| Next changeset 1:3c170cc50eeb (2025-02-24) |
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Commit message:
planemo upload for repository https://github.com/TGAC/earlham-galaxytools/tree/master/tools/smina/ commit b0a69750ca69548162f9b660eb45fc70c1e4f319-dirty |
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added:
smina.xml test-data/ligand.pdbqt test-data/ligand_out.pdbqt test-data/output_smina test-data/protein.pdbqt |
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| diff -r 000000000000 -r 7c0bb0c48a27 smina.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/smina.xml Tue May 08 19:08:15 2018 -0400 |
| [ |
| b'@@ -0,0 +1,197 @@\n+<tool id="smina" name="smina" version="1.0">\n+ <description>Scoring and Minimization with AutoDock Vina</description>\n+ <requirements>\n+ <requirement type="package" version="2017.11.9">smina</requirement>\n+ </requirements>\n+ <command detect_errors="exit_code"><![CDATA[\n+ln -s \'$input.receptor\' receptor.pdbqt &&\n+ln -s \'$input.ligand\' ligand.pdbqt &&\n+smina\n+--receptor receptor.pdbqt\n+--ligand ligand.pdbqt\n+#if $input.flex\n+ --flex \'$input.flex\'\n+#end if\n+#if $input.flexres\n+ --flexres \'$input.flexres\'\n+#end if\n+#if $input.flexdist_ligand\n+ --flexdist_ligand \'$input.flexdist_ligand\'\n+#end if\n+#if str($input.flexdist)\n+ --flexdist $input.flexdist\n+#end if\n+\n+--center_x $search_space.center_x\n+--center_y $search_space.center_y\n+--center_z $search_space.center_z\n+--size_x $search_space.size_x\n+--size_y $search_space.size_y\n+--size_z $search_space.size_z\n+#if $search_space.autobox_ligand\n+ --autobox_ligand \'$search_space.autobox_ligand\'\n+#end if\n+#if str($search_space.autobox_add)\n+ --autobox_add $search_space.autobox_add\n+#end if\n+$search_space.no_lig\n+\n+--out ligand_out.pdbqt\n+#if $output_sect.out_flex\n+ --out_flex \'$out_flex_output\'\n+#end if\n+#if $output_sect.log\n+ --log \'$output_log\'\n+#end if\n+#if $output_sect.atom_terms\n+ --atom_terms \'$atom_terms_output\'\n+#end if\n+$output_sect.atom_term_data\n+\n+--scoring $scoring_and_minimization.scoring\n+#if $scoring_and_minimization.custom_scoring\n+ --custom_scoring \'$scoring_and_minimization.custom_scoring\'\n+#end if\n+#if $scoring_and_minimization.custom_atoms\n+ --custom_atoms \'$scoring_and_minimization.custom_atoms\'\n+#end if\n+$scoring_and_minimization.score_only\n+$scoring_and_minimization.local_only\n+$scoring_and_minimization.minimize\n+$scoring_and_minimization.randomize_only\n+--minimize_iters $scoring_and_minimization.minimize_iters\n+$scoring_and_minimization.accurate_line\n+$scoring_and_minimization.minimize_early_term\n+#if $scoring_and_minimization.approximation\n+ --approximation $scoring_and_minimization.approximation\n+#end if\n+#if $scoring_and_minimization.factor\n+ --factor $scoring_and_minimization.factor\n+#end if\n+#if str($scoring_and_minimization.force_cap)\n+ --force_cap $scoring_and_minimization.force_cap\n+#end if\n+#if str($scoring_and_minimization.user_grid)\n+ --user_grid $scoring_and_minimization.user_grid\n+#end if\n+--user_grid_lambda $scoring_and_minimization.user_grid_lambda\n+$scoring_and_minimization.print_terms\n+$scoring_and_minimization.print_atom_types\n+\n+--cpu \\${GALAXY_SLOTS:-1}\n+#if