diff --git a/package/CHANGELOG b/package/CHANGELOG index 645a561a3ef..a283ff2fed5 100644 --- a/package/CHANGELOG +++ b/package/CHANGELOG @@ -91,6 +91,8 @@ Fixes * Fixed documentation of MDAnalysis.analysis.contacts * Enforced consistent dtype (numpy.float32) of Universe.dimensions and Timestep.dimensions for all Universes and Readers (Issue #2190, PR #2213) + * Fixed analysis.nucleic.hydroxyl() function: correctly recognize the + 2'-hydroxyl hydrogen H2'; gave wrong results (Issue #2218) Deprecations * analysis.polymer.PersistenceLength no longer requires the perform_fit() diff --git a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py index b707e329d49..c8918c34955 100644 --- a/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py +++ b/testsuite/MDAnalysisTests/analysis/test_nuclinfo.py @@ -25,7 +25,7 @@ import MDAnalysis as mda import pytest from MDAnalysis.analysis import nuclinfo -from MDAnalysisTests.datafiles import NUCL +from MDAnalysisTests.datafiles import RNA_PSF, RNA_PDB from numpy.testing import ( assert_almost_equal, assert_allclose, @@ -34,12 +34,12 @@ @pytest.fixture(scope='module') def u(): - return mda.Universe(NUCL) + return mda.Universe(RNA_PSF, RNA_PDB) @pytest.mark.parametrize('i, bp, seg1, seg2, expected_value', ( - (1, 2, 'RNAA', 'RNAA', 4.449), - (22, 23, 'RNAA', 'RNAA', 4.601) + ( 1, 2, 'RNAA', 'RNAA', 4.3874702), + (22, 23, 'RNAA', 'RNAA', 4.1716404), )) def test_wc_pair(u, i, bp, seg1, seg2, expected_value): val = nuclinfo.wc_pair(u, i, bp, seg1=seg1, seg2=seg2) @@ -47,8 +47,8 @@ def test_wc_pair(u, i, bp, seg1, seg2, expected_value): @pytest.mark.parametrize('i, bp, seg1, seg2, expected_value', ( - (3, 17, 'RNAA', 'RNAA', 16.649), - (20, 5, 'RNAA', 'RNAA', 4.356) + ( 3, 17, 'RNAA', 'RNAA', 15.06506), + (20, 5, 'RNAA', 'RNAA', 3.219116), )) def test_minor_pair(u, i, bp, seg1, seg2, expected_value): val = nuclinfo.minor_pair(u, i, bp, seg1=seg1, seg2=seg2) @@ -56,8 +56,8 @@ def test_minor_pair(u, i, bp, seg1, seg2, expected_value): @pytest.mark.parametrize('i, bp, seg1, seg2, expected_value', ( - (2, 12, 'RNAA', 'RNAA', 30.001), - (5, 9, 'RNAA', 'RNAA', 12.581) + (2, 12, 'RNAA', 'RNAA', 26.884272), + (5, 9, 'RNAA', 'RNAA', 13.578535), )) def test_major_pair(u, i, bp, seg1, seg2, expected_value): val = nuclinfo.major_pair(u, i, bp, seg1=seg1, seg2=seg2) @@ -65,8 +65,8 @@ def test_major_pair(u, i, bp, seg1, seg2, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 9, 14.846), - ('RNAA', 21, 16.199) + ('RNAA', 9, 3.16497), + ('RNAA', 21, 22.07721), )) def test_phase_cp(u, seg, i, expected_value): val = nuclinfo.phase_cp(u, seg=seg, i=i) @@ -74,8 +74,8 @@ def test_phase_cp(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 1, 8.565), - ('RNAA', 11, 151.397) + ('RNAA', 1, 359.57580), + ('RNAA', 11, 171.71645), )) def test_phase_as(u, seg, i, expected_value): val = nuclinfo.phase_as(u, seg=seg, i=i) @@ -83,10 +83,10 @@ def test_phase_as(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 5, [296.103016, 179.084427, 47.712818, 81.49588, 205.350479, - 284.046562, 198.58165]), - ('RNAA', 21, [300.047634, 172.476593, 50.744877, 82.144211, 206.106445, - 286.208565, 195.652176]) + ('RNAA', 5, [302.203802, 179.043077, 35.271411, 79.499729, 201.000393, + 282.14321 , 210.709327]), + ('RNAA', 21, [280.388619, 185.12919 , 56.616215, 64.87354 , 187.153367, + 279.340915, 215.332144]), )) def test_tors(u, seg, i, expected_value): val = nuclinfo.tors(u, seg=seg, i=i) @@ -94,8 +94,8 @@ def test_tors(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 6, 299.278), - ('RNAA', 18, 304.093) + ('RNAA', 6, 279.15103), + ('RNAA', 18, 298.09936), )) def test_tors_alpha(u, seg, i, expected_value): val = nuclinfo.tors_alpha(u, seg=seg, i=i) @@ -103,8 +103,8 @@ def test_tors_alpha(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 7, 177.041), - ('RNAA', 15, 162.441) + ('RNAA', 7, 184.20501), + ('RNAA', 15, 169.70042), )) def test_tors_beta(u, seg, i, expected_value): val = nuclinfo.tors_beta(u, seg=seg, i=i) @@ -112,8 +112,8 @@ def test_tors_beta(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 7, 47.201), - ('RNAA', 15, 64.276) + ('RNAA', 7, 52.72022), + ('RNAA', 15, 54.59684), )) def test_tors_gamma(u, seg, i, expected_value): val = nuclinfo.tors_gamma(u, seg=seg, i=i) @@ -121,8 +121,8 @@ def test_tors_gamma(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 7, 80.223), - ('RNAA', 15, 81.553) + ('RNAA', 7, 84.80554), + ('RNAA', 15, 82.00043), )) def test_tors_delta(u, seg, i, expected_value): val = nuclinfo.tors_delta(u, seg=seg, i=i) @@ -130,8 +130,8 @@ def test_tors_delta(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 7, 207.476), - ('RNAA', 15, 202.352) + ('RNAA', 7, 200.40990), + ('RNAA', 15, 210.96953), )) def test_tors_eps(u, seg, i, expected_value): val = nuclinfo.tors_eps(u, seg=seg, i=i) @@ -139,8 +139,8 @@ def test_tors_eps(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 7, 289.429), - ('RNAA', 15, 289.318) + ('RNAA', 7, 297.84736), + ('RNAA', 15, 330.24898) )) def test_tors_zeta(u, seg, i, expected_value): val = nuclinfo.tors_zeta(u, seg=seg, i=i) @@ -148,8 +148,10 @@ def test_tors_zeta(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 1, 198.601), - ('RNAA', 2, 198.932) + ('RNAA', 1, 177.12643), + ('RNAA', 2, 212.08998), + ('RNAA', 7, 209.56533), + ('RNAA', 15, 209.32109), )) def test_tors_chi(u, seg, i, expected_value): val = nuclinfo.tors_chi(u, seg=seg, i=i) @@ -157,8 +159,10 @@ def test_tors_chi(u, seg, i, expected_value): @pytest.mark.parametrize('seg, i, expected_value', ( - ('RNAA', 20, 122.689), - ('RNAA', 5, 122.965) + ('RNAA', 20, 103.07024), + ('RNAA', 5, 156.62223), + ('RNAA', 7 , 77.94538), + ('RNAA', 15, 130.18539), )) def test_hydroxyl(u, seg, i, expected_value): val = nuclinfo.hydroxyl(u, seg=seg, i=i) @@ -166,8 +170,8 @@ def test_hydroxyl(u, seg, i, expected_value): @pytest.mark.parametrize('bp1, bp2, i, seg1, seg2, seg3, expected_value', ( - (16, 2, 3, 'RNAA', 'RNAA', 'RNAA', 308.244), - (8, 9, 10, 'RNAA', 'RNAA', 'RNAA', 25.224), + (16, 2, 3, 'RNAA', 'RNAA', 'RNAA', 314.69804), + (8, 9, 10, 'RNAA', 'RNAA', 'RNAA', 34.50106), )) def test_pseudo_dihe_baseflip(u, bp1, bp2, i, seg1, seg2, seg3, expected_value): val = nuclinfo.pseudo_dihe_baseflip(u, bp1, bp2, i, seg1, seg2, seg3) diff --git a/testsuite/MDAnalysisTests/core/test_atomselections.py b/testsuite/MDAnalysisTests/core/test_atomselections.py index 537d8739a84..b18af932db1 100644 --- a/testsuite/MDAnalysisTests/core/test_atomselections.py +++ b/testsuite/MDAnalysisTests/core/test_atomselections.py @@ -42,7 +42,7 @@ PSF, DCD, PRMpbc, TRJpbc_bz2, PSF_NAMD, PDB_NAMD, - GRO, NUCL, NUCLsel, TPR, XTC, + GRO, RNA_PSF, NUCLsel, TPR, XTC, TRZ_psf, TRZ, PDB_icodes, PDB_HOLE, @@ -449,20 +449,22 @@ def