17 00:00:00 2001 From: dcliebschner Date: Fri, 15 Mar 2024 10:10:54 -0700 Subject: [PATCH] Add test --- mmtbx/hydrogens/tst_add_hydrogen_3.py | 117 +++++++++++++++++++++++++- 1 file changed, 116 insertions(+), 1 deletion(-) diff --git a/mmtbx/hydrogens/tst_add_hydrogen_3.py b/mmtbx/hydrogens/tst_add_hydrogen_3.py index 0d9f3b75be..143fcf64a0 100644 --- a/mmtbx/hydrogens/tst_add_hydrogen_3.py +++ b/mmtbx/hydrogens/tst_add_hydrogen_3.py @@ -5,7 +5,6 @@ from mmtbx.hydrogens import reduce_hydrogen from mmtbx.hydrogens.tst_add_hydrogen import compare_models from libtbx.utils import null_out -#from libtbx.test_utils import approx_equal # ------------------------------------------------------------------------------ @@ -15,6 +14,7 @@ def run(): test_002() test_003() test_004() + test_005() # ------------------------------------------------------------------------------ @@ -119,6 +119,15 @@ def test_004(): # ------------------------------------------------------------------------------ +def test_005(): + ''' + Carbohydrate (BMA) forms covlalent link to ASN. Make sure valence is correct for + the NAG and protein links. This example is from Russel (6vw1). + ''' + compare_models(pdb_str = pdb_str_005) + +# ------------------------------------------------------------------------------ + pdb_str_000 = """ REMARK Make sure reduce does not crash for single_atom_residue models CRYST1 22.029 33.502 24.035 90.00 90.00 90.00 P 1 @@ -483,6 +492,112 @@ def test_004(): END """ +pdb_str_005 = """ +CRYST1 80.435 118.034 112.075 90.00 93.12 90.00 P 1 21 1 +SCALE1 0.012432 0.000000 0.000678 0.00000 +SCALE2 0.000000 0.008472 0.000000 0.00000 +SCALE3 0.000000 0.000000 0.008936 0.00000 +ATOM 1 N ASN A 90 76.017 -20.785 155.731 1.00 -1.00 N +ANISOU 1 N ASN A 90 17156 21970 15197 -6703 124 870 N +ATOM 2 CA ASN A 90 75.942 -19.415 156.227 1.00 -1.00 C +ANISOU 2 CA ASN A 90 17577 22797 16129 -6189 29 1252 C +ATOM 3 C ASN A 90 77.350 -18.831 156.235 1.00 -1.00 C +ANISOU 3 C ASN A 90 17170 21823 15645 -5768 103 1134 C +ATOM 4 O ASN A 90 78.239 -19.359 156.912 1.00 -1.00 O +ANISOU 4 O ASN A 90 17802 21588 16095 -5569 283 881 O +ATOM 5 CB ASN A 90 75.320 -19.390 157.626 1.00 -1.00 C +ANISOU 5 CB ASN A 90 18758 23893 17672 -5918 105 1419 C +ATOM 6 CG ASN A 90 75.068 -17.982 158.153 1.00 -1.00 C +ANISOU 6 CG ASN A 90 19640 25239 19120 -5436 46 1805 C +ATOM 7 OD1 ASN A 90 75.922 -17.100 158.061 1.00 -1.00 O +ANISOU 7 OD1 ASN A 90 18832 24282 18399 -5077 50 1839 O +ATOM 8 ND2 ASN A 90 73.886 -17.776 158.730 1.00 -1.00 N +ANISOU 8 ND2 ASN A 90 21686 27829 21572 -5430 16 2088 N +ATOM 9 H ASN A 90 76.270 -20.847 154.911 1.00142.97 H +ATOM 10 HA ASN A 90 75.375 -18.865 155.664 1.00148.71 H +ATOM 11 HB2 ASN A 90 75.921 -19.835 158.244 1.00158.76 H +ATOM 12 HB3 ASN A 90 74.468 -19.854 157.599 1.00158.76 H +ATOM 13 HD21 ASN A 90 73.315 -18.418 158.763 1.00187.09 H +TER +HETATM 15 C1 NAG C 1 73.523 -16.504 159.309 1.00103.52 C +HETATM 16 C2 NAG C 1 72.427 -15.749 158.564 1.00114.27 C +HETATM 17 C3 NAG C 1 72.112 -14.434 159.280 1.00117.99 C +HETATM 18 C4 NAG C 1 71.829 -14.658 160.763 1.00124.42 C +HETATM 19 C5 NAG C 1 72.930 -15.509 161.403 1.00121.57 C +HETATM 20 C6 NAG C 1 72.619 -15.937 162.820 1.00122.81 C +HETATM 21 C7 NAG C 1 71.992 -15.651 156.147 1.00125.03 C +HETATM 22 C8 NAG C 1 72.570 -15.344 154.798 1.00127.15 C +HETATM 23 N2 NAG C 1 72.819 -15.497 157.186 1.00121.51 N +HETATM 24 O3 NAG C 1 70.990 -13.814 158.662 1.00116.89 O +HETATM 25 O4 NAG C 1 71.791 -13.386 161.404 1.00133.35 O +HETATM 26 O5 NAG C 1 73.123 -16.717 160.654 1.00114.93 O +HETATM 27 O6 NAG C 1 73.745 -15.787 163.673 1.00121.65 O +HETATM 28 O7 NAG C 1 70.831 -16.020 156.289 1.00125.47 O +HETATM 29 H1 NAG C 1 74.336 -15.975 159.299 1.00103.52 H +HETATM 30 H2 NAG C 1 71.632 -16.305 158.561 1.00114.27 H +HETATM 31 H3 NAG C 1 72.914 -13.895 159.195 1.00117.99 H +HETATM 32 H4 NAG C 1 70.979 -15.124 160.802 1.00124.42 H +HETATM 33 H5 NAG C 1 73.736 -14.970 161.406 1.00121.57 H +HETATM 34 H61 NAG C 1 71.867 -15.409 163.130 1.00122.81 H +HETATM 35 H62 NAG C 1 72.316 -16.858 162.792 1.00122.81 H +HETATM 36 H81 NAG C 1 73.509 -15.120 154.894 1.00127.15 H +HETATM 37 H82 NAG C 1 72.095 -14.593 154.409 1.00127.15 H +HETATM 38 H83 NAG C 1 72.477 -16.121 154.225 1.00127.15 H +HETATM 39 HN2 NAG C 1 73.625 -15.236 157.040 1.00121.51 H +HETATM 41 HO3 NAG C 1 70.851 -13.074 159.056 1.00116.89 H +HETATM 43 HO6 NAG C 1 74.400 -16.202 163.325 1.00121.65 H +HETATM 44 C1 NAG C 2 70.691 -13.209 162.330 1.00143.22 C +HETATM 45 C2 NAG C 2 71.046 -12.013 163.217 1.00149.90 C +HETATM 46 C3 NAG C 2 69.929 -11.751 164.223 1.00153.90 C +HETATM 47 C4 NAG C 2 68.594 -11.600 163.506 1.00157.09 C +HETATM 48 C5 NAG C 2 68.339 -12.806 162.605 1.00152.27 C +HETATM 49 C6 NAG C 2 67.082 -12.672 161.777 1.00151.75 C +HETATM 50 C7 NAG C 2 73.401 -11.485 163.670 1.00150.52 C +HETATM 51 C8 NAG C 2 74.621 -11.843 164.465 1.00149.56 C +HETATM 52 N2 NAG C 2 72.312 -12.226 163.901 1.00151.39 N +HETATM 53 O3 NAG C 2 70.226 -10.571 164.961 1.00153.21 O +HETATM 54 O4 NAG C 2 67.540 -11.490 164.456 1.00163.16 O +HETATM 55 O5 NAG C 2 69.429 -12.972 161.684 1.00147.83 O +HETATM 56 O6 NAG C 2 67.313 -11.906 160.602 1.00151.36 O +HETATM 57 O7 NAG C 2 73.402 -10.566 162.856 1.00149.17 O +HETATM 58 H1 NAG C 2 70.621 -14.004 162.882 1.00143.22 H +HETATM 59 H2 NAG C 2 71.140 -11.238 162.641 1.00149.90 H +HETATM 60 H3 NAG C 2 69.893 -12.528 164.802 1.00153.90 H +HETATM 61 H4 NAG C 2 68.684 -10.788 162.984 1.00157.09 H +HETATM 62 H5 NAG C 2 68.256 -13.586 163.175 1.00152.27 H +HETATM 63 H61 NAG C 2 66.399 -12.268 162.336 1.00151.75 H +HETATM 64 H62 NAG C 2 66.770 -13.565 161.563 1.00151.75 H +HETATM 65 H81 NAG C 2 74.432 -12.623 165.009 1.00149.56 H +HETATM 66 H82 NAG C 2 74.862 -11.097 165.037 1.00149.56 H +HETATM 67 H83 NAG C 2 75.353 -12.038 163.859 1.00149.56 H +HETATM 68 HN2 NAG C 2 72.354 -12.860 164.480 1.00151.39 H +HETATM 70 HO3 NAG C 2 70.256 -9.922 164.413 1.00153.21 H +HETATM 72 HO6 NAG C 2 67.657 -11.163 160.832 1.00151.36 H +HETATM 73 C1 BMA C 3 67.036 -10.135 164.465 1.00164.84 C +HETATM 74 C2 BMA C 3 65.513 -10.187 164.205 1.00164.51 C +HETATM 75 C3 BMA C 3 64.912 -8.784 164.326 1.00164.84 C +HETATM 76 C4 BMA C 3 65.353 -8.085 165.626 1.00165.75 C +HETATM 77 C5 BMA C 3 66.886 -8.117 165.760 1.00164.34 C +HETATM 78 C6 BMA C 3 67.377 -7.517 167.067 1.00159.95 C +HETATM 79 O2 BMA C 3 64.864 -10.998 165.174 1.00162.15 O +HETATM 80 O3 BMA C 3 63.491 -8.819 164.251 1.00162.71 O +HETATM 81 O4 BMA C 3 64.902 -6.737 165.632 1.00164.98 O +HETATM 82 O5 BMA C 3 67.321 -9.489 165.704 1.00164.62 O +HETATM 83 O6 BMA C 3 66.718 -6.271 167.265 1.00154.88 O +HETATM 84 H1 BMA C 3 67.454 -9.653 163.734 1.00164.84 H +HETATM 85 H2 BMA C 3 65.448 -10.536 163.302 1.00164.51 H +HETATM 86 H3 BMA C 3 65.260 -8.317 163.550 1.00164.84 H +HETATM 87 H4 BMA C 3 64.914 -8.536 166.365 1.00165.75 H +HETATM 88 H5 BMA C 3 67.297 -7.591 165.056 1.00164.34 H +HETATM 89 H61 BMA C 3 67.191 -8.125 167.800 1.00159.95 H +HETATM 90 H62 BMA C 3 68.339 -7.396 167.035 1.00159.95 H +HETATM 92 HO2 BMA C 3 65.200 -10.810 165.932 1.00162.15 H +HETATM 93 HO3 BMA C 3 63.182 -9.145 164.973 1.00162.71 H +HETATM 94 HO4 BMA C 3 65.175 -6.362 166.344 1.00164.98 H +HETATM 95 HO6 BMA C 3 65.881 -6.399 167.190 1.00154.88 H +END +""" + # ------------------------------------------------------------------------------ if (__name__ == "__main__"):