str($misc.seed)\n+ --seed $misc.seed\n+#end if\n+--exhaustiveness $misc.exhaustiveness\n+--num_modes $misc.num_modes\n+--energy_range $misc.energy_range\n+--min_rmsd_filter $misc.min_rmsd_filter\n+$misc.addH\n+ ]]></command>\n+ <inputs>\n+ <section name="input" title="Input" expanded="True">\n+ <param argument="--receptor" type="data" format="pdbqt" label="Rigid part of the receptore" />\n+ <param argument="--ligand" type="data" format="pdbqt" label="Ligand(s)" />\n+ <param argument="--flex" type="data" format="pdbqt" optional="true" label="Flexible side chains, if any" />\n+ <param argument="--flexres" type="text" optional="true" label="Flexible side chains specified by comma separated list of chain:resid" />\n+ <param argument="--flexdist_ligand" type="data" format="data" optional="true" label="Ligand to use for flexdist" />\n+ <param argument="--flexdist" type="float" optional="true" label="Set all side chains within specified distance to flexdist_ligand to flexible" />\n+ </section>\n+ <section name="search_space" title="Search space" expanded="True">\n+ <param argument="--center_x" type="float" value="0" label="X coordinate of the center" />\n+ <param argument="--center_y" type="float" value="0" label="Y coordinate of the center" />\n+ <param argument="--center_z" type="float" value="0" label="Z coo'..b' conditions are fully met" />\n+ <param argument="--approximation" type="select" optional="true" label="Approximation">\n+ <option value="linear">linear</option>\n+ <option value="spline">spline</option>\n+ <option value="exact">exact</option>\n+ </param>\n+ <param argument="--factor" type="float" min="0" optional="true" label="Approximation factor: higher results in a finer-grained approximation" />\n+ <param argument="--force_cap" type="float" optional="true" label="Max allowed force; lower values more gently minimize clashing structures" />\n+ <param argument="--user_grid" type="float" optional="true" label="Autodock map file for user grid data based calculations" />\n+ <param argument="--user_grid_lambda" type="float" value="-1" label="Scales user_grid and functional scoring" />\n+ <param argument="--print_terms" type="boolean" truevalue="--print_terms" falsevalue="" label="Print all available terms with default parameterizations" />\n+ <param argument="--print_atom_types" type="boolean" truevalue="--print_atom_types" falsevalue="" label="Print all available atom types" />\n+ </section>\n+ <section name="misc" title="Misc">\n+ <param argument="--seed" type="integer" optional="true" label="Explicit random seed" />\n+ <param argument="--exhaustiveness" type="integer" value="8" label="Exhaustiveness of the global search" />\n+ <param argument="--num_modes" type="integer" min="1" value="9" label="Maximum number of binding modes to generate" />\n+ <param argument="--energy_range" type="float" value="3" label="Maximum energy difference between the best binding mode and the worst one displayed (kcal/mol)" />\n+ <param argument="--min_rmsd_filter" type="float" value="1" label="Rmsd value used to filter final poses to remove redundancy" />\n+ <param argument="--addH" type="boolean" truevalue="" falsevalue="--addH false" checked="true" label="Automatically add hydrogens in ligands" />\n+ </section>\n+ </inputs>\n+ <outputs>\n+ <data name="output" format="pdbqt" from_work_dir="ligand_out.pdbqt" />\n+ <data name="out_flex_output" format="txt" label="smina: flexible receptor residues">\n+ <filter>output_sect[\'out_flex\']</filter>\n+ </data>\n+ <data name="output_log" format="txt" label="smina: log file">\n+ <filter>output_sect[\'log\']</filter>\n+ </data>\n+ <data name="atom_terms_output" format="txt" label="smima: per-atom interaction term values">\n+ <filter>output_sect[\'atom_terms\']</filter>\n+ </data>\n+ </outputs>\n+ <tests>\n+ <test>\n+ <param name="receptor" value="protein.pdbqt" />\n+ <param name="ligand" value="ligand.pdbqt" />\n+ <param name="center_x" value="11" />\n+ <param name="center_y" value="90.5" />\n+ <param name="center_z" value="57.5" />\n+ <param name="size_x" value="22" />\n+ <param name="size_y" value="24" />\n+ <param name="size_z" value="28" />\n+ <param name="log" value="True" />\n+ <param name="seed" value="1000" />\n+ <param name="num_modes" value="5" />\n+ <output name="output" file="ligand_out.pdbqt" />\n+ <output name="output_log" file="output_smina" />\n+ </test>\n+ </tests>\n+ <help><![CDATA[\n+************\n+Description\n+************\n+\n+`smina <https://sourceforge.net/projects/smina/>`_ is a fork of `AutoDock Vina <http://vina.scripps.edu/>`_ that is customized to better support scoring function development and high-performance energy minimization. smina is maintained by David Koes at the University of Pittsburgh and is not directly affiliated with the AutoDock project.\n+ ]]></help>\n+ <citations>\n+ <citation type="doi">10.1021/ci300604z</citation>\n+ </citations>\n+</tool>\n' |
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| diff -r 000000000000 -r 7c0bb0c48a27 test-data/ligand.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand.pdbqt Tue May 08 19:08:15 2018 -0400 |
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| @@ -0,0 +1,66 @@ +REMARK 7 active torsions: +REMARK status: ('A' for Active; 'I' for Inactive) +REMARK 1 A between atoms: C5_5 and C7_7 +REMARK 2 A between atoms: C9_9 and N13_13 +REMARK 3 A between atoms: N13_13 and C14_14 +REMARK 4 A between atoms: C16_16 and N21_21 +REMARK I between atoms: N21_21 and C22_22 +REMARK 5 A between atoms: C22_22 and C23_23 +REMARK 6 A between atoms: C27_26 and C46_30 +REMARK 7 A between atoms: C46_30 and N48_31 +ROOT +HETATM 1 C1 STI 202 15.290 78.984 63.105 1.00 0.00 -0.001 A +HETATM 2 C2 STI 202 14.162 78.322 62.514 1.00 0.00 0.095 A +HETATM 3 N3 STI 202 14.348 77.405 61.475 1.00 0.00 -0.243 NA +HETATM 4 C4 STI 202 15.604 77.088 60.967 1.00 0.00 0.097 A +HETATM 5 C5 STI 202 16.790 77.718 61.516 1.00 0.00 0.020 A +HETATM 6 C6 STI 202 16.610 78.678 62.599 1.00 0.00 0.057 A +ENDROOT +BRANCH 5 7 +HETATM 7 C7 STI 202 18.135 77.365 60.950 1.00 0.00 0.099 A +HETATM 8 N8 STI 202 18.991 76.649 61.763 1.00 0.00 -0.061 NA +HETATM 9 C9 STI 202 20.233 76.272 61.350 1.00 0.00 0.728 A +HETATM 10 N10 STI 202 20.667 76.608 60.078 1.00 0.00 -0.059 NA +HETATM 11 C11 STI 202 19.854 77.325 59.216 1.00 0.00 0.119 A +HETATM 12 C12 STI 202 18.556 77.729 59.622 1.00 0.00 0.041 A +BRANCH 9 13 +HETATM 13 N13 STI 202 21.026 75.546 62.243 1.00 0.00 -0.190 N +HETATM 14 H STI 202 20.822 74.493 62.382 