test_molnum(self, universe, selection_string, reference): class TestSelectionsNucleicAcids(object): - @pytest.fixture() + @pytest.fixture(scope='class') def universe(self): - return MDAnalysis.Universe(NUCL) + return MDAnalysis.Universe(RNA_PSF) + + @pytest.fixture(scope='class') + def universe2(self): + return MDAnalysis.Universe(NUCLsel) + def test_nucleic(self, universe): rna = universe.select_atoms("nucleic") assert_equal(rna.n_atoms, 739) assert_equal(rna.n_residues, 23) - def test_nucleic_all(self, universe): - u = mda.Universe(NUCLsel) - - sel = u.select_atoms('nucleic') - + def test_nucleic_all(self, universe2): + sel = universe2.select_atoms('nucleic') assert len(sel) == 34 def test_nucleicbackbone(self, universe): diff --git a/testsuite/MDAnalysisTests/data/1k5i.pdb b/testsuite/MDAnalysisTests/data/1k5i.pdb deleted file mode 100644 index 00d64486914..00000000000 --- a/testsuite/MDAnalysisTests/data/1k5i.pdb +++ /dev/null @@ -1,739 +0,0 @@ -ATOM 1 H5T GUA 1 7.974 6.430 9.561 1.00 0.00 RNAA -ATOM 2 O5' GUA 1 8.440 6.906 8.870 1.00 0.00 RNAA -ATOM 3 C5' GUA 1 8.311 8.289 9.189 1.00 0.00 RNAA -ATOM 4 H5' GUA 1 8.751 8.483 10.167 1.00 0.00 RNAA -ATOM 5 H5'' GUA 1 7.258 8.569 9.214 1.00 0.00 RNAA -ATOM 6 C4' GUA 1 9.016 9.132 8.153 1.00 0.00 RNAA -ATOM 7 H4' GUA 1 8.736 10.171 8.326 1.00 0.00 RNAA -ATOM 8 O4' GUA 1 10.447 8.893 8.241 1.00 0.00 RNAA -ATOM 9 C1' GUA 1 11.013 8.887 6.946 1.00 0.00 RNAA -ATOM 10 H1' GUA 1 11.844 9.592 6.958 1.00 0.00 RNAA -ATOM 11 N9 GUA 1 11.554 7.557 6.683 1.00 0.00 RNAA -ATOM 12 C4 GUA 1 12.378 7.199 5.643 1.00 0.00 RNAA -ATOM 13 N2 GUA 1 14.168 8.054 2.793 1.00 0.00 RNAA -ATOM 14 H21 GUA 1 14.781 7.562 2.159 1.00 0.00 RNAA -ATOM 15 H22 GUA 1 13.988 9.043 2.682 1.00 0.00 RNAA -ATOM 16 N3 GUA 1 12.842 8.021 4.677 1.00 0.00 RNAA -ATOM 17 C2 GUA 1 13.617 7.384 3.815 1.00 0.00 RNAA -ATOM 18 N1 GUA 1 13.912 6.044 3.888 1.00 0.00 RNAA -ATOM 19 H1 GUA 1 14.513 5.631 3.189 1.00 0.00 RNAA -ATOM 20 C6 GUA 1 13.443 5.180 4.871 1.00 0.00 RNAA -ATOM 21 O6 GUA 1 13.766 3.986 4.840 1.00 0.00 RNAA -ATOM 22 C5 GUA 1 12.613 5.850 5.807 1.00 0.00 RNAA -ATOM 23 N7 GUA 1 11.952 5.368 6.929 1.00 0.00 RNAA -ATOM 24 C8 GUA 1 11.342 6.414 7.416 1.00 0.00 RNAA -ATOM 25 H8 GUA 1 10.735 6.383 8.309 1.00 0.00 RNAA -ATOM 26 C2' GUA 1 9.918 9.307 5.968 1.00 0.00 RNAA -ATOM 27 H2'' GUA 1 10.046 8.745 5.018 1.00 0.00 RNAA -ATOM 28 O2' GUA 1 9.928 10.716 5.858 1.00 0.00 RNAA -ATOM 29 H2' GUA 1 10.022 8.806 5.005 1.00 0.00 RNAA -ATOM 30 C3' GUA 1 8.674 8.817 6.702 1.00 0.00 RNAA -ATOM 31 H3' GUA 1 8.494 7.753 6.552 1.00 0.00 RNAA -ATOM 32 O3' GUA 1 7.490 9.486 6.282 1.00 0.00 RNAA -ATOM 33 P GUA 2 6.525 8.797 5.198 1.00 0.00 RNAA -ATOM 34 O1P GUA 2 5.252 9.560 5.159 1.00 0.00 RNAA -ATOM 35 O2P GUA 2 6.497 7.341 5.491 1.00 0.00 RNAA -ATOM 36 O5' GUA 2 7.284 9.013 3.814 1.00 0.00 RNAA -ATOM 37 C5' GUA 2 7.629 10.321 3.367 1.00 0.00 RNAA -ATOM 38 H5' GUA 2 8.176 10.845 4.150 1.00 0.00 RNAA -ATOM 39 H5'' GUA 2 6.723 10.880 3.133 1.00 0.00 RNAA -ATOM 40 C4' GUA 2 8.488 10.242 2.128 1.00 0.00 RNAA -ATOM 41 H4' GUA 2 8.539 11.241 1.695 1.00 0.00 RNAA -ATOM 42 O4' GUA 2 9.788 9.695 2.479 1.00 0.00 RNAA -ATOM 43 C1' GUA 2 10.281 8.915 1.408 1.00 0.00 RNAA -ATOM 44 H1' GUA 2 11.248 9.332 1.129 1.00 0.00 RNAA -ATOM 45 N9 GUA 2 10.501 7.555 1.889 1.00 0.00 RNAA -ATOM 46 C4 GUA 2 11.196 6.563 1.237 1.00 0.00 RNAA -ATOM 47 N2 GUA 2 13.015 5.485 -1.513 1.00 0.00 RNAA -ATOM 48 H21 GUA 2 13.494 4.632 -1.768 1.00 0.00 RNAA -ATOM 49 H22 GUA 2 13.027 6.294 -2.118 1.00 0.00 RNAA -ATOM 50 N3 GUA 2 11.788 6.671 0.029 1.00 0.00 RNAA -ATOM 51 C2 GUA 2 12.385 5.548 -0.331 1.00 0.00 RNAA -ATOM 52 N1 GUA 2 12.403 4.406 0.432 1.00 0.00 RNAA -ATOM 53 H1 GUA 2 12.890 3.592 0.088 1.00 0.00 RNAA -ATOM 54 C6 GUA 2 11.793 4.271 1.675 1.00 0.00 RNAA -ATOM 55 O6 GUA 2 11.861 3.191 2.273 1.00 0.00 RNAA -ATOM 56 C5 GUA 2 11.149 5.470 2.078 1.00 0.00 RNAA -ATOM 57 N7 GUA 2 10.436 5.766 3.231 1.00 0.00 RNAA -ATOM 58 C8 GUA 2 10.071 7.009 3.074 1.00 0.00 RNAA -ATOM 59 H8 GUA 2 9.484 7.552 3.800 1.00 0.00 RNAA -ATOM 60 C2' GUA 2 9.271 9.007 0.265 1.00 0.00 RNAA -ATOM 61 H2'' GUA 2 9.196 8.014 -0.230 1.00 0.00 RNAA -ATOM 62 O2' GUA 2 9.638 10.086 -0.571 1.00 0.00 RNAA -ATOM 63 H2' GUA 2 9.187 8.064 -0.275 1.00 0.00 RNAA -ATOM 64 C3' GUA 2 7.988 9.309 1.031 1.00 0.00 RNAA -ATOM 65 H3' GUA 2 7.526 8.413 1.445 1.00 0.00 RNAA -ATOM 66 O3' GUA 2 6.996 9.931 0.221 1.00 0.00 RNAA -ATOM 67 P ADE 3 5.920 9.027 -0.558 1.00 0.00 RNAA -ATOM 68 O1P ADE 3 4.920 9.931 -1.181 1.00 0.00 RNAA -ATOM 69 O2P ADE 3 5.465 7.962 0.370 1.00 0.00 RNAA -ATOM 70 O5' ADE 3 6.763 8.339 -1.720 1.00 0.00 RNAA -ATOM 71 C5' ADE 3 7.364 9.119 -2.752 1.00 0.00 RNAA -ATOM 72 H5' ADE 3 8.077 9.817 -2.315 1.00 0.00 RNAA -ATOM 73 H5'' ADE 3 6.596 9.683 -3.282 1.00 0.00 RNAA -ATOM 74 C4' ADE 3 8.079 8.224 -3.734 1.00 0.00 RNAA -ATOM 75 H4' ADE 3 8.326 8.826 -4.609 1.00 0.00 RNAA -ATOM 76 O4' ADE 3 9.241 7.637 -3.088 1.00 0.00 RNAA -ATOM 77 C1' ADE 3 9.431 6.316 -3.556 1.00 0.00 RNAA -ATOM 78 H1' ADE 3 10.451 6.257 -3.935 1.00 0.00 RNAA -ATOM 79 N9 ADE 3 9.317 5.402 -2.420 1.00 0.00 RNAA -ATOM 80 C5 ADE 3 9.434 3.642 -1.107 1.00 0.00 RNAA -ATOM 81 N7 ADE 3 8.831 4.644 -0.360 1.00 0.00 RNAA -ATOM 82 C8 ADE 3 8.782 5.663 -1.183 1.00 0.00 RNAA -ATOM 83 H8 ADE 3 8.351 6.617 -0.916 1.00 0.00 RNAA -ATOM 84 N1 ADE 3 10.359 1.575 -1.775 1.00 0.00 RNAA -ATOM 85 C2 ADE 3 10.587 2.150 -2.963 1.00 0.00 RNAA -ATOM 86 H2 ADE 3 11.053 1.508 -3.710 1.00 0.00 RNAA -ATOM 87 N3 ADE 3 10.320 3.390 -3.364 1.00 0.00 RNAA -ATOM 88 C4 ADE 3 9.737 4.094 -2.379 1.00 0.00 RNAA -ATOM 89 C6 ADE 3 9.772 2.311 -0.805 1.00 0.00 RNAA -ATOM 90 N6 ADE 3 9.544 1.742 0.381 1.00 0.00 RNAA -ATOM 91 H61 ADE 3 9.802 0.779 0.541 1.00 0.00 RNAA -ATOM 92 H62 ADE 3 9.107 2.278 1.118 1.00 0.00 RNAA -ATOM 93 C2' ADE 3 8.399 6.066 -4.655 1.00 0.00 RNAA -ATOM 94 H2'' ADE 3 8.046 5.015 -4.585 1.00 0.00 RNAA -ATOM 95 O2' ADE 3 8.963 6.447 -5.894 1.00 0.00 RNAA -ATOM 96 H2' ADE 3 8.047 5.034 -4.649 1.00 0.00 RNAA -ATOM 97 C3' ADE 3 7.288 7.022 -4.233 1.00 0.00 RNAA -ATOM 98 H3' ADE 3 6.652 6.606 -3.450 1.00 0.00 RNAA -ATOM 99 O3' ADE 3 6.421 7.361 -5.309 1.00 0.00 RNAA -ATOM 100 P CYT 4 5.106 6.479 -5.583 1.00 0.00 RNAA -ATOM 101 O1P CYT 4 4.339 7.152 -6.662 1.00 0.00 RNAA -ATOM 102 O2P CYT 4 4.446 6.194 -4.284 1.00 0.00 RNAA -ATOM 103 O5' CYT 4 5.673 5.107 -6.159 1.00 0.00 RNAA -ATOM 104 C5' CYT 4 6.384 5.068 -7.394 1.00 0.00 RNAA -ATOM 105 H5' CYT 4 7.246 5.733 -7.342 1.00 0.00 RNAA -ATOM 106 H5'' CYT 4 5.732 5.395 -8.205 1.00 0.00 RNAA -ATOM 107 C4' CYT 4 6.856 3.663 -7.682 1.00 0.00 RNAA -ATOM 108 H4' CYT 4 7.204 3.637 -8.715 1.00 0.00 RNAA -ATOM 109 O4' CYT 4 7.879 3.293 -6.718 1.00 0.00 RNAA -ATOM 110 C1' CYT 4 7.793 1.909 -6.443 1.00 0.00 RNAA -ATOM 111 H1' CYT 4 8.765 1.476 -6.680 1.00 0.00 RNAA -ATOM 112 N1 CYT 4 7.559 1.731 -5.002 1.00 0.00 RNAA -ATOM 113 C6 CYT 4 7.098 2.762 -4.232 1.00 0.00 RNAA -ATOM 114 H6 CYT 4 6.899 3.731 -4.690 1.00 0.00 RNAA -ATOM 115 C5 CYT 4 6.883 2.603 -2.920 1.00 0.00 RNAA -ATOM 116 H5 CYT 4 6.527 3.426 -2.301 1.00 0.00 RNAA -ATOM 117 C2 CYT 4 7.815 0.483 -4.428 1.00 0.00 RNAA -ATOM 118 O2 CYT 4 8.239 -0.434 -5.146 1.00 0.00 RNAA -ATOM 119 N3 CYT 4 7.597 0.303 -3.105 1.00 0.00 RNAA -ATOM 120 C4 CYT 4 7.144 1.317 -2.363 1.00 0.00 RNAA -ATOM 121 N4 CYT 4 6.937 1.095 -1.063 1.00 0.00 RNAA -ATOM 122 H41 CYT 4 7.113 0.175 -0.686 1.00 0.00 RNAA -ATOM 123 H42 CYT 4 6.594 1.832 -0.464 1.00 0.00 RNAA -ATOM 124 C2' CYT 4 6.682 1.331 -7.319 1.00 0.00 RNAA -ATOM 125 H2'' CYT 4 6.124 0.568 -6.735 1.00 0.00 RNAA -ATOM 126 O2' CYT 4 7.254 0.882 -8.530 1.00 0.00 RNAA -ATOM 127 H2' CYT 4 6.126 0.551 -6.800 1.00 0.00 RNAA -ATOM 128 C3' CYT 4 5.812 2.564 -7.538 1.00 0.00 RNAA -ATOM 129 H3' CYT 4 5.138 2.754 -6.702 1.00 0.00 RNAA -ATOM 130 O3' CYT 4 4.990 2.455 -8.695 1.00 0.00 RNAA -ATOM 131 P CYT 5 3.506 1.851 -8.566 1.00 0.00 RNAA -ATOM 132 O1P CYT 5 2.836 2.047 -9.877 1.00 0.00 RNAA -ATOM 133 O2P CYT 5 2.878 2.393 -7.333 1.00 0.00 RNAA -ATOM 134 O5' CYT 5 3.741 0.290 -8.357 1.00 0.00 RNAA -ATOM 135 C5' CYT 5 4.348 -0.499 -9.377 1.00 0.00 RNAA -ATOM 136 H5' CYT 5 5.338 -0.106 -9.605 1.00 0.00 RNAA -ATOM 137 H5'' CYT 5 3.737 -0.467 -10.280 1.00 0.00 RNAA -ATOM 138 C4' CYT 5 4.476 -1.934 -8.924 1.00 0.00 RNAA -ATOM 139 H4' CYT 5 4.729 -2.534 -9.798 1.00 0.00 RNAA -ATOM 140 O4' CYT 5 5.465 -2.016 -7.863 1.00 0.00 RNAA -ATOM 141 C1' CYT 5 5.097 -3.027 -6.945 1.00 0.00 RNAA -ATOM 142 H1' CYT 5 5.931 -3.727 -6.892 1.00 0.00 RNAA -ATOM 143 N1 CYT 5 4.932 -2.418 -5.618 1.00 0.00 RNAA -ATOM 144 C6 CYT 5 4.758 -1.069 -5.480 1.00 0.00 RNAA -ATOM 145 H6 CYT 5 4.743 -0.434 -6.367 1.00 0.00 RNAA -ATOM 146 C5 CYT 5 4.605 -0.509 -4.274 1.00 0.00 RNAA -ATOM 147 H5 CYT 5 4.473 0.567 -4.159 1.00 0.00 RNAA -ATOM 148 C2 CYT 5 4.958 -3.242 -4.490 1.00 0.00 RNAA -ATOM 149 O2 CYT 5 5.126 -4.461 -4.638 1.00 0.00 RNAA -ATOM 150 N3 CYT 5 4.801 -2.694 -3.263 1.00 0.00 RNAA -ATOM 151 C4 CYT 5 4.628 -1.376 -3.142 1.00 0.00 RNAA -ATOM 152 N4 CYT 5 4.473 -0.877 -1.913 1.00 0.00 RNAA -ATOM 153 H41 CYT 5 4.464 -1.501 -1.119 1.00 0.00 RNAA -ATOM 154 H42 CYT 5 4.340 0.115 -1.777 1.00 0.00 RNAA -ATOM 155 C2' CYT 5 3.832 -3.695 -7.484 1.00 0.00 RNAA -ATOM 156 H2'' CYT 5 3.165 -3.945 -6.632 1.00 0.00 RNAA -ATOM 157 O2' CYT 5 4.213 -4.777 -8.310 1.00 0.00 RNAA -ATOM 158 H2' CYT 5 3.158 -3.991 -6.681 1.00 0.00 RNAA -ATOM 159 C3' CYT 5 3.232 -2.557 -8.304 1.00 0.00 RNAA -ATOM 160 H3' CYT 5 2.686 -1.842 -7.689 1.00 0.00 RNAA -ATOM 161 O3' CYT 5 2.310 -3.017 -9.286 1.00 0.00 RNAA -ATOM 162 P CYT 6 0.748 -3.130 -8.921 1.00 0.00 RNAA -ATOM 163 O1P CYT 6 0.015 -3.382 -10.188 1.00 0.00 RNAA -ATOM 164 O2P CYT 6 0.374 -1.967 -8.077 1.00 0.00 RNAA -ATOM 165 O5' CYT 6 0.657 -4.443 -8.024 1.00 0.00 RNAA -ATOM 166 C5' CYT 6 1.044 -5.711 -8.547 1.00 0.00 RNAA -ATOM 167 H5' CYT 6 2.058 -5.648 -8.944 1.00 0.00 RNAA -ATOM 168 H5'' CYT 6 0.368 -6.001 -9.352 1.00 0.00 RNAA -ATOM 169 C4' CYT 6 1.001 -6.765 -7.467 1.00 0.00 RNAA -ATOM 170 H4' CYT 6 1.115 -7.735 -7.952 1.00 0.00 RNAA -ATOM 171 O4' CYT 6 2.034 -6.489 -6.485 1.00 0.00 RNAA -ATOM 172 C1' CYT 6 1.587 -6.876 -5.201 1.00 0.00 RNAA -ATOM 173 H1' CYT 6 2.322 -7.579 -4.808 1.00 0.00 RNAA -ATOM 174 N1 CYT 6 1.588 -5.689 -4.332 1.00 0.00 RNAA -ATOM 175 C6 CYT 6 1.598 -4.430 -4.861 1.00 0.00 RNAA -ATOM 176 H6 CYT 6 1.601 -4.300 -5.943 1.00 0.00 RNAA -ATOM 177 C5 CYT 6 1.602 -3.347 -4.073 1.00 0.00 RNAA -ATOM 178 H5 CYT 6 1.623 -2.341 -4.493 1.00 0.00 RNAA -ATOM 179 C2 CYT 6 1.578 -5.870 -2.946 1.00 0.00 RNAA -ATOM 180 O2 CYT 6 1.575 -7.023 -2.490 1.00 0.00 RNAA -ATOM 181 N3 CYT 6 1.575 -4.787 -2.135 1.00 0.00 RNAA -ATOM 182 C4 CYT 6 1.586 -3.561 -2.664 1.00 0.00 RNAA -ATOM 183 N4 CYT 6 1.579 -2.519 -1.831 1.00 0.00 RNAA -ATOM 184 H41 CYT 6 1.530 -2.677 -0.834 1.00 0.00 RNAA -ATOM 185 H42 CYT 6 1.586 -1.575 -2.192 1.00 0.00 RNAA -ATOM 186 C2' CYT 6 0.213 -7.522 -5.369 1.00 0.00 RNAA -ATOM 187 H2'' CYT 6 -0.428 -7.234 -4.509 1.00 0.00 RNAA -ATOM 188 O2' CYT 6 0.393 -8.909 -5.569 1.00 0.00 RNAA -ATOM 189 H2' CYT 6 -0.445 -7.299 -4.529 1.00 0.00 RNAA -ATOM 190 C3' CYT 6 -0.277 -6.837 -6.640 1.00 0.00 RNAA -ATOM 191 H3' CYT 6 -0.694 -5.848 -6.447 1.00 0.00 RNAA -ATOM 192 O3' CYT 6 -1.297 -7.574 -7.306 1.00 0.00 RNAA -ATOM 193 P GUA 7 -2.842 -7.288 -6.965 1.00 0.00 RNAA -ATOM 194 O1P GUA 7 -3.655 -7.999 -7.984 1.00 0.00 RNAA -ATOM 195 O2P GUA 7 -3.026 -5.828 -6.770 1.00 0.00 RNAA -ATOM 196 O5' GUA 7 -3.065 -8.009 -5.562 1.00 0.00 RNAA -ATOM 197 C5' GUA 7 -2.818 -9.405 -5.414 1.00 0.00 RNAA -ATOM 198 H5' GUA 7 -1.790 -9.630 -5.701 1.00 0.00 RNAA -ATOM 199 H5'' GUA 7 -3.496 -9.970 -6.053 1.00 0.00 RNAA -ATOM 200 C4' GUA 7 -3.034 -9.825 -3.979 1.00 0.00 RNAA -ATOM 201 H4' GUA 7 -3.070 -10.915 -3.954 1.00 0.00 RNAA -ATOM 202 O4' GUA 7 -1.990 -9.260 -3.141 1.00 0.00 RNAA -ATOM 203 C1' GUA 7 -2.506 -9.013 -1.848 1.00 0.00 RNAA -ATOM 204 H1' GUA 7 -1.908 -9.602 -1.152 1.00 0.00 RNAA -ATOM 205 N9 GUA 7 -2.307 -7.603 -1.529 1.00 0.00 RNAA -ATOM 206 C4 GUA 7 -2.450 -7.022 -0.291 1.00 0.00 RNAA -ATOM 207 N2 GUA 7 -3.207 -7.276 3.092 1.00 0.00 RNAA -ATOM 208 H21 GUA 7 -3.198 -6.601 3.843 1.00 0.00 RNAA -ATOM 209 H22 GUA 7 -3.440 -8.248 3.241 1.00 0.00 RNAA -ATOM 210 N3 GUA 7 -2.810 -7.656 0.845 1.00 0.00 RNAA -ATOM 211 C2 GUA 7 -2.859 -6.828 1.877 1.00 0.00 RNAA -ATOM 212 N1 GUA 7 -2.573 -5.488 1.800 1.00 0.00 RNAA -ATOM 213 H1 GUA 7 -2.644 -4.968 2.663 1.00 0.00 RNAA -ATOM 214 C6 GUA 7 -2.205 -4.814 0.640 1.00 0.00 RNAA -ATOM 215 O6 GUA 7 -1.974 -3.600 0.687 1.00 0.00 RNAA -ATOM 216 C5 GUA 7 -2.150 -5.689 -0.476 1.00 0.00 RNAA -ATOM 217 N7 GUA 7 -1.829 -5.436 -1.803 1.00 0.00 RNAA -ATOM 218 C8 GUA 7 -1.940 -6.597 -2.389 1.00 0.00 RNAA -ATOM 219 H8 GUA 7 -1.768 -6.747 -3.444 1.00 0.00 RNAA -ATOM 220 C2' GUA 7 -3.974 -9.437 -1.843 1.00 0.00 RNAA -ATOM 221 H2'' GUA 7 -4.560 -8.695 -1.259 1.00 0.00 RNAA -ATOM 222 O2' GUA 7 -4.051 -10.776 -1.396 1.00 0.00 RNAA -ATOM 223 H2' GUA 7 -4.588 -8.759 -1.251 1.00 0.00 RNAA -ATOM 224 C3' GUA 7 -4.317 -9.326 -3.324 1.00 0.00 RNAA -ATOM 225 H3' GUA 7 -4.549 -8.304 -3.625 1.00 0.00 RNAA -ATOM 226 O3' GUA 7 -5.441 -10.117 -3.694 1.00 0.00 RNAA -ATOM 227 P GUA 8 -6.908 -9.461 -3.703 1.00 0.00 RNAA -ATOM 228 O1P GUA 8 -7.856 -10.462 -4.253 1.00 0.00 RNAA -ATOM 229 O2P GUA 8 -6.802 -8.124 -4.342 1.00 0.00 RNAA -ATOM 230 O5' GUA 8 -7.243 -9.246 -2.161 1.00 0.00 RNAA -ATOM 231 C5' GUA 8 -7.338 -10.356 -1.272 1.00 0.00 RNAA -ATOM 232 H5' GUA 8 -6.384 -10.881 -1.236 1.00 0.00 RNAA -ATOM 233 H5'' GUA 8 -8.107 -11.045 -1.623 1.00 0.00 RNAA -ATOM 234 C4' GUA 8 -7.700 -9.887 0.117 1.00 0.00 RNAA -ATOM 235 H4' GUA 8 -8.048 -10.755 0.678 1.00 0.00 RNAA -ATOM 236 O4' GUA 8 -6.553 -9.229 0.720 1.00 0.00 RNAA -ATOM 237 C1' GUA 8 -6.996 -8.189 1.571 1.00 0.00 RNAA -ATOM 238 H1' GUA 8 -6.595 -8.402 2.563 1.00 0.00 RNAA -ATOM 239 N9 GUA 8 -6.411 -6.935 1.111 1.00 0.00 RNAA -ATOM 240 C4 GUA 8 -6.322 -5.763 1.825 1.00 0.00 RNAA -ATOM 241 N2 GUA 8 -6.921 -3.967 4.732 1.00 0.00 RNAA -ATOM 242 H21 GUA 8 -6.732 -3.028 5.052 1.00 0.00 RNAA -ATOM 243 H22 GUA 8 -7.384 -4.640 5.327 1.00 0.00 RNAA -ATOM 244 N3 GUA 8 -6.764 -5.566 3.085 1.00 0.00 RNAA -ATOM 245 C2 GUA 8 -6.535 -4.331 3.501 1.00 0.00 RNAA -ATOM 246 N1 GUA 8 -5.918 -3.366 2.744 1.00 0.00 RNAA -ATOM 247 H1 GUA 8 -5.764 -2.438 3.113 1.00 0.00 RNAA -ATOM 248 C6 GUA 8 -5.455 -3.548 1.444 1.00 0.00 RNAA -ATOM 249 O6 GUA 8 -4.915 -2.607 0.852 1.00 0.00 RNAA -ATOM 250 C5 GUA 8 -5.695 -4.868 0.983 1.00 0.00 RNAA -ATOM 251 N7 GUA 8 -5.399 -5.462 -0.236 1.00 0.00 RNAA -ATOM 252 C8 GUA 8 -5.842 -6.683 -0.115 1.00 0.00 RNAA -ATOM 253 H8 GUA 8 -5.769 -7.423 -0.899 1.00 0.00 RNAA -ATOM 254 C2' GUA 8 -8.523 -8.201 1.559 1.00 0.00 RNAA -ATOM 255 H2'' GUA 8 -8.891 -7.153 1.572 1.00 0.00 RNAA -ATOM 256 O2' GUA 8 -8.971 -9.028 2.615 1.00 0.00 RNAA -ATOM 257 H2' GUA 8 -8.935 -7.194 1.608 1.00 0.00 RNAA -ATOM 258 C3' GUA 8 -8.801 -8.837 0.201 1.00 0.00 RNAA -ATOM 259 H3' GUA 8 -8.737 -8.120 -0.617 1.00 0.00 RNAA -ATOM 260 O3' GUA 8 -10.094 -9.423 0.118 1.00 0.00 RNAA -ATOM 261 P GUA 9 -11.335 -8.546 -0.406 1.00 0.00 RNAA -ATOM 262 O1P GUA 9 -12.503 -9.449 -0.572 1.00 0.00 RNAA -ATOM 263 O2P GUA 9 -10.867 -7.735 -1.559 1.00 0.00 RNAA -ATOM 264 O5' GUA 9 -11.639 -7.551 0.800 1.00 0.00 RNAA -ATOM 265 C5' GUA 9 -11.967 -8.048 2.094 1.00 0.00 RNAA -ATOM 266 H5' GUA 9 -11.166 -8.693 2.456 1.00 0.00 RNAA -ATOM 267 H5'' GUA 9 -12.891 -8.624 2.045 1.00 0.00 RNAA -ATOM 268 C4' GUA 9 -12.158 -6.903 3.061 1.00 0.00 RNAA -ATOM 269 H4' GUA 9 -12.648 -7.300 3.950 1.00 0.00 RNAA -ATOM 270 O4' GUA 9 -10.875 -6.278 3.333 1.00 0.00 RNAA -ATOM 271 C1' GUA 9 -11.055 -4.890 3.536 1.00 0.00 RNAA -ATOM 272 H1' GUA 9 -10.663 -4.663 4.528 1.00 0.00 RNAA -ATOM 273 N9 GUA 9 -10.246 -4.172 2.558 1.00 0.00 RNAA -ATOM 274 C4 GUA 9 -9.881 -2.848 2.613 1.00 0.00 RNAA -ATOM 275 N2 GUA 9 -9.947 0.217 4.240 1.00 0.00 RNAA -ATOM 276 H21 GUA 9 -9.561 1.134 4.067 1.00 0.00 RNAA -ATOM 277 H22 GUA 9 -10.501 0.034 5.065 1.00 0.00 RNAA -ATOM 278 N3 GUA 9 -10.212 -1.974 3.588 1.00 0.00 RNAA -ATOM 279 C2 GUA 9 -9.712 -0.769 3.362 1.00 0.00 RNAA -ATOM 280 N1 GUA 9 -8.952 -0.445 2.266 1.00 0.00 RNAA -ATOM 281 H1 GUA 9 -8.603 0.495 2.144 1.00 0.00 RNAA -ATOM 282 C6 GUA 9 -8.601 -1.329 1.250 1.00 0.00 RNAA -ATOM 283 O6 GUA 9 -7.911 -0.930 0.304 1.00 0.00 RNAA -ATOM 284 C5 GUA 9 -9.128 -2.627 1.480 1.00 0.00 RNAA -ATOM 285 N7 GUA 9 -9.019 -3.787 0.726 1.00 0.00 RNAA -ATOM 286 C8 GUA 9 -9.696 -4.675 1.403 1.00 0.00 RNAA -ATOM 287 H8 GUA 9 -9.814 -5.701 1.087 1.00 0.00 RNAA -ATOM 288 C2' GUA 9 -12.551 -4.596 3.431 1.00 0.00 RNAA -ATOM 289 H2'' GUA 9 -12.690 -3.632 2.896 1.00 0.00 RNAA -ATOM 290 O2' GUA 9 -13.115 -4.673 4.724 1.00 0.00 RNAA -ATOM 291 H2' GUA 9 -12.741 -3.640 2.943 1.00 0.00 RNAA -ATOM 292 C3' GUA 9 -13.020 -5.753 2.555 1.00 0.00 RNAA -ATOM 293 H3' GUA 9 -12.858 -5.566 1.492 1.00 0.00 RNAA -ATOM 294 O3' GUA 9 -14.406 -6.037 2.704 1.00 0.00 RNAA -ATOM 295 P CYT 10 -15.419 -5.732 1.495 1.00 0.00 RNAA -ATOM 296 O1P CYT 10 -16.726 -6.361 1.817 1.00 0.00 RNAA -ATOM 297 O2P CYT 10 -14.733 -6.083 0.225 1.00 0.00 RNAA -ATOM 298 O5' CYT 10 -15.599 -4.150 1.532 1.00 0.00 RNAA -ATOM 299 C5' CYT 10 -16.492 -3.535 2.458 1.00 0.00 RNAA -ATOM 300 H5' CYT 10 -16.152 -3.721 3.477 1.00 0.00 RNAA -ATOM 301 H5'' CYT 10 -17.493 -3.948 2.337 1.00 0.00 RNAA -ATOM 302 C4' CYT 10 -16.544 -2.044 2.217 1.00 0.00 RNAA -ATOM 303 H4' CYT 10 -17.346 -1.639 2.834 1.00 0.00 RNAA -ATOM 304 O4' CYT 10 -15.241 -1.472 2.509 1.00 0.00 RNAA -ATOM 305 C1' CYT 10 -14.912 -0.506 1.531 1.00 0.00 RNAA -ATOM 306 H1' CYT 10 -14.572 0.384 2.061 1.00 0.00 RNAA -ATOM 307 N1 CYT 10 -13.788 -1.016 0.731 1.00 0.00 RNAA -ATOM 308 C6 CYT 10 -13.474 -2.347 0.724 1.00 0.00 RNAA -ATOM 309 H6 CYT 10 -14.072 -3.044 1.309 1.00 0.00 RNAA -ATOM 310 C5 CYT 10 -12.444 -2.811 0.005 1.00 0.00 RNAA -ATOM 311 H5 CYT 10 -12.192 -3.871 -0.003 1.00 0.00 RNAA -ATOM 312 C2 CYT 10 -13.036 -0.111 -0.021 1.00 0.00 RNAA -ATOM 313 O2 CYT 10 -13.348 1.089 -0.003 1.00 0.00 RNAA -ATOM 314 N3 CYT 10 -11.991 -0.564 -0.752 1.00 0.00 RNAA -ATOM 315 C4 CYT 10 -11.691 -1.865 -0.749 1.00 0.00 RNAA -ATOM 316 N4 CYT 10 -10.649 -2.267 -1.481 1.00 0.00 RNAA -ATOM 317 H41 CYT 10 -10.119 -1.590 -2.011 1.00 0.00 RNAA -ATOM 318 H42 CYT 10 -10.391 -3.243 -1.502 1.00 0.00 RNAA -ATOM 319 C2' CYT 10 -16.185 -0.243 0.726 1.00 0.00 RNAA -ATOM 320 H2'' CYT 10 -15.910 0.007 -0.321 1.00 0.00 RNAA -ATOM 321 O2' CYT 10 -16.958 0.720 1.414 1.00 0.00 RNAA -ATOM 322 H2' CYT 10 -15.962 0.044 -0.302 1.00 0.00 RNAA -ATOM 323 C3' CYT 10 -16.835 -1.621 0.782 1.00 0.00 RNAA -ATOM 324 H3' CYT 10 -16.400 -2.317 0.064 1.00 0.00 RNAA -ATOM 325 O3' CYT 10 -18.231 -1.582 0.507 1.00 0.00 RNAA -ATOM 326 P URA 11 -18.804 -2.301 -0.812 1.00 0.00 RNAA -ATOM 327 O1P URA 11 -20.286 -2.253 -0.731 1.00 0.00 RNAA -ATOM 328 O2P URA 11 -18.120 -3.611 -0.969 1.00 0.00 RNAA -ATOM 329 O5' URA 11 -18.342 -1.350 -2.003 1.00 0.00 RNAA -ATOM 330 C5' URA 11 -18.788 0.002 -2.075 1.00 0.00 RNAA -ATOM 331 H5' URA 11 -18.586 0.506 -1.130 1.00 0.00 RNAA -ATOM 332 H5'' URA 11 -19.861 0.026 -2.264 1.00 0.00 RNAA -ATOM 333 C4' URA 11 -18.079 0.733 -3.189 1.00 0.00 RNAA -ATOM 334 H4' URA 11 -18.117 1.797 -2.949 1.00 0.00 RNAA -ATOM 335 O4' URA 11 -16.724 0.221 -3.304 1.00 0.00 RNAA -ATOM 336 C1' URA 11 -16.446 -0.061 -4.662 1.00 0.00 RNAA -ATOM 337 H1' URA 11 -16.016 0.842 -5.095 1.00 0.00 RNAA -ATOM 338 N1 URA 11 -15.444 -1.132 -4.727 1.00 0.00 RNAA -ATOM 339 C6 URA 11 -15.059 -1.817 -3.599 1.00 0.00 RNAA -ATOM 340 H6 URA 11 -15.502 -1.544 -2.641 1.00 0.00 RNAA -ATOM 341 C2 URA 11 -14.901 -1.430 -5.962 1.00 0.00 RNAA -ATOM 342 O2 URA 11 -15.209 -0.840 -6.983 1.00 0.00 RNAA -ATOM 343 N3 URA 11 -13.977 -2.446 -5.960 1.00 0.00 RNAA -ATOM 344 H3 URA 11 -13.573 -2.684 -6.855 1.00 0.00 RNAA -ATOM 345 C4 URA 11 -13.547 -3.176 -4.871 1.00 0.00 RNAA -ATOM 346 O4 URA 11 -12.700 -4.056 -5.029 1.00 0.00 RNAA -ATOM 347 C5 URA 11 -14.155 -2.802 -3.630 1.00 0.00 RNAA -ATOM 348 H5 URA 11 -13.882 -3.322 -2.712 1.00 0.00 RNAA -ATOM 349 C2' URA 11 -17.800 -0.411 -5.278 1.00 0.00 RNAA -ATOM 350 H2'' URA 11 -18.071 -1.448 -4.986 1.00 0.00 RNAA -ATOM 351 O2' URA 11 -17.754 -0.154 -6.667 1.00 0.00 RNAA -ATOM 352 H2' URA 11 -18.094 -1.434 -5.046 1.00 0.00 RNAA -ATOM 353 C3' URA 11 -18.708 0.588 -4.569 1.00 0.00 RNAA -ATOM 354 H3' URA 11 -19.741 0.245 -4.509 1.00 0.00 RNAA -ATOM 355 O3' URA 11 -18.747 1.834 -5.256 1.00 0.00 RNAA -ATOM 356 P CYT 12 -19.723 3.004 -4.744 1.00 0.00 RNAA -ATOM 357 O1P CYT 12 -20.299 2.587 -3.440 1.00 0.00 RNAA -ATOM 358 O2P CYT 12 -20.631 3.360 -5.865 1.00 0.00 RNAA -ATOM 359 O5' CYT 12 -18.742 4.230 -4.478 1.00 0.00 RNAA -ATOM 360 C5' CYT 12 -18.946 5.488 -5.116 1.00 0.00 RNAA -ATOM 361 H5' CYT 12 -19.995 5.596 -5.390 1.00 0.00 RNAA -ATOM 362 H5'' CYT 12 -18.339 5.546 -6.020 1.00 0.00 RNAA -ATOM 363 C4' CYT 12 -18.558 6.614 -4.189 1.00 0.00 RNAA -ATOM 364 H4' CYT 12 -18.763 7.553 -4.703 1.00 0.00 RNAA -ATOM 365 O4' CYT 12 -19.276 6.471 -2.934 1.00 0.00 RNAA -ATOM 366 C1' CYT 12 -18.511 7.033 -1.886 1.00 0.00 RNAA -ATOM 367 H1' CYT 12 -19.084 7.874 -1.491 1.00 0.00 RNAA -ATOM 368 N1 CYT 12 -18.385 6.032 -0.817 1.00 0.00 RNAA -ATOM 369 C6 CYT 12 -17.757 4.840 -1.050 1.00 0.00 RNAA -ATOM 370 H6 CYT 12 -17.335 4.634 -2.033 1.00 0.00 RNAA -ATOM 371 C5 CYT 12 -17.642 3.919 -0.083 1.00 0.00 RNAA -ATOM 372 H5 CYT 12 -17.131 2.973 -0.259 1.00 0.00 RNAA -ATOM 373 C2 CYT 12 -18.917 6.316 0.443 1.00 0.00 RNAA -ATOM 374 O2 CYT 12 -19.473 7.408 0.628 1.00 0.00 RNAA -ATOM 375 N3 CYT 12 -18.813 5.394 1.427 1.00 0.00 RNAA -ATOM 376 C4 CYT 12 -18.205 4.229 1.189 1.00 0.00 RNAA -ATOM 377 N4 CYT 12 -18.139 3.339 2.181 1.00 0.00 RNAA -ATOM 378 H41 CYT 12 -18.539 3.547 3.085 1.00 0.00 RNAA -ATOM 379 H42 CYT 12 -17.687 2.453 2.001 1.00 0.00 RNAA -ATOM 380 C2' CYT 12 -17.170 7.479 -2.467 1.00 0.00 RNAA -ATOM 381 H2'' CYT 12 -16.362 7.169 -1.770 1.00 0.00 RNAA -ATOM 382 O2' CYT 12 -17.237 8.861 -2.753 1.00 0.00 RNAA -ATOM 383 H2' CYT 12 -16.342 7.227 -1.804 1.00 0.00 RNAA -ATOM 384 C3' CYT 12 -17.099 6.657 -3.750 1.00 0.00 RNAA -ATOM 385 H3' CYT 12 -16.697 5.657 -3.583 1.00 0.00 RNAA -ATOM 386 O3' CYT 12 -16.269 7.260 -4.736 1.00 0.00 RNAA -ATOM 387 P ADE 13 -15.417 6.340 -5.741 1.00 0.00 RNAA -ATOM 388 O1P ADE 13 -15.998 6.480 -7.101 1.00 0.00 RNAA -ATOM 389 O2P ADE 13 -15.284 4.990 -5.137 1.00 0.00 RNAA -ATOM 390 O5' ADE 13 -13.972 7.011 -5.749 1.00 0.00 RNAA -ATOM 391 C5' ADE 13 -13.812 8.412 -5.955 1.00 0.00 RNAA -ATOM 392 H5' ADE 13 -14.751 8.839 -6.310 1.00 0.00 RNAA -ATOM 393 H5'' ADE 13 -13.040 8.592 -6.703 1.00 0.00 RNAA -ATOM 394 C4' ADE 13 -13.419 9.089 -4.664 1.00 0.00 RNAA -ATOM 395 H4' ADE 13 -13.468 10.166 -4.828 1.00 0.00 RNAA -ATOM 396 O4' ADE 13 -14.289 8.628 -3.596 1.00 0.00 RNAA -ATOM 397 C1' ADE 13 -13.588 8.666 -2.369 1.00 0.00 RNAA -ATOM 398 H1' ADE 13 -14.122 9.361 -1.720 1.00 0.00 RNAA -ATOM 399 N9 ADE 13 -13.649 7.341 -1.754 1.00 0.00 RNAA -ATOM 400 C5 ADE 13 -13.669 5.709 -0.279 1.00 0.00 RNAA -ATOM 401 N7 ADE 13 -13.806 5.110 -1.524 1.00 0.00 RNAA -ATOM 402 C8 ADE 13 -13.789 6.118 -2.362 1.00 0.00 RNAA -ATOM 403 H8 ADE 13 -13.874 5.997 -3.432 1.00 0.00 RNAA -ATOM 404 N1 ADE 13 -13.474 6.060 2.046 1.00 0.00 RNAA -ATOM 405 C2 ADE 13 -13.388 7.367 1.766 1.00 0.00 RNAA -ATOM 406 H2 ADE 13 -13.263 8.023 2.627 1.00 0.00 RNAA -ATOM 407 N3 ADE 13 -13.427 7.979 0.584 1.00 0.00 RNAA -ATOM 408 C4 ADE 13 -13.571 7.082 -0.407 1.00 0.00 RNAA -ATOM 409 C6 ADE 13 -13.612 5.186 1.025 1.00 0.00 RNAA -ATOM 410 N6 ADE 13 -13.674 3.885 1.317 1.00 0.00 RNAA -ATOM 411 H61 ADE 13 -13.629 3.619 2.290 1.00 0.00 RNAA -ATOM 412 H62 ADE 13 -13.765 3.153 0.627 1.00 0.00 RNAA -ATOM 413 C2' ADE 13 -12.162 9.134 -2.656 1.00 0.00 RNAA -ATOM 414 H2'' ADE 13 -11.458 8.522 -2.052 1.00 0.00 RNAA -ATOM 415 O2' ADE 13 -12.095 10.531 -2.447 1.00 0.00 RNAA -ATOM 416 H2' ADE 13 -11.433 8.585 -2.060 1.00 0.00 RNAA -ATOM 417 C3' ADE 13 -12.023 8.786 -4.134 1.00 0.00 RNAA -ATOM 418 H3' ADE 13 -11.745 7.743 -4.292 1.00 0.00 RNAA -ATOM 419 O3' ADE 13 -11.027 9.567 -4.784 1.00 0.00 RNAA -ATOM 420 P ADE 14 -9.496 9.081 -4.774 1.00 0.00 RNAA -ATOM 421 O1P ADE 14 -8.674 10.190 -5.320 1.00 0.00 RNAA -ATOM 422 O2P ADE 14 -9.429 7.739 -5.409 1.00 0.00 RNAA -ATOM 423 O5' ADE 14 -9.146 8.913 -3.229 1.00 0.00 RNAA -ATOM 424 C5' ADE 14 -8.832 10.041 -2.417 1.00 0.00 RNAA -ATOM 425 H5' ADE 14 -9.522 10.855 -2.634 1.00 0.00 RNAA -ATOM 426 H5'' ADE 14 -7.815 10.374 -2.624 1.00 0.00 RNAA -ATOM 427 C4' ADE 14 -8.940 9.675 -0.956 1.00 0.00 RNAA -ATOM 428 H4' ADE 14 -8.870 10.596 -0.376 1.00 0.00 RNAA -ATOM 429 O4' ADE 14 -10.179 8.946 -0.745 1.00 0.00 RNAA -ATOM 430 C1' ADE 14 -9.972 7.904 0.188 1.00 0.00 RNAA -ATOM 431 H1' ADE 14 -10.739 8.006 0.956 1.00 0.00 RNAA -ATOM 432 N9 ADE 14 -10.171 6.623 -0.486 1.00 0.00 RNAA -ATOM 433 C5 ADE 14 -10.561 4.498 -0.904 1.00 0.00 RNAA -ATOM 434 N7 ADE 14 -10.371 5.107 -2.137 1.00 0.00 RNAA -ATOM 435 C8 ADE 14 -10.140 6.362 -1.834 1.00 0.00 RNAA -ATOM 436 H8 ADE 14 -9.935 7.118 -2.577 1.00 0.00 RNAA -ATOM 437 N1 ADE 14 -10.968 2.894 0.778 1.00 0.00 RNAA -ATOM 438 C2 ADE 14 -10.816 3.892 1.659 1.00 0.00 RNAA -ATOM 439 H2 ADE 14 -10.925 3.610 2.707 1.00 0.00 RNAA -ATOM 440 N3 ADE 14 -10.553 5.177 1.438 1.00 0.00 RNAA -ATOM 441 C4 ADE 14 -10.436 5.419 0.121 1.00 0.00 RNAA -ATOM 442 C6 ADE 14 -10.847 3.170 -0.538 1.00 0.00 RNAA -ATOM 443 N6 ADE 14 -11.005 2.180 -1.419 1.00 0.00 RNAA -ATOM 444 H61 ADE 14 -11.268 1.251 -1.122 1.00 0.00 RNAA -ATOM 445 H62 ADE 14 -10.915 2.381 -2.404 1.00 0.00 RNAA -ATOM 446 C2' ADE 14 -8.565 8.084 0.755 1.00 0.00 RNAA -ATOM 447 H2'' ADE 14 -8.126 7.084 0.958 1.00 0.00 RNAA -ATOM 448 O2' ADE 14 -8.642 8.965 1.857 1.00 0.00 RNAA -ATOM 449 H2' ADE 14 -8.104 7.129 1.006 1.00 0.00 RNAA -ATOM 450 C3' ADE 14 -7.861 8.734 -0.432 1.00 0.00 RNAA -ATOM 451 H3' ADE 14 -7.562 8.014 -1.194 1.00 0.00 RNAA -ATOM 452 O3' ADE 14 -6.671 9.408 -0.040 1.00 0.00 RNAA -ATOM 453 P CYT 15 -5.328 8.565 0.220 1.00 0.00 RNAA -ATOM 454 O1P CYT 15 -4.234 9.519 0.537 1.00 0.00 RNAA -ATOM 455 O2P CYT 15 -5.168 7.619 -0.913 1.00 0.00 RNAA -ATOM 456 O5' CYT 15 -5.639 7.709 1.527 1.00 0.00 RNAA -ATOM 457 C5' CYT 15 -6.082 8.345 2.723 1.00 0.00 RNAA -ATOM 458 H5' CYT 15 -6.822 9.105 2.472 1.00 0.00 RNAA -ATOM 459 H5'' CYT 15 -5.241 8.824 3.225 1.00 0.00 RNAA -ATOM 460 C4' CYT 15 -6.710 7.340 3.659 1.00 0.00 RNAA -ATOM 461 H4' CYT 15 -7.094 7.889 4.519 1.00 0.00 RNAA -ATOM 462 O4' CYT 15 -7.740 6.603 2.945 1.00 0.00 RNAA -ATOM 463 C1' CYT 15 -7.812 5.282 3.446 1.00 0.00 RNAA -ATOM 464 H1' CYT 15 -8.837 5.127 3.784 1.00 0.00 RNAA -ATOM 465 N1 CYT 15 -7.554 4.349 2.341 1.00 0.00 RNAA -ATOM 466 C6 CYT 15 -6.927 4.764 1.199 1.00 0.00 RNAA -ATOM 467 H6 CYT 15 -6.616 5.803 1.104 1.00 0.00 RNAA -ATOM 468 C5 CYT 15 -6.690 3.911 0.193 1.00 0.00 RNAA -ATOM 469 H5 CYT 15 -6.198 4.238 -0.724 1.00 0.00 RNAA -ATOM 470 C2 CYT 15 -7.961 3.019 2.478 1.00 0.00 RNAA -ATOM 471 O2 CYT 15 -8.532 2.670 3.522 1.00 0.00 RNAA -ATOM 472 N3 CYT 15 -7.725 2.144 1.474 1.00 0.00 RNAA -ATOM 473 C4 CYT 15 -7.110 2.560 0.363 1.00 0.00 RNAA -ATOM 474 N4 CYT 15 -6.891 1.664 -0.602 1.00 