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testing_get_matching_atoms.ipynb
{
"cells": [
{
"cell_type": "markdown",
"metadata": {},
"source": [
"# Testing `align.get_matching_atoms()` "
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {},
"outputs": [],
"source": [
"import MDAnalysis as mda\n",
"from MDAnalysis.tests.datafiles import PSF, DCD\n",
"from MDAnalysis.analysis import align"
]
},
{
"cell_type": "code",
"execution_count": 23,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"MDAnalysis : INFO MDAnalysis 0.17.1-dev STARTED logging to 'testing.log'\n"
]
}
],
"source": [
"mda.start_logging(logfile=\"testing.log\")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Use a normal MD system (universe `u`) with hydrogens. Create someting that looks like a PDB structure with all hydrogens stripped and the first CA removed (as if it were not resolved)."
]
},
{
"cell_type": "code",
"execution_count": 28,
"metadata": {},
"outputs": [],
"source": [
"u = mda.Universe(PSF, DCD)\n",
"structure = mda.Merge(u.select_atoms(\"not name H* and not atom 4AKE 1 CA\"))"
]
},
{
"cell_type": "code",
"execution_count": 29,
"metadata": {},
"outputs": [],
"source": [
"mobile = u.select_atoms(\"protein and backbone\")\n",
"ref = structure.select_atoms(\"protein and backbone \")"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"No matching atoms should be found and a SelectionError should be raised (strict=True):"
]
},
{
"cell_type": "code",
"execution_count": 30,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"MDAnalysis.analysis.align: ERROR Reference and trajectory atom selections do not contain the same number of atoms: \n",
"atoms: N_ref=854, N_traj=855\n"
]
},
{
"ename": "SelectionError",
"evalue": "Reference and trajectory atom selections do not contain the same number of atoms: \natoms: N_ref=854, N_traj=855",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mSelectionError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-30-ff896ce5ce59>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mgroups\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0malign\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_matching_atoms\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mref\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmobile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstrict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mTrue\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/package/MDAnalysis/analysis/align.py\u001b[0m in \u001b[0;36mget_matching_atoms\u001b[0;34m(ag1, ag2, tol_mass, strict)\u001b[0m\n\u001b[1;32m 1045\u001b[0m \u001b[0;32mif\u001b[0m \u001b[0mstrict\u001b[0m\u001b[0;34m:\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1046\u001b[0m \u001b[0mlogger\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0merror\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1047\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mSelectionError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1048\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1049\u001b[0m \u001b[0;31m# continue with trying to creating a valid selection\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mSelectionError\u001b[0m: Reference and trajectory atom selections do not contain the same number of atoms: \natoms: N_ref=854, N_traj=855"
]
}
],
"source": [
"groups = align.get_matching_atoms(ref, mobile, strict=True)"
]
},
{
"cell_type": "markdown",
"metadata": {},
"source": [
"Now try strict=False: the atom matcher should be figuring out that there are the same residues in both structures and only one CA is missing.\n",
"\n",
"However, the current algorithm just checks sizes of residues when looking for residue matches. Because hydrogens were removed from `structure`, *all residues are now flagged as non-matching* and an empty selection would be generated. This is caught with a SelectionError but could be improved."