1.00 0.00 0.184 HD +BRANCH 13 15 +HETATM 15 C14 STI 202 22.078 76.132 62.968 1.00 0.00 0.052 A +HETATM 16 C15 STI 202 21.784 76.754 64.221 1.00 0.00 0.087 A +HETATM 17 C16 STI 202 22.842 77.373 65.022 1.00 0.00 0.042 A +HETATM 18 C17 STI 202 24.173 77.343 64.522 1.00 0.00 0.013 A +HETATM 19 C18 STI 202 24.483 76.718 63.261 1.00 0.00 -0.002 A +HETATM 20 C19 STI 202 23.455 76.105 62.465 1.00 0.00 -0.009 A +HETATM 21 C20 STI 202 23.868 75.449 61.126 1.00 0.00 0.032 C +BRANCH 17 22 +HETATM 22 N21 STI 202 22.625 78.015 66.297 1.00 0.00 -0.325 N +HETATM 23 C22 STI 202 21.459 78.556 66.802 1.00 0.00 0.253 C +HETATM 24 O29 STI 202 20.459 78.777 66.146 1.00 0.00 -0.268 OA +HETATM 25 H STI 202 23.491 78.080 66.943 1.00 0.00 0.169 HD +BRANCH 23 26 +HETATM 26 C23 STI 202 21.395 78.922 68.248 1.00 0.00 0.034 A +HETATM 27 C25 STI 202 22.608 78.977 69.064 1.00 0.00 0.036 A +HETATM 28 C26 STI 202 22.516 79.314 70.461 1.00 0.00 0.029 A +HETATM 29 C27 STI 202 21.216 79.597 71.045 1.00 0.00 -0.011 A +HETATM 30 C28 STI 202 20.031 79.541 70.215 1.00 0.00 -0.007 A +HETATM 31 C29 STI 202 20.112 79.211 68.845 1.00 0.00 -0.000 A +BRANCH 29 32 +HETATM 32 C46 STI 202 21.035 79.941 72.527 1.00 0.00 0.273 C +BRANCH 32 33 +HETATM 33 N48 STI 202 21.864 81.048 73.091 1.00 0.00 0.145 N +HETATM 34 C49 STI 202 23.277 80.579 73.421 1.00 0.00 0.286 C +HETATM 35 C50 STI 202 24.142 81.743 73.995 1.00 0.00 0.286 C +HETATM 36 N51 STI 202 23.461 82.314 75.230 1.00 0.00 0.143 N +HETATM 37 C52 STI 202 22.054 82.791 74.907 1.00 0.00 0.286 C +HETATM 38 C54 STI 202 24.311 83.368 75.810 1.00 0.00 0.285 C +HETATM 39 C53 STI 202 21.211 81.634 74.310 1.00 0.00 0.286 C +ENDBRANCH 32 33 +ENDBRANCH 29 32 +ENDBRANCH 23 26 +ENDBRANCH 17 22 +ENDBRANCH 13 15 +ENDBRANCH 9 13 +ENDBRANCH 5 7 +TORSDOF 7 |
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| diff -r 000000000000 -r 7c0bb0c48a27 test-data/ligand_out.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/ligand_out.pdbqt Tue May 08 19:08:15 2018 -0400 |
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| b"@@ -0,0 +1,350 @@\n+MODEL 1\n+REMARK minimizedAffinity -10.8892946\n+REMARK minimizedRMSD -1\n+REMARK 7 active torsions:\n+REMARK status: ('A' for Active; 'I' for Inactive)\n+REMARK 1 A between atoms: C5_5 and C7_7 \n+REMARK 2 A between atoms: C9_9 and N13_13 \n+REMARK 3 A between atoms: N13_13 and C14_14 \n+REMARK 4 A between atoms: C16_16 and N21_21 \n+REMARK I between atoms: N21_21 and C22_22 \n+REMARK 5 A between atoms: C22_22 and C23_23 \n+REMARK 6 A between atoms: C27_26 and C46_30 \n+REMARK 7 A between atoms: C46_30 and N48_31 \n+ROOT\n+HETATM 1 C1 STI 202 7.561 86.944 59.932 1.00 0.00 -0.001 A \n+HETATM 2 C2 STI 202 6.623 86.724 58.868 1.00 0.00 0.095 A \n+HETATM 3 N3 STI 202 5.753 87.746 58.474 1.00 0.00 -0.243 NA\n+HETATM 4 C4 STI 202 5.746 89.001 59.074 1.00 0.00 0.097 A \n+HETATM 5 C5 STI 202 6.667 89.295 60.156 1.00 0.00 0.020 A \n+HETATM 6 C6 STI 202 7.578 88.238 60.578 1.00 0.00 0.057 A \n+ENDROOT\n+BRANCH 5 7\n+HETATM 7 C7 STI 202 6.639 90.655 60.792 1.00 0.00 0.099 A \n+HETATM 8 N8 STI 202 7.383 90.826 61.943 1.00 0.00 -0.061 NA\n+HETATM 9 C9 STI 202 7.433 92.018 62.599 1.00 0.00 0.728 A \n+HETATM 10 N10 STI 202 6.723 93.103 62.112 1.00 0.00 -0.059 NA\n+HETATM 11 