0.00 RNAA -ATOM 475 H41 CYT 15 -7.192 0.711 -0.451 1.00 0.00 RNAA -ATOM 476 H42 CYT 15 -6.429 1.925 -1.461 1.00 0.00 RNAA -ATOM 477 C2' CYT 15 -6.809 5.169 4.594 1.00 0.00 RNAA -ATOM 478 H2'' CYT 15 -6.331 4.167 4.555 1.00 0.00 RNAA -ATOM 479 O2' CYT 15 -7.474 5.485 5.800 1.00 0.00 RNAA -ATOM 480 H2' CYT 15 -6.337 4.188 4.618 1.00 0.00 RNAA -ATOM 481 C3' CYT 15 -5.801 6.247 4.209 1.00 0.00 RNAA -ATOM 482 H3' CYT 15 -5.084 5.901 3.465 1.00 0.00 RNAA -ATOM 483 O3' CYT 15 -5.036 6.701 5.319 1.00 0.00 RNAA -ATOM 484 P CYT 16 -3.671 5.947 5.708 1.00 0.00 RNAA -ATOM 485 O1P CYT 16 -3.011 6.707 6.799 1.00 0.00 RNAA -ATOM 486 O2P CYT 16 -2.929 5.681 4.448 1.00 0.00 RNAA -ATOM 487 O5' CYT 16 -4.155 4.546 6.292 1.00 0.00 RNAA -ATOM 488 C5' CYT 16 -4.907 4.478 7.500 1.00 0.00 RNAA -ATOM 489 H5' CYT 16 -5.828 5.052 7.393 1.00 0.00 RNAA -ATOM 490 H5'' CYT 16 -4.325 4.895 8.322 1.00 0.00 RNAA -ATOM 491 C4' CYT 16 -5.252 3.044 7.823 1.00 0.00 RNAA -ATOM 492 H4' CYT 16 -5.660 3.019 8.832 1.00 0.00 RNAA -ATOM 493 O4' CYT 16 -6.166 2.537 6.812 1.00 0.00 RNAA -ATOM 494 C1' CYT 16 -5.914 1.163 6.592 1.00 0.00 RNAA -ATOM 495 H1' CYT 16 -6.847 0.632 6.783 1.00 0.00 RNAA -ATOM 496 N1 CYT 16 -5.568 0.969 5.177 1.00 0.00 RNAA -ATOM 497 C6 CYT 16 -5.161 2.016 4.399 1.00 0.00 RNAA -ATOM 498 H6 CYT 16 -5.097 3.015 4.831 1.00 0.00 RNAA -ATOM 499 C5 CYT 16 -4.835 1.838 3.113 1.00 0.00 RNAA -ATOM 500 H5 CYT 16 -4.532 2.675 2.484 1.00 0.00 RNAA -ATOM 501 C2 CYT 16 -5.653 -0.317 4.637 1.00 0.00 RNAA -ATOM 502 O2 CYT 16 -6.041 -1.248 5.358 1.00 0.00 RNAA -ATOM 503 N3 CYT 16 -5.314 -0.518 3.342 1.00 0.00 RNAA -ATOM 504 C4 CYT 16 -4.912 0.513 2.595 1.00 0.00 RNAA -ATOM 505 N4 CYT 16 -4.572 0.265 1.327 1.00 0.00 RNAA -ATOM 506 H41 CYT 16 -4.600 -0.691 1.004 1.00 0.00 RNAA -ATOM 507 H42 CYT 16 -4.257 1.007 0.718 1.00 0.00 RNAA -ATOM 508 C2' CYT 16 -4.805 0.732 7.552 1.00 0.00 RNAA -ATOM 509 H2'' CYT 16 -4.131 0.023 7.026 1.00 0.00 RNAA -ATOM 510 O2' CYT 16 -5.402 0.241 8.735 1.00 0.00 RNAA -ATOM 511 H2' CYT 16 -4.133 0.011 7.088 1.00 0.00 RNAA -ATOM 512 C3' CYT 16 -4.090 2.058 7.790 1.00 0.00 RNAA -ATOM 513 H3' CYT 16 -3.380 2.299 6.999 1.00 0.00 RNAA -ATOM 514 O3' CYT 16 -3.345 2.064 9.003 1.00 0.00 RNAA -ATOM 515 P URA 17 -1.826 1.539 9.008 1.00 0.00 RNAA -ATOM 516 O1P URA 17 -1.309 1.698 10.391 1.00 0.00 RNAA -ATOM 517 O2P URA 17 -1.105 2.173 7.878 1.00 0.00 RNAA -ATOM 518 O5' URA 17 -1.954 -0.020 8.702 1.00 0.00 RNAA -ATOM 519 C5' URA 17 -2.541 -0.907 9.651 1.00 0.00 RNAA -ATOM 520 H5' URA 17 -3.563 -0.593 9.862 1.00 0.00 RNAA -ATOM 521 H5'' URA 17 -1.966 -0.890 10.576 1.00 0.00 RNAA -ATOM 522 C4' URA 17 -2.556 -2.317 9.111 1.00 0.00 RNAA -ATOM 523 H4' URA 17 -2.865 -2.977 9.922 1.00 0.00 RNAA -ATOM 524 O4' URA 17 -3.430 -2.377 7.951 1.00 0.00 RNAA -ATOM 525 C1' URA 17 -2.911 -3.293 7.008 1.00 0.00 RNAA -ATOM 526 H1' URA 17 -3.697 -4.022 6.810 1.00 0.00 RNAA -ATOM 527 N1 URA 17 -2.641 -2.569 5.757 1.00 0.00 RNAA -ATOM 528 C6 URA 17 -2.492 -1.203 5.742 1.00 0.00 RNAA -ATOM 529 H6 URA 17 -2.578 -0.653 6.681 1.00 0.00 RNAA -ATOM 530 C2 URA 17 -2.542 -3.308 4.596 1.00 0.00 RNAA -ATOM 531 O2 URA 17 -2.683 -4.519 4.562 1.00 0.00 RNAA -ATOM 532 N3 URA 17 -2.277 -2.579 3.462 1.00 0.00 RNAA -ATOM 533 H3 URA 17 -2.163 -3.082 2.594 1.00 0.00 RNAA -ATOM 534 C4 URA 17 -2.116 -1.211 3.374 1.00 0.00 RNAA -ATOM 535 O4 URA 17 -1.891 -0.696 2.278 1.00 0.00 RNAA -ATOM 536 C5 URA 17 -2.244 -0.519 4.620 1.00 0.00 RNAA -ATOM 537 H5 URA 17 -2.147 0.566 4.651 1.00 0.00 RNAA -ATOM 538 C2' URA 17 -1.678 -3.943 7.632 1.00 0.00 RNAA -ATOM 539 H2'' URA 17 -0.913 -4.098 6.842 1.00 0.00 RNAA -ATOM 540 O2' URA 17 -2.094 -5.104 8.324 1.00 0.00 RNAA -ATOM 541 H2' URA 17 -0.907 -4.149 6.890 1.00 0.00 RNAA -ATOM 542 C3' URA 17 -1.225 -2.848 8.592 1.00 0.00 RNAA -ATOM 543 H3' URA 17 -0.647 -2.069 8.095 1.00 0.00 RNAA -ATOM 544 O3' URA 17 -0.399 -3.342 9.641 1.00 0.00 RNAA -ATOM 545 P GUA 18 1.200 -3.294 9.483 1.00 0.00 RNAA -ATOM 546 O1P GUA 18 1.781 -3.524 10.831 1.00 0.00 RNAA -ATOM 547 O2P GUA 18 1.569 -2.072 8.725 1.00 0.00 RNAA -ATOM 548 O5' GUA 18 1.533 -4.561 8.578 1.00 0.00 RNAA -ATOM 549 C5' GUA 18 1.116 -5.866 8.972 1.00 0.00 RNAA -ATOM 550 H5' GUA 18 0.046 -5.859 9.183 1.00 0.00 RNAA -ATOM 551 H5'' GUA 18 1.653 -6.167 9.872 1.00 0.00 RNAA -ATOM 552 C4' GUA 18 1.398 -6.865 7.876 1.00 0.00 RNAA -ATOM 553 H4' GUA 18 1.345 -7.860 8.316 1.00 0.00 RNAA -ATOM 554 O4' GUA 18 0.450 -6.663 6.794 1.00 0.00 RNAA -ATOM 555 C1' GUA 18 1.058 -7.003 5.564 1.00 0.00 RNAA -ATOM 556 H1' GUA 18 0.453 -7.791 5.116 1.00 0.00 RNAA -ATOM 557 N9 GUA 18 1.005 -5.840 4.684 1.00 0.00 RNAA -ATOM 558 C4 GUA 18 1.162 -5.848 3.318 1.00 0.00 RNAA -ATOM 559 N2 GUA 18 1.731 -7.596 0.376 1.00 0.00 RNAA -ATOM 560 H21 GUA 18 1.799 -7.358 -0.603 1.00 0.00 RNAA -ATOM 561 H22 GUA 18 1.823 -8.553 0.688 1.00 0.00 RNAA -ATOM 562 N3 GUA 18 1.392 -6.937 2.553 1.00 0.00 RNAA -ATOM 563 C2 GUA 18 1.498 -6.626 1.272 1.00 0.00 RNAA -ATOM 564 N1 GUA 18 1.388 -5.350 0.778 1.00 0.00 RNAA -ATOM 565 H1 GUA 18 1.477 -5.199 -0.218 1.00 0.00 RNAA -ATOM 566 C6 GUA 18 1.154 -4.215 1.548 1.00 0.00 RNAA -ATOM 567 O6 GUA 18 1.080 -3.108 1.000 1.00 0.00 RNAA -ATOM 568 C5 GUA 18 1.036 -4.531 2.926 1.00 0.00 RNAA -ATOM 569 N7 GUA 18 0.803 -3.712 4.022 1.00 0.00 RNAA -ATOM 570 C8 GUA 18 0.793 -4.529 5.039 1.00 0.00 RNAA -ATOM 571 H8 GUA 18 0.638 -4.206 6.058 1.00 0.00 RNAA -ATOM 572 C2' GUA 18 2.480 -7.475 5.864 1.00 0.00 RNAA -ATOM 573 H2'' GUA 18 3.160 -7.091 5.074 1.00 0.00 RNAA -ATOM 574 O2' GUA 18 2.459 -8.878 6.029 1.00 0.00 RNAA -ATOM 575 H2' GUA 18 3.183 -7.150 5.096 1.00 0.00 RNAA -ATOM 576 C3' GUA 18 2.752 -6.760 7.183 1.00 0.00 RNAA -ATOM 577 H3' GUA 18 3.057 -5.724 7.041 1.00 0.00 RNAA -ATOM 578 O3' GUA 18 3.792 -7.379 7.934 1.00 0.00 RNAA -ATOM 579 P GUA 19 5.320 -6.957 7.675 1.00 0.00 RNAA -ATOM 580 O1P GUA 19 6.154 -7.693 8.659 1.00 0.00 RNAA -ATOM 581 O2P GUA 19 5.396 -5.475 7.615 1.00 0.00 RNAA -ATOM 582 O5' GUA 19 5.642 -7.534 6.225 1.00 0.00 RNAA -ATOM 583 C5' GUA 19 5.607 -8.936 5.975 1.00 0.00 RNAA -ATOM 584 H5' GUA 19 4.617 -9.327 6.211 1.00 0.00 RNAA -ATOM 585 H5'' GUA 19 6.345 -9.441 6.598 1.00 0.00 RNAA -ATOM 586 C4' GUA 19 5.917 -9.220 4.524 1.00 0.00 RNAA -ATOM 587 H4' GUA 19 6.078 -10.294 4.425 1.00 0.00 RNAA -ATOM 588 O4' GUA 19 4.837 -8.719 3.691 1.00 0.00 RNAA -ATOM 589 C1' GUA 19 5.354 -8.323 2.437 1.00 0.00 RNAA -ATOM 590 H1' GUA 19 4.845 -8.920 1.679 1.00 0.00 RNAA -ATOM 591 N9 GUA 19 5.010 -6.923 2.212 1.00 0.00 RNAA -ATOM 592 C4 GUA 19 5.059 -6.258 1.009 1.00 0.00 RNAA -ATOM 593 N2 GUA 19 5.732 -6.254 -2.395 1.00 0.00 RNAA -ATOM 594 H21 GUA 19 5.654 -5.576 -3.139 1.00 0.00 RNAA -ATOM 595 H22 GUA 19 6.041 -7.199 -2.577 1.00 0.00 RNAA -ATOM 596 N3 GUA 19 5.440 -6.784 -0.174 1.00 0.00 RNAA -ATOM 597 C2 GUA 19 