]
},
{
"cell_type": "code",
"execution_count": 31,
"metadata": {},
"outputs": [
{
"name": "stderr",
"output_type": "stream",
"text": [
"MDAnalysis.analysis.align: INFO Reference and trajectory atom selections do not contain the same number of atoms: \n",
"atoms: N_ref=854, N_traj=855\n",
"but we attempt to create a valid selection (use strict=True to disable this heuristic).\n",
"/Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/package/MDAnalysis/analysis/align.py:1053: SelectionWarning: Reference and trajectory atom selections do not contain the same number of atoms: \n",
"atoms: N_ref=854, N_traj=855\n",
"but we attempt to create a valid selection (use strict=True to disable this heuristic).\n",
" warnings.warn(msg, category=SelectionWarning)\n",
"MDAnalysis.analysis.align: WARNING Removed 214 residues with non-matching numbers of atoms\n",
"MDAnalysis.analysis.align: ERROR Failed to automatically find matching atoms: created empty selections. Try to improve your selections for mobile and reference.\n"
]
},
{
"ename": "SelectionError",
"evalue": "Failed to automatically find matching atoms: created empty selections. Try to improve your selections for mobile and reference.",
"output_type": "error",
"traceback": [
"\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
"\u001b[0;31mSelectionError\u001b[0m Traceback (most recent call last)",
"\u001b[0;32m<ipython-input-31-05959bc58ccb>\u001b[0m in \u001b[0;36m<module>\u001b[0;34m()\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0mgroups\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0malign\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mget_matching_atoms\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mref\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mmobile\u001b[0m\u001b[0;34m,\u001b[0m \u001b[0mstrict\u001b[0m\u001b[0;34m=\u001b[0m\u001b[0;32mFalse\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m",
"\u001b[0;32m/Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/package/MDAnalysis/analysis/align.py\u001b[0m in \u001b[0;36mget_matching_atoms\u001b[0;34m(ag1, ag2, tol_mass, strict)\u001b[0m\n\u001b[1;32m 1140\u001b[0m \"Try to improve your selections for mobile and reference.\")\n\u001b[1;32m 1141\u001b[0m \u001b[0mlogger\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0merror\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merrmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m-> 1142\u001b[0;31m \u001b[0;32mraise\u001b[0m \u001b[0mSelectionError\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0merrmsg\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m 1143\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m 1144\u001b[0m \u001b[0mmass_mismatches\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0;34m(\u001b[0m\u001b[0mnp\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mabsolute\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0mag1\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmasses\u001b[0m \u001b[0;34m-\u001b[0m \u001b[0mag2\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mmasses\u001b[0m\u001b[0;34m)\u001b[0m \u001b[0;34m>\u001b[0m \u001b[0mtol_mass\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
"\u001b[0;31mSelectionError\u001b[0m: Failed to automatically find matching atoms: created empty selections. Try to improve your selections for mobile and reference."
]
}
],
"source": [
"groups = align.get_matching_atoms(ref, mobile, strict=False)"
]
},
{
"cell_type": "code",
"execution_count": 32,
"metadata": {},
"outputs": [
{
"name": "stdout",
"output_type": "stream",
"text": [
"2018-03-07 13:43:14,809 MDAnalysis INFO MDAnalysis 0.17.1-dev STARTED logging to 'testing.log'\r\n",
"2018-03-07 13:43:26,778 MDAnalysis.analysis.align INFO Reference and trajectory atom selections do not contain the same number of atoms: \r\n",
"atoms: N_ref=854, N_traj=855\r\n",
"but we attempt to create a valid selection (use strict=True to disable this heuristic).\r\n",
"2018-03-07 13:43:26,794 MDAnalysis.analysis.align WARNING Removed 214 residues with non-matching numbers of atoms\r\n",
"2018-03-07 13:43:26,796 MDAnalysis.analysis.align DEBUG Removed residue ids: group 1: [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18\r\n",
" 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36\r\n",
" 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54\r\n",
" 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72\r\n",
" 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\r\n",
" 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108\r\n",
" 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126\r\n",
" 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144\r\n",
" 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162\r\n",
" 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\r\n",
" 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198\r\n",
" 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214]\r\n",
"2018-03-07 13:43:26,797 MDAnalysis.analysis.align DEBUG Removed residue ids: group 2: [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18\r\n",
" 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36\r\n",
" 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54\r\n",
" 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72\r\n",
" 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\r\n",
" 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108\r\n",
" 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126\r\n",
" 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144\r\n",
" 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162\r\n",
" 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\r\n",
" 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198\r\n",
" 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214]\r\n",
"2018-03-07 13:43:26,797 MDAnalysis.analysis.align ERROR Failed to automatically find matching atoms: created empty selections. Try to improve your selections for mobile and reference.\r\n",
"2018-03-07 13:46:24,417 MDAnalysis.topology.PSF DEBUG PSF file /Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/testsuite/MDAnalysisTests/data/adk.psf: format STANDARD\r\n",
"2018-03-07 13:46:24,590 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomids object at 0x107d21a90> to topology\r\n",