C11 STI 202 5.960 92.994 60.962 1.00 0.00 0.119 A \n+HETATM 12 C12 STI 202 5.891 91.763 60.259 1.00 0.00 0.041 A \n+BRANCH 9 13\n+HETATM 13 N13 STI 202 8.217 92.095 63.754 1.00 0.00 -0.190 N \n+HETATM 14 H STI 202 7.871 91.599 64.651 1.00 0.00 0.184 HD\n+BRANCH 13 15\n+HETATM 15 C14 STI 202 9.437 92.792 63.795 1.00 0.00 0.052 A \n+HETATM 16 C15 STI 202 9.632 93.885 62.894 1.00 0.00 0.087 A \n+HETATM 17 C16 STI 202 10.880 94.651 62.898 1.00 0.00 0.042 A \n+HETATM 18 C17 STI 202 11.897 94.280 63.820 1.00 0.00 0.013 A \n+HETATM 19 C18 STI 202 11.712 93.181 64.734 1.00 0.00 -0.002 A \n+HETATM 20 C19 STI 202 10.492 92.421 64.743 1.00 0.00 -0.009 A \n+HETATM 21 C20 STI 202 10.367 91.260 65.758 1.00 0.00 0.032 C \n+BRANCH 17 22\n+HETATM 22 N21 STI 202 11.149 95.768 62.024 1.00 0.00 -0.325 N \n+HETATM 23 C22 STI 202 12.328 96.097 61.384 1.00 0.00 0.253 C \n+HETATM 24 O29 STI 202 13.411 95.605 61.636 1.00 0.00 -0.268 OA\n+HETATM 25 H STI 202 10.317 96.437 61.847 1.00 0.00 0.169 HD\n+BRANCH 23 26\n+HETATM 26 C23 STI 202 12.307 97.137 60.314 1.00 0.00 0.034 A \n+HETATM 27 C25 STI 202 11.261 98.159 60.279 1.00 0.00 0.036 A \n+HETATM 28 C26 STI 202 11.253 99.140 59.224 1.00 0.00 0.029 A \n+HETATM 29 C27 STI 202 12.288 99.103 58.205 1.00 0.00 -0.011 A \n+HETATM 30 C28 STI 202 13.315 98.085 58.264 1.00 0.00 -0.007 A \n+HETATM 31 C29 STI 202 13.330 97.119 59.294 1.00 0.00 -0.000 A \n+BRANCH 29 32\n+HETATM 32 C46 STI 202 12.334 100.097 57.040 1.00 0.00 0.273 C \n+BRANCH 32 33\n+HETATM 33 N48 STI 202 13.077 99.693 55.809 1.00 0.00 0.145 N \n+HETATM 34 C49 STI 202 14.377 100.475 55.656 1.00 0.00 0.286 C \n+HETATM 35 C50 STI 202 15.156 100.038 54.377 1.00 0.00 0.286 C \n+HETATM 36 N51 STI 202 14.266 100.228 53.158 1.00 0.00 0.143 N \n+HETATM 37 C52 STI 202 12.970 99.445 53.299 1.00 0.00 0.286 C \n+HETATM 38 C54 STI 202 15.024 99.878 51.944 1.00 0.00 0.285 C \n+HETATM 39 C53 STI 202 12.218 99.866 54.589 1.00 0.00 0.286 C \n+ENDBRANCH 32 33\n+ENDBRANCH 29 32\n+ENDBRANCH 23 26\n+ENDBRANCH 17 22\n+ENDBRANCH 13 15\n+ENDBRANCH 9"..b"dAffinity -10.1429949\n+REMARK minimizedRMSD -1\n+REMARK 7 active torsions:\n+REMARK status: ('A' for Active; 'I' for Inactive)\n+REMARK 1 A between atoms: C5_5 and C7_7 \n+REMARK 2 A between atoms: C9_9 and N13_13 \n+REMARK 3 A between atoms: N13_13 and C14_14 \n+REMARK 4 A between atoms: C16_16 and N21_21 \n+REMARK I between atoms: N21_21 and C22_22 \n+REMARK 5 A between atoms: C22_22 and C23_23 \n+REMARK 6 A between atoms: C27_26 and C46_30 \n+REMARK 7 A between atoms: C46_30 and N48_31 \n+ROOT\n+HETATM 1 C1 STI 202 5.231 90.115 68.570 1.00 0.00 -0.001 A \n+HETATM 2 C2 STI 202 3.814 89.956 68.734 1.00 0.00 0.095 A \n+HETATM 3 N3 STI 202 2.934 90.427 67.756 1.00 0.00 -0.243 NA\n+HETATM 4 C4 STI 202 3.368 91.059 66.595 1.00 0.00 0.097 A \n+HETATM 5 C5 STI 202 4.786 91.254 66.360 1.00 0.00 0.020 A \n+HETATM 6 C6 STI 202 5.715 90.770 67.374 1.00 0.00 0.057 A \n+ENDROOT\n+BRANCH 5 7\n+HETATM 7 C7 STI 202 5.232 91.943 65.103 1.00 0.00 0.099 A \n+HETATM 8 N8 STI 202 6.527 91.710 64.684 1.00 0.00 -0.061 NA\n+HETATM 9 C9 STI 202 7.035 92.280 63.556 1.00 0.00 0.728 A \n+HETATM 10 N10 STI 202 6.241 93.121 62.792 1.00 0.00 -0.059 NA\n+HETATM 11 C11 STI 202 4.934 93.393 63.160 1.00 0.00 0.119 A \n+HETATM 12 C12 STI 202 4.382 92.812 64.331 1.00 0.00 0.041 A \n+BRANCH 9 13\n+HETATM 13 N13 STI 202 8.356 91.981 63.211 1.00 0.00 -0.190 N \n+HETATM 14 H STI 202 8.567 91.035 62.732 1.00 0.00 0.184 HD\n+BRANCH 13 15\n+HETATM 15 C14 STI 202 9.421 92.863 63.463 1.00 0.00 0.052 A \n+HETATM 16 C15 STI 202 9.697 93.894 62.512 1.00 0.00 0.087 A \n+HETATM 17 C16 STI 202 10.789 94.845 62.727 1.00 0.00 0.042 A \n+HETATM 18 C17 STI 202 11.573 94.718 63.907 1.00 0.00 0.013 A \n+HETATM 19 C18 STI 202 11.304 93.684 64.875 1.00 0.00 -0.002 A \n+HETATM 20 C19 STI 202 10.234 92.745 64.677 1.00 0.00 -0.009 A \n+HETATM 21 C20 STI 202 10.004 91.668 65.764 1.00 0.00 0.032 C \n+BRANCH 17 22\n+HETATM 22 N21 STI 202 11.127 95.914 61.817 1.00 0.00 -0.325 N \n+HETATM 23 C22 STI 202 12.376 96.328 61.399 1.00 0.00 0.253 C \n+HETATM 24 O29 STI 202 13.424 95.989 61.915 1.00 0.00 -0.268 OA\n+HETATM 25 H STI 202 10.289 96.463 61.407 1.00 0.00 0.169 HD\n+BRANCH 23 26\n+HETATM 26 C23 STI 202 12.481 97.271 60.246 1.00 0.00 0.034 A \n+HETATM 27 C25 STI 202 13.624 97.220 59.335 1.00 0.00 0.036 A \n+HETATM 28 C26 STI 202 13.710 98.154 58.242 1.00 0.00 0.029 A \n+HETATM 29 C27 STI 202 12.657 99.137 58.056 1.00 0.00 -0.011 A \n+HETATM 30 C28 STI 202 11.533 99.164 58.969 1.00 0.00 -0.007 A \n+HETATM 31 C29 STI 202 11.441 98.252 60.043 1.00 0.00 -0.000 A \n+BRANCH 29 32\n+HETATM 32 C46 STI 202 12.689 100.177 56.931 1.00 0.00 0.273 C \n+BRANCH 32 33\n+HETATM 33 N48 STI 202 13.454 99.840 55.694 1.00 0.00 0.145 N \n+HETATM 34 C49 STI 202 14.800 100.555 55.654 1.00 0.00 0.286 C \n+HETATM 35 C50 STI 202 15.601 100.187 54.367 1.00 0.00 0.286 C \n+HETATM 36 N51 STI 202 14.769 100.535 53.141 1.00 0.00 0.143 N \n+HETATM 37 C52 STI 202 13.428 99.820 53.170 1.00 0.00 0.286 C \n+HETATM 38 C54 STI 202 15.552 100.250 51.926 1.00 0.00 0.285 C \n+HETATM 39 C53 STI 202 12.653 100.170 54.467 1.00 0.00 0.286 C \n+ENDBRANCH 32 33\n+ENDBRANCH 29 32\n+ENDBRANCH 23 26\n+ENDBRANCH 17 22\n+ENDBRANCH 13 15\n+ENDBRANCH 9 13\n+ENDBRANCH 5 7\n+TORSDOF 7\n+ENDMDL\n" |
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| diff -r 000000000000 -r 7c0bb0c48a27 test-data/output_smina --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/output_smina Tue May 08 19:08:15 2018 -0400 |
| b |
| @@ -0,0 +1,30 @@ + _______ _______ _________ _ _______ + ( ____ \( )\__ __/( ( /|( ___ ) + | ( \/| () () | ) ( | \ ( || ( ) | + | (_____ | || || | | | | \ | || (___) | + (_____ )| |(_)| | | | | (\ \) || ___ | + ) || | | | | | | | \ || ( ) | + /\____) || ) ( |___) (___| ) \ || ) ( | + \_______)|/ \|\_______/|/ )_)|/ \| + + +smina is based off AutoDock Vina. Please cite appropriately. + +Weights Terms +-0.035579 gauss(o=0,_w=0.5,_c=8) +-0.005156 gauss(o=3,_w=2,_c=8) +0.840245 repulsion(o=0,_c=8) +-0.035069 hydrophobic(g=0.5,_b=1.5,_c=8) +-0.587439 non_dir_h_bond(g=-0.7,_b=0,_c=8) +1.923 num_tors_div + +Using random seed: 1000 + +mode | affinity | dist from best mode + | (kcal/mol) | rmsd l.b.| rmsd u.b. +-----+------------+----------+---------- +1 -10.9 0.000 0.000 +2 -10.8 2.596 3.684 +3 -10.5 2.869 4.597 +4 -10.4 2.255 3.321 +5 -10.1 2.651 3.907 |
| b |
| diff -r 000000000000 -r 7c0bb0c48a27 test-data/protein.pdbqt --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/protein.pdbqt Tue May 08 19:08:15 2018 -0400 |