5.380 -5.896 -1.152 1.00 0.00 RNAA -ATOM 598 N1 GUA 19 4.979 -4.593 -0.985 1.00 0.00 RNAA -ATOM 599 H1 GUA 19 4.957 -3.979 -1.786 1.00 0.00 RNAA -ATOM 600 C6 GUA 19 4.586 -4.030 0.225 1.00 0.00 RNAA -ATOM 601 O6 GUA 19 4.248 -2.841 0.262 1.00 0.00 RNAA -ATOM 602 C5 GUA 19 4.644 -4.971 1.285 1.00 0.00 RNAA -ATOM 603 N7 GUA 19 4.340 -4.830 2.632 1.00 0.00 RNAA -ATOM 604 C8 GUA 19 4.575 -6.009 3.141 1.00 0.00 RNAA -ATOM 605 H8 GUA 19 4.446 -6.240 4.188 1.00 0.00 RNAA -ATOM 606 C2' GUA 19 6.861 -8.581 2.451 1.00 0.00 RNAA -ATOM 607 H2'' GUA 19 7.375 -7.742 1.937 1.00 0.00 RNAA -ATOM 608 O2' GUA 19 7.100 -9.867 1.916 1.00 0.00 RNAA -ATOM 609 H2' GUA 19 7.408 -7.799 1.927 1.00 0.00 RNAA -ATOM 610 C3' GUA 19 7.150 -8.535 3.948 1.00 0.00 RNAA -ATOM 611 H3' GUA 19 7.257 -7.516 4.321 1.00 0.00 RNAA -ATOM 612 O3' GUA 19 8.349 -9.217 4.300 1.00 0.00 RNAA -ATOM 613 P GUA 20 9.744 -8.420 4.319 1.00 0.00 RNAA -ATOM 614 O1P GUA 20 10.766 -9.340 4.878 1.00 0.00 RNAA -ATOM 615 O2P GUA 20 9.526 -7.095 4.952 1.00 0.00 RNAA -ATOM 616 O5' GUA 20 10.077 -8.189 2.778 1.00 0.00 RNAA -ATOM 617 C5' GUA 20 10.304 -9.292 1.905 1.00 0.00 RNAA -ATOM 618 H5' GUA 20 9.436 -9.951 1.912 1.00 0.00 RNAA -ATOM 619 H5'' GUA 20 11.177 -9.853 2.239 1.00 0.00 RNAA -ATOM 620 C4' GUA 20 10.545 -8.804 0.497 1.00 0.00 RNAA -ATOM 621 H4' GUA 20 10.896 -9.653 -0.092 1.00 0.00 RNAA -ATOM 622 O4' GUA 20 9.325 -8.205 -0.021 1.00 0.00 RNAA -ATOM 623 C1' GUA 20 9.655 -7.159 -0.913 1.00 0.00 RNAA -ATOM 624 H1' GUA 20 9.204 -7.408 -1.874 1.00 0.00 RNAA -ATOM 625 N9 GUA 20 9.038 -5.927 -0.434 1.00 0.00 RNAA -ATOM 626 C4 GUA 20 8.863 -4.769 -1.154 1.00 0.00 RNAA -ATOM 627 N2 GUA 20 9.252 -2.978 -4.102 1.00 0.00 RNAA -ATOM 628 H21 GUA 20 9.000 -2.049 -4.408 1.00 0.00 RNAA -ATOM 629 H22 GUA 20 9.717 -3.625 -4.721 1.00 0.00 RNAA -ATOM 630 N3 GUA 20 9.242 -4.566 -2.435 1.00 0.00 RNAA -ATOM 631 C2 GUA 20 8.939 -3.347 -2.851 1.00 0.00 RNAA -ATOM 632 N1 GUA 20 8.313 -2.402 -2.077 1.00 0.00 RNAA -ATOM 633 H1 GUA 20 8.111 -1.492 -2.466 1.00 0.00 RNAA -ATOM 634 C6 GUA 20 7.918 -2.590 -0.758 1.00 0.00 RNAA -ATOM 635 O6 GUA 20 7.363 -1.667 -0.150 1.00 0.00 RNAA -ATOM 636 C5 GUA 20 8.236 -3.893 -0.294 1.00 0.00 RNAA -ATOM 637 N7 GUA 20 8.022 -4.485 0.943 1.00 0.00 RNAA -ATOM 638 C8 GUA 20 8.515 -5.687 0.814 1.00 0.00 RNAA -ATOM 639 H8 GUA 20 8.516 -6.416 1.610 1.00 0.00 RNAA -ATOM 640 C2' GUA 20 11.178 -7.083 -1.000 1.00 0.00 RNAA -ATOM 641 H2'' GUA 20 11.483 -6.016 -1.037 1.00 0.00 RNAA -ATOM 642 O2' GUA 20 11.606 -7.881 -2.085 1.00 0.00 RNAA -ATOM 643 H2' GUA 20 11.524 -6.052 -1.071 1.00 0.00 RNAA -ATOM 644 C3' GUA 20 11.578 -7.696 0.338 1.00 0.00 RNAA -ATOM 645 H3' GUA 20 11.527 -6.979 1.158 1.00 0.00 RNAA -ATOM 646 O3' GUA 20 12.908 -8.203 0.334 1.00 0.00 RNAA -ATOM 647 P URA 21 14.117 -7.278 0.848 1.00 0.00 RNAA -ATOM 648 O1P URA 21 15.318 -8.144 0.966 1.00 0.00 RNAA -ATOM 649 O2P URA 21 13.654 -6.504 2.030 1.00 0.00 RNAA -ATOM 650 O5' URA 21 14.360 -6.255 -0.349 1.00 0.00 RNAA -ATOM 651 C5' URA 21 14.716 -6.719 -1.647 1.00 0.00 RNAA -ATOM 652 H5' URA 21 14.004 -7.478 -1.973 1.00 0.00 RNAA -ATOM 653 H5'' URA 21 15.714 -7.158 -1.624 1.00 0.00 RNAA -ATOM 654 C4' URA 21 14.707 -5.576 -2.633 1.00 0.00 RNAA -ATOM 655 H4' URA 21 15.146 -5.938 -3.563 1.00 0.00 RNAA -ATOM 656 O4' URA 21 13.346 -5.089 -2.787 1.00 0.00 RNAA -ATOM 657 C1' URA 21 13.365 -3.698 -3.042 1.00 0.00 RNAA -ATOM 658 H1' URA 21 12.879 -3.547 -4.005 1.00 0.00 RNAA -ATOM 659 N1 URA 21 12.553 -3.027 -2.018 1.00 0.00 RNAA -ATOM 660 C6 URA 21 12.181 -3.668 -0.859 1.00 0.00 RNAA -ATOM 661 H6 URA 21 12.501 -4.698 -0.697 1.00 0.00 RNAA -ATOM 662 C2 URA 21 12.168 -1.724 -2.265 1.00 0.00 RNAA -ATOM 663 O2 URA 21 12.481 -1.121 -3.277 1.00 0.00 RNAA -ATOM 664 N3 URA 21 11.403 -1.145 -1.282 1.00 0.00 RNAA -ATOM 665 H3 URA 21 11.075 -0.205 -1.455 1.00 0.00 RNAA -ATOM 666 C4 URA 21 10.998 -1.727 -0.099 1.00 0.00 RNAA -ATOM 667 O4 URA 21 10.323 -1.070 0.696 1.00 0.00 RNAA -ATOM 668 C5 URA 21 11.438 -3.077 0.082 1.00 0.00 RNAA -ATOM 669 H5 URA 21 11.164 -3.625 0.983 1.00 0.00 RNAA -ATOM 670 C2' URA 21 14.827 -3.250 -3.073 1.00 0.00 RNAA -ATOM 671 H2'' URA 21 14.909 -2.266 -2.564 1.00 0.00 RNAA -ATOM 672 O2' URA 21 15.276 -3.293 -4.411 1.00 0.00 RNAA -ATOM 673 H2' URA 21 14.957 -2.269 -2.616 1.00 0.00 RNAA -ATOM 674 C3' URA 21 15.490 -4.333 -2.229 1.00 0.00 RNAA -ATOM 675 H3' URA 21 15.415 -4.137 -1.160 1.00 0.00 RNAA -ATOM 676 O3' URA 21 16.879 -4.470 -2.509 1.00 0.00 RNAA -ATOM 677 P CYT 22 17.952 -3.636 -1.651 1.00 0.00 RNAA -ATOM 678 O1P CYT 22 19.309 -4.128 -1.999 1.00 0.00 RNAA -ATOM 679 O2P CYT 22 17.508 -3.653 -0.233 1.00 0.00 RNAA -ATOM 680 O5' CYT 22 17.804 -2.144 -2.190 1.00 0.00 RNAA -ATOM 681 C5' CYT 22 18.115 -1.822 -3.543 1.00 0.00 RNAA -ATOM 682 H5' CYT 22 17.504 -2.427 -4.213 1.00 0.00 RNAA -ATOM 683 H5'' CYT 22 19.167 -2.028 -3.739 1.00 0.00 RNAA -ATOM 684 C4' CYT 22 17.844 -0.360 -3.810 1.00 0.00 RNAA -ATOM 685 H4' CYT 22 18.297 -0.111 -4.769 1.00 0.00 RNAA -ATOM 686 O4' CYT 22 16.411 -0.127 -3.769 1.00 0.00 RNAA -ATOM 687 C1' CYT 22 16.151 1.153 -3.226 1.00 0.00 RNAA -ATOM 688 H1' CYT 22 15.559 1.695 -3.964 1.00 0.00 RNAA -ATOM 689 N1 CYT 22 15.329 0.989 -2.019 1.00 0.00 RNAA -ATOM 690 C6 CYT 22 15.265 -0.212 -1.367 1.00 0.00 RNAA -ATOM 691 H6 CYT 22 15.837 -1.060 -1.745 1.00 0.00 RNAA -ATOM 692 C5 CYT 22 14.514 -0.365 -0.270 1.00 0.00 RNAA -ATOM 693 H5 CYT 22 14.459 -1.323 0.248 1.00 0.00 RNAA -ATOM 694 C2 CYT 22 14.607 2.086 -1.543 1.00 0.00 RNAA -ATOM 695 O2 CYT 22 14.682 3.164 -2.151 1.00 0.00 RNAA -ATOM 696 N3 CYT 22 13.845 1.949 -0.433 1.00 0.00 RNAA -ATOM 697 C4 CYT 22 13.789 0.770 0.192 1.00 0.00 RNAA -ATOM 698 N4 CYT 22 13.022 0.679 1.281 1.00 0.00 RNAA -ATOM 699 H41 CYT 22 12.532 1.495 1.617 1.00 0.00 RNAA -ATOM 700 H42 CYT 22 12.948 -0.195 1.784 1.00 0.00 RNAA -ATOM 701 C2' CYT 22 17.497 1.830 -2.970 1.00 0.00 RNAA -ATOM 702 H2'' CYT 22 17.434 2.406 -2.023 1.00 0.00 RNAA -ATOM 703 O2' CYT 22 17.849 2.575 -4.118 1.00 0.00 RNAA -ATOM 704 H2' CYT 22 17.475 2.437 -2.064 1.00 0.00 RNAA -ATOM 705 C3' CYT 22 18.407 0.620 -2.787 1.00 0.00 RNAA -ATOM 706 H3' CYT 22 18.367 0.215 -1.776 1.00 0.00 RNAA -ATOM 707 O3' CYT 22 19.775 0.921 -3.040 1.00 0.00 RNAA -ATOM 708 P CYT 23 20.711 1.442 -1.843 1.00 0.00 RNAA -ATOM 709 O1P CYT 23 22.109 1.506 -2.342 1.00 0.00 RNAA -ATOM 710 O2P CYT 23 20.400 0.627 -0.641 1.00 0.00 RNAA -ATOM 711 O5' CYT 23 20.202 2.927 -1.571 1.00 0.00 RNAA -ATOM 712 C5' CYT 23 20.353 3.945 -2.557 1.00 0.00 RNAA -ATOM 713 H5' CYT 23 19.804 3.668 -3.458 1.00 0.00 RNAA -ATOM 714 H5'' CYT 23 21.408 4.063 -2.807 1.00 0.00 RNAA -ATOM 715 C4' CYT 23 19.824 5.260 -2.037 1.00 0.00 RNAA -ATOM 716 H4' CYT 23 20.147 6.043 -2.724 1.00 0.00 RNAA -ATOM 717 O4' CYT 23 18.381 5.164 -1.902 1.00 0.00 RNAA -ATOM 718 