"2018-03-07 13:46:24,590 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomnames object at 0x107d21b70> to topology\r\n",
"2018-03-07 13:46:24,590 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomtypes object at 0x107d21c50> to topology\r\n",
"2018-03-07 13:46:24,590 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Charges object at 0x107d21c88> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Masses object at 0x107d21cc0> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resids object at 0x107d21d30> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resnums object at 0x107d21cf8> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resnames object at 0x107d21d68> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Segids object at 0x107d21da0> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomindices object at 0x107d1dda0> to topology\r\n",
"2018-03-07 13:46:24,591 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resindices object at 0x107d1dcf8> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Segindices object at 0x107d1dc50> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Bonds object at 0x1189b6908> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Angles object at 0x1189b66d8> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Dihedrals object at 0x1175b9908> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Impropers object at 0x1174df048> to topology\r\n",
"2018-03-07 13:46:24,592 MDAnalysis.core.universe DEBUG Universe.load_new(): loading /Volumes/Data/oliver/Biop/Projects/Methods/MDAnalysis/mdanalysis/testsuite/MDAnalysisTests/data/adk_dims.dcd...\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Segids object at 0x1189254e0> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resnames object at 0x118925400> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resnums object at 0x1189253c8> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Charges object at 0x118925630> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomnames object at 0x1189257b8> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Masses object at 0x118925320> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resids object at 0x1189259b0> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomids object at 0x118925908> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomtypes object at 0x118925b70> to topology\r\n",
"2018-03-07 13:46:24,774 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Dihedrals object at 0x118925be0> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Impropers object at 0x118925f28> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Angles object at 0x118925fd0> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Bonds object at 0x118925cc0> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Atomindices object at 0x1189250b8> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Resindices object at 0x1189251d0> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG _process_attr: Adding <MDAnalysis.core.topologyattrs.Segindices object at 0x118925ac8> to topology\r\n",
"2018-03-07 13:46:24,775 MDAnalysis.core.universe DEBUG Universe.load_new(): loading [[[ 11.736044 8.500797 -10.445281 ]\r\n",
" [ 10.739638 9.569928 -8.590751 ]\r\n",
" [ 10.556571 9.934239 -7.112363 ]\r\n",
" ...\r\n",
" [ 6.512604 18.447018 -7.134053 ]\r\n",
" [ 6.300186 19.363485 -7.935916 ]\r\n",
" [ 5.5854015 17.589624 -6.9656615]]]...\r\n",
"2018-03-07 13:46:35,048 MDAnalysis.analysis.align ERROR Reference and trajectory atom selections do not contain the same number of atoms: \r\n",
"atoms: N_ref=854, N_traj=855\r\n",
"2018-03-07 13:49:11,686 MDAnalysis.analysis.align INFO Reference and trajectory atom selections do not contain the same number of atoms: \r\n",
"atoms: N_ref=854, N_traj=855\r\n",
"but we attempt to create a valid selection (use strict=True to disable this heuristic).\r\n",
"2018-03-07 13:49:11,705 MDAnalysis.analysis.align WARNING Removed 214 residues with non-matching numbers of atoms\r\n",
"2018-03-07 13:49:11,708 MDAnalysis.analysis.align DEBUG Removed residue ids: group 1: [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18\r\n",
" 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36\r\n",
" 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54\r\n",
" 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72\r\n",
" 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\r\n",
" 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108\r\n",
" 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126\r\n",
" 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144\r\n",
" 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162\r\n",
" 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\r\n",
" 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198\r\n",
" 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214]\r\n",
"2018-03-07 13:49:11,709 MDAnalysis.analysis.align DEBUG Removed residue ids: group 2: [ 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18\r\n",
" 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36\r\n",
" 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54\r\n",
" 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72\r\n",
" 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90\r\n",
" 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108\r\n",
" 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126\r\n",
" 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144\r\n",
" 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162\r\n",
" 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180\r\n",
" 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198\r\n",
" 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214]\r\n",
"2018-03-07 13:49:11,709 MDAnalysis.analysis.align ERROR Failed to automatically find matching atoms: created empty selections. Try to improve your selections for mobile and reference.\r\n"
]
}
],
"source": [
"%cat testing.log"
]
},
{
"cell_type": "code",
"execution_count": null,
"metadata": {},
"outputs": [],
"source": []
}
],
"metadata": {
"kernelspec": {
"display_name": "Python 3",
"language": "python",
"name": "python3"
},
"language_info": {
"codemirror_mode": {
"name": "ipython",
"version": 3
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"file_extension": ".py",
"mimetype": "text/x-python",
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