| b |
| b'@@ -0,0 +1,2704 @@\n+REMARK 4 XXXX COMPLIES WITH FORMAT V. 2.0\n+ATOM 1 N MET B 225 8.895 115.777 72.069 1.00 66.21 -0.058 N \n+ATOM 2 HN1 MET B 225 9.110 116.757 71.885 1.00 0.00 0.276 HD\n+ATOM 3 HN2 MET B 225 8.532 115.302 71.243 1.00 0.00 0.276 HD\n+ATOM 4 HN3 MET B 225 9.737 115.217 72.203 1.00 0.00 0.276 HD\n+ATOM 5 CA MET B 225 7.964 115.677 73.229 1.00 67.57 0.256 C \n+ATOM 6 C MET B 225 8.577 116.332 74.473 1.00 67.86 0.259 C \n+ATOM 7 O MET B 225 9.799 116.348 74.640 1.00 65.18 -0.271 OA\n+ATOM 8 CB MET B 225 7.641 114.206 73.505 1.00 69.59 0.051 C \n+ATOM 9 CG MET B 225 6.364 113.982 74.294 1.00 74.31 0.060 C \n+ATOM 10 SD MET B 225 5.924 112.234 74.408 1.00 78.96 -0.139 SA\n+ATOM 11 CE MET B 225 5.398 111.927 72.771 1.00 75.85 0.069 C \n+ATOM 12 N ASP B 226 7.720 116.875 75.335 1.00 67.79 -0.337 N \n+ATOM 13 HN ASP B 226 6.722 116.819 75.133 1.00 0.00 0.164 HD\n+ATOM 14 CA ASP B 226 8.152 117.550 76.561 1.00 65.70 0.170 C \n+ATOM 15 C ASP B 226 8.642 116.583 77.638 1.00 60.19 0.255 C \n+ATOM 16 O ASP B 226 7.934 115.651 78.012 1.00 58.11 -0.270 OA\n+ATOM 17 CB ASP B 226 7.001 118.404 77.109 1.00 72.35 0.129 C \n+ATOM 18 CG ASP B 226 7.265 118.916 78.515 1.00 77.69 0.188 C \n+ATOM 19 OD1 ASP B 226 8.325 119.540 78.739 1.00 80.27 -0.647 OA\n+ATOM 20 OD2 ASP B 226 6.406 118.698 79.397 1.00 80.93 -0.647 OA\n+ATOM 21 N PRO B 227 9.864 116.804 78.156 1.00 57.95 -0.312 N \n+ATOM 22 CA PRO B 227 10.484 115.970 79.194 1.00 56.85 0.163 C \n+ATOM 23 C PRO B 227 9.616 115.766 80.431 1.00 59.80 0.251 C \n+ATOM 24 O PRO B 227 9.603 114.682 81.013 1.00 60.52 -0.271 OA\n+ATOM 25 CB PRO B 227 11.767 116.724 79.522 1.00 56.20 0.034 C \n+ATOM 26 CG PRO B 227 12.113 117.376 78.233 1.00 58.49 0.027 C \n+ATOM 27 CD PRO B 227 10.774 117.891 77.754 1.00 57.18 0.105 C \n+ATOM 28 N SER B 228 8.899 116.812 80.833 1.00 61.30 -0.336 N \n+ATOM 29 HN SER B 228 8.956 117.684 80.308 1.00 0.00 0.164 HD\n+ATOM 30 CA SER B 228 8.032 116.744 82.007 1.00 64.43 0.189 C \n+ATOM 31 C SER B 228 6.834 115.817 81.792 1.00 66.62 0.254 C \n+ATOM 32 O SER B 228 6.408 115.119 82.714 1.00 66.74 -0.270 OA\n+ATOM 33 CB SER B 228 7.537 118.146 82.373 1.00 61.78 0.169 C \n+ATOM 34 OG SER B 228 8.629 119.010 82.648 1.00 60.05 -0.380 OA\n+ATOM 35 HG SER B 228 8.322 119.880 82.875 1.00 0.00 0.211 HD\n+ATOM 36 N SER B 229 6.299 115.818 80.574 1.00 68.62 -0.335 N \n+ATOM 37 HN SER B 229 6.705 116.422 79.859 1.00 0.00 0.164 HD\n+ATOM 38 CA SER B 229 5.151 114.985 80.225 1.00 71.77 0.189 C \n+ATOM 39 C SER B 229 5.192 113.597 80.847 1.00 72.94 0.257 C \n+ATOM 40 O SER B 229 6.250 112.971 80.936 1.00 73.97 -0.270 OA\n+ATOM 41 CB SER B 229 5.040 114.835 78.708 1.00 73.74 0.169 C \n+ATOM 42 OG SER B 229 4.090 113.836 78.376 1.00 73.66 -0.380 OA\n+ATOM 43 HG SER B 229 4.021 113.743 77.433 1.00 0.00 0.211 HD\n+ATOM 44 N PRO B 230 4.028 113.098 81.287 1.00 74.05 -0.312 N \n+ATOM 45 CA PRO B 230 3.893 111.777 81.908 1.00 73.39 0.163 C \n+ATOM 46 C PRO B 230 4.091 110.662 80.885 1.00 71.08 0.251 C \n+ATOM 47 O PRO B 230 4.531 109.563 81.220 1.00 72.24 -0.271 OA\n+ATOM 48 CB PRO B 230 2.462 111.792 82.449 1.00 73.99 0.034 C \n+ATOM 49 CG PRO B 230 2.173 113.250'..b'\n+ATOM 2654 C GLU B 494 