C1' CYT 23 17.955 5.904 -0.775 1.00 0.00 RNAA -ATOM 719 H1' CYT 23 17.236 6.640 -1.136 1.00 0.00 RNAA -ATOM 720 N1 CYT 23 17.247 4.994 0.137 1.00 0.00 RNAA -ATOM 721 C6 CYT 23 17.446 3.643 0.075 1.00 0.00 RNAA -ATOM 722 H6 CYT 23 18.137 3.232 -0.662 1.00 0.00 RNAA -ATOM 723 C5 CYT 23 16.805 2.811 0.906 1.00 0.00 RNAA -ATOM 724 H5 CYT 23 16.955 1.733 0.855 1.00 0.00 RNAA -ATOM 725 C2 CYT 23 16.363 5.533 1.075 1.00 0.00 RNAA -ATOM 726 O2 CYT 23 16.192 6.761 1.104 1.00 0.00 RNAA -ATOM 727 N3 CYT 23 15.712 4.707 1.926 1.00 0.00 RNAA -ATOM 728 C4 CYT 23 15.917 3.390 1.859 1.00 0.00 RNAA -ATOM 729 N4 CYT 23 15.260 2.610 2.721 1.00 0.00 RNAA -ATOM 730 H41 CYT 23 14.657 3.033 3.413 1.00 0.00 RNAA -ATOM 731 H42 CYT 23 15.386 1.608 2.705 1.00 0.00 RNAA -ATOM 732 C2' CYT 23 19.182 6.569 -0.155 1.00 0.00 RNAA -ATOM 733 H2'' CYT 23 19.099 6.507 0.951 1.00 0.00 RNAA -ATOM 734 O2' CYT 23 19.290 7.873 -0.689 1.00 0.00 RNAA -ATOM 735 H2' CYT 23 19.136 6.565 0.935 1.00 0.00 RNAA -ATOM 736 C3' CYT 23 20.305 5.663 -0.648 1.00 0.00 RNAA -ATOM 737 H3' CYT 23 20.459 4.796 -0.007 1.00 0.00 RNAA -ATOM 738 O3' CYT 23 21.555 6.342 -0.700 1.00 0.00 RNAA -ATOM 739 H3T CYT 23 21.687 7.002 -0.015 1.00 0.00 RNAA diff --git a/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.pdb.gz b/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.pdb.gz new file mode 100644 index 00000000000..55d8c06a6ad Binary files /dev/null and b/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.pdb.gz differ diff --git a/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz b/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz new file mode 100644 index 00000000000..90063ab42f8 Binary files /dev/null and b/testsuite/MDAnalysisTests/data/analysis/1k5i_c36.psf.gz differ diff --git a/testsuite/MDAnalysisTests/datafiles.py b/testsuite/MDAnalysisTests/datafiles.py index a987d26ebf0..235e3d586df 100644 --- a/testsuite/MDAnalysisTests/datafiles.py +++ b/testsuite/MDAnalysisTests/datafiles.py @@ -58,7 +58,7 @@ "XPDB_small", "PDB_full", # PDB 4E43 (full HEADER, TITLE, COMPND, REMARK, altloc) "ALIGN", # Various way to align atom names in PDB files - "NUCL", # nucleic acid (PDB) + "RNA_PSF", "RNA_PDB", # nucleic acid (PDB 1K5I in CHARMM36m) "INC_PDB", # incomplete PDB file (Issue #396) # for testing cryst before/after model headers "PDB_cm", "PDB_cm_bz2", "PDB_cm_gz", @@ -230,7 +230,8 @@ PDB_closed = resource_filename(__name__, 'data/adk_closed.pdb') ALIGN = resource_filename(__name__, 'data/align.pdb') -NUCL = resource_filename(__name__, 'data/1k5i.pdb') +RNA_PSF = resource_filename(__name__, 'data/analysis/1k5i_c36.psf.gz') +RNA_PDB = resource_filename(__name__, 'data/analysis/1k5i_c36.pdb.gz') INC_PDB = resource_filename(__name__, 'data/incomplete.pdb') PDB_cm = resource_filename(__name__, 'data/cryst_then_model.pdb') PDB_cm_gz = resource_filename(__name__, 'data/cryst_then_model.pdb.gz') diff --git a/testsuite/MDAnalysisTests/utils/test_nuclinfo.py b/testsuite/MDAnalysisTests/utils/test_nuclinfo.py deleted file mode 100644 index d45df072709..00000000000 --- a/testsuite/MDAnalysisTests/utils/test_nuclinfo.py +++ /dev/null @@ -1,101 +0,0 @@ -# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*- -# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 fileencoding=utf-8 -# -# MDAnalysis --- https://www.mdanalysis.org -# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors -# (see the file AUTHORS for the full list of names) -# -# Released under the GNU Public Licence, v2 or any higher version -# -# Please cite your use of MDAnalysis in published work: -# -# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler, -# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein. -# MDAnalysis: A Python package for the rapid analysis of molecular dynamics -# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th -# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy. -# doi: 10.25080/majora-629e541a-00e -# -# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein. -# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations. -# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787 -# - -""" -:Author: Elizabeth Denning -:Contact: denniej0@gmail.com - -Sample code to use the routine for nucleic acid analysis -For the example provided below, the backbone dihedrals and WC distances - -""" -from __future__ import absolute_import - -import numpy as np -import MDAnalysis -import pytest - -from MDAnalysis.analysis import nuclinfo -from MDAnalysis.tests.datafiles import NUCL - -from numpy.testing import assert_almost_equal ,assert_array_almost_equal - - -PREC = 4 - -@pytest.fixture() -def universe(): - return MDAnalysis.Universe(NUCL) - - -def test_wc_pair(universe): - seg1 = universe.residues[3].atoms.segids[0] - seg2 = universe.residues[19].atoms.segids[0] - wc = nuclinfo.wc_pair(universe, 4, 20, seg1, seg2) - assert_almost_equal(wc, 2.9810174, err_msg="Watson-Crick distance does not match expected value.") - - -def test_major_pair(universe): - seg1 = universe.residues[3].atoms.segids[0] - seg2 = universe.residues[19].atoms.segids[0] - maj = nuclinfo.major_pair(universe, 4, 20, seg1, seg2) - assert_almost_equal(maj, 2.9400151, err_msg="Watson-Crick distance does not match expected value.") - - -def test_minor_pair(universe): - seg1 = universe.residues[3].atoms.segids[0] - seg2 = universe.residues[19].atoms.segids[0] - - minor = nuclinfo.minor_pair(universe, 4, 20, seg1, seg2) - assert_almost_equal(minor, 3.7739358, err_msg="Watson-Crick distance does not match expected value.") - - -def test_torsions(universe): - nucl_acid = np.array(nuclinfo.tors(universe, "RNAA", 4), dtype=np.float32) - expected_nucl_acid = np.array( - [296.45596313, 177.79353333, 48.67910767, 81.81109619, 205.58882141, 286.37353516, 198.09187317], - dtype=np.float32) - assert_almost_equal(nucl_acid, expected_nucl_acid, PREC, - err_msg="Backbone torsion does not have expected values for " - "alpha, beta, gamma, epsilon, zeta, chi.") - - -def test_hydroxyl(universe): - hydroxyls = np.array([nuclinfo.hydroxyl(universe, - universe.atoms.segids[0], resid) - for resid in (7, 10, 11, 22)]) - expected_hydroxyls = np.array( - [ 122.73991394, 123.34986115, 123.20658112, 122.57156372], - dtype=np.float32) - assert_array_almost_equal(hydroxyls, expected_hydroxyls, PREC, - err_msg="RNA hydroxyl dihedrals do not match") - - -def test_pseudo_dihe_baseflip(universe): - seg1 = universe.residues[3].atoms.segids[0] - seg2 = universe.residues[19].atoms.segids[0] - - # There is not really a baseflip, just testing the code... - flip = nuclinfo.pseudo_dihe_baseflip(universe, 4, 20, 5, seg1=seg1, seg2=seg2, seg3=seg1) - assert_almost_equal(flip, 322.0826, PREC, - err_msg="pseudo_dihedral for resid 5 against 4--20 do not match")