36.358 83.980 62.758 1.00 74.90 0.251 C \n+ATOM 2655 O GLU B 494 37.407 84.611 62.661 1.00 75.94 -0.271 OA\n+ATOM 2656 CB GLU B 494 34.721 85.146 64.247 1.00 74.74 0.043 C \n+ATOM 2657 CG GLU B 494 35.660 86.227 64.764 1.00 82.17 0.100 C \n+ATOM 2658 CD GLU B 494 35.327 86.660 66.179 1.00 87.43 0.185 C \n+ATOM 2659 OE1 GLU B 494 34.384 86.089 66.769 1.00 90.63 -0.647 OA\n+ATOM 2660 OE2 GLU B 494 36.009 87.570 66.702 1.00 88.07 -0.647 OA\n+ATOM 2661 N THR B 495 36.317 82.653 62.817 1.00 77.31 -0.336 N \n+ATOM 2662 HN THR B 495 35.416 82.184 62.914 1.00 0.00 0.164 HD\n+ATOM 2663 CA THR B 495 37.536 81.853 62.746 1.00 80.18 0.186 C \n+ATOM 2664 C THR B 495 38.042 81.872 61.310 1.00 80.90 0.253 C \n+ATOM 2665 O THR B 495 39.239 82.018 61.066 1.00 81.34 -0.270 OA\n+ATOM 2666 CB THR B 495 37.285 80.396 63.173 1.00 80.26 0.140 C \n+ATOM 2667 CG2 THR B 495 38.523 79.548 62.921 1.00 80.29 0.034 C \n+ATOM 2668 OG1 THR B 495 36.961 80.356 64.568 1.00 80.67 -0.382 OA\n+ATOM 2669 HG1 THR B 495 36.188 80.885 64.725 1.00 0.00 0.210 HD\n+ATOM 2670 N MET B 496 37.121 81.723 60.362 1.00 82.31 -0.337 N \n+ATOM 2671 HN MET B 496 36.148 81.580 60.632 1.00 0.00 0.164 HD\n+ATOM 2672 CA MET B 496 37.468 81.759 58.946 1.00 84.62 0.160 C \n+ATOM 2673 C MET B 496 37.860 83.196 58.616 1.00 87.04 0.251 C \n+ATOM 2674 O MET B 496 37.836 83.618 57.460 1.00 86.75 -0.271 OA\n+ATOM 2675 CB MET B 496 36.269 81.338 58.096 1.00 81.82 0.043 C \n+ATOM 2676 CG MET B 496 35.860 79.888 58.278 1.00 80.74 0.060 C \n+ATOM 2677 SD MET B 496 34.320 79.500 57.429 1.00 75.91 -0.139 SA\n+ATOM 2678 CE MET B 496 33.187 79.402 58.804 1.00 78.90 0.069 C \n+ATOM 2679 N PHE B 497 38.211 83.936 59.663 1.00 90.42 -0.337 N \n+ATOM 2680 HN PHE B 497 38.193 83.501 60.585 1.00 0.00 0.164 HD\n+ATOM 2681 CA PHE B 497 38.620 85.332 59.572 1.00 93.05 0.164 C \n+ATOM 2682 C PHE B 497 39.740 85.555 60.585 1.00 94.67 0.251 C \n+ATOM 2683 O PHE B 497 40.909 85.261 60.324 1.00 92.26 -0.271 OA\n+ATOM 2684 CB PHE B 497 37.450 86.253 59.933 1.00 93.91 0.058 C \n+ATOM 2685 CG PHE B 497 36.866 86.994 58.768 1.00 93.96 -0.020 A \n+ATOM 2686 CD1 PHE B 497 35.755 86.498 58.095 1.00 94.24 -0.004 A \n+ATOM 2687 CD2 PHE B 497 37.420 88.200 58.351 1.00 93.85 -0.004 A \n+ATOM 2688 CE1 PHE B 497 35.202 87.197 57.023 1.00 94.81 -0.000 A \n+ATOM 2689 CE2 PHE B 497 36.877 88.904 57.282 1.00 94.40 -0.000 A \n+ATOM 2690 CZ PHE B 497 35.764 88.402 56.616 1.00 95.25 -0.000 A \n+ATOM 2691 N GLN B 498 39.346 86.074 61.747 1.00 97.48 -0.339 N \n+ATOM 2692 HN GLN B 498 38.354 86.278 61.866 1.00 0.00 0.164 HD\n+ATOM 2693 CA GLN B 498 40.241 86.370 62.861 1.00 99.26 0.146 C \n+ATOM 2694 C GLN B 498 41.016 87.663 62.621 1.00 99.49 0.229 C \n+ATOM 2695 O GLN B 498 42.257 87.648 62.759 1.00100.35 -0.286 OA\n+ATOM 2696 CB GLN B 498 41.211 85.205 63.093 1.00100.80 0.040 C \n+ATOM 2697 CG GLN B 498 41.391 84.831 64.556 1.00102.53 0.090 C \n+ATOM 2698 CD GLN B 498 40.090 84.391 65.210 1.00103.58 0.227 C \n+ATOM 2699 NE2 GLN B 498 40.041 83.136 65.647 1.00102.89 -0.369 N \n+ATOM 2700 1HE2 GLN B 498 39.169 82.841 66.086 1.00 0.00 0.159 HD\n+ATOM 2701 2HE2 GLN B 498 40.827 82.492 65.558 1.00 0.00 0.159 HD\n+ATOM 2702 OE1 GLN B 498 39.140 85.169 65.318 1.00103.62 -0.273 OA\n+TER 2703 GLN